[med-svn] [trinityrnaseq] 02/04: Imported Upstream version 2.1.0+dfsg
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue Sep 29 19:43:34 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch test/2.1.0
in repository trinityrnaseq.
commit 7f4bee0021c33f6f6a0c2a650d02f2c0ec156652
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Tue Sep 29 12:11:14 2015 -0700
Imported Upstream version 2.1.0+dfsg
---
Analysis/DifferentialExpression/DE_graph_to_dot.pl | 55 +
Analysis/DifferentialExpression/PtR | 48 +-
.../group_isoforms_by_tissue_enrichment.pl | 54 +
.../add_blastx_hit_to_trinity_id.pl | 11 +-
.../DifferentialExpression/analyze_diff_expr.pl | 8 +-
.../define_clusters_by_cutting_tree.pl | 3 +
Analysis/DifferentialExpression/run_DE_analysis.pl | 343 +-
.../FL_trans_analysis_pipeline.pl | 8 +-
.../util/blat_full_length_mappings.pl | 13 +-
Butterfly/src/src/TransAssembly_allProbPaths.java | 7 +
Chrysalis/GraphFromFasta_MPI.cc | 30 +-
.../Contents/Resources/DWARF/MakeDepend | Bin 875386 -> 960753 bytes
Chrysalis/Makefile | 3 +
Chrysalis/ReadsToTranscripts_MPI.cc | 2 +-
Chrysalis/ReadsToTranscripts_MPI_chang.cc | 2 +-
Chrysalis/analysis/BreakTransByPairs.cc | 4 +-
Chrysalis/analysis/Chrysalis.cc | 16 +-
Chrysalis/analysis/CreateIwormFastaBundle.cc | 8 +-
Chrysalis/analysis/DNAVector.cc | 52 +-
Chrysalis/analysis/DNAVector.h | 14 +-
Chrysalis/analysis/GraphFromFasta.cc | 40 +-
Chrysalis/analysis/IsoformAugment.cc | 4 +-
Chrysalis/analysis/JoinTransByPairs.cc | 10 +-
Chrysalis/analysis/KmerTable.cc | 12 +-
Chrysalis/analysis/NonRedKmerTable.cc | 35 +-
Chrysalis/analysis/NonRedKmerTable.h | 12 +-
Chrysalis/analysis/QuantifyGraph.cc | 2 +-
Chrysalis/analysis/ReadsToTranscripts.cc | 4 +-
Chrysalis/analysis/TranscriptomeFromVaryK.cc | 8 +-
Chrysalis/analysis/TranscriptomeGraph.cc | 23 +-
Chrysalis/base/SVector.h | 30 +-
Chrysalis/util/mutil.h | 6 +-
Inchworm/configure | 2 +-
Inchworm/src/Cigar.hpp | 2 +-
Inchworm/src/DeBruijnGraph.cpp | 9 +-
Inchworm/src/FastaToDeBruijn.cpp | 10 +-
Inchworm/src/IRKE.cpp | 21 +-
Inchworm/src/IRKE_run.cpp | 1 +
Inchworm/src/fastaToKmerCoverageStats.cpp | 12 +-
Inchworm/src/sequenceUtil.cpp | 8 +-
PerlLib/Fastq_reader.pm | 4 +
PerlLib/HPC/PBS_handler.pm | 19 +-
PerlLib/HPC/SGE_handler.pm | 2 +-
PerlLib/Pipeliner.pm | 60 +-
PerlLib/Process_cmd.pm | 15 +-
PerlLib/SAM_entry.pm | 14 +
Release.Notes | 16 +
Trinity | 610 +-
galaxy-plugin/EdgeR_differentialExpression.xml | 21 +-
.../EdgeR_differentialExpression_wrapper.py | 40 +
.../EdgeR_differentialExpression.xml | 21 +-
.../EdgeR_differentialExpression_wrapper.py | 40 +
.../GauravGalaxy/RSEM_estimates_to_matrix.xml | 51 +
Trinity => galaxy-plugin/GauravGalaxy/Trinity | 1554 ++---
.../GauravGalaxy/__add_to_PATH_setting.txt | 1 +
.../abundance_estimation_to_matrix.xml | 42 +
.../abundance_estimation_to_matrix_wrapper.py | 2 +-
.../GauravGalaxy/align_and_estimate_abundance.xml | 90 +
galaxy-plugin/GauravGalaxy/alignreads.xml | 138 +
galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml | 41 +
galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml~ | 41 +
.../GauravGalaxy/analyze_diff_exp_wrapper.py | 63 +
.../GauravGalaxy/bash_command_executer.py | 44 +
galaxy-plugin/GauravGalaxy/cat.xml | 41 +
.../diffExpress_edgeR.xml} | 8 +-
galaxy-plugin/GauravGalaxy/transcriptsToOrfs.xml | 53 +
.../{ => GauravGalaxy}/trinityToolWrapper.py | 3 +-
galaxy-plugin/{ => GauravGalaxy}/trinityrnaseq.xml | 4 +-
.../trinityrnaseq.xml.Graham_version_022014} | 12 +-
galaxy-plugin/GauravGalaxy/trinityrnaseq_norm.xml | 102 +
Trinity => galaxy-plugin/Trinity | 1554 ++---
.../abundance_estimation_to_matrix_wrapper.py | 2 +-
galaxy-plugin/analyze_diff_exp.xml | 41 +
galaxy-plugin/analyze_diff_exp_wrapper.py | 63 +
galaxy-plugin/trinityToolWrapper.py | 3 +-
galaxy-plugin/trinityrnaseq.xml | 4 +-
notes | 22 +
sample_data/Makefile | 8 +-
.../Sp_ds.10k.left.fq.gz | Bin
.../Sp_ds.10k.right.fq.gz | Bin
.../Sp_hs.10k.left.fq.gz | Bin
.../Sp_hs.10k.right.fq.gz | Bin
.../Sp_log.10k.left.fq.gz | Bin
.../Sp_log.10k.right.fq.gz | Bin
.../Sp_plat.10k.left.fq.gz | Bin
.../Sp_plat.10k.right.fq.gz | Bin
sample_data/test_DATA/Trinity.fasta | 4443 ++++++++++++
sample_data/test_DE_analysis/Makefile | 30 +
.../test_DE_analysis/Trinity_trans.TMM.EXPR.matrix | 7240 ++++++++++++++++++++
.../Trinity_trans.TPM.not_cross_norm | 7240 ++++++++++++++++++++
.../test_DE_analysis/Trinity_trans.counts.matrix | 7240 ++++++++++++++++++++
.../example_DESeq2_analysis_pipeline/Makefile | 0
.../example_DESeq2_analysis_pipeline/cleanme.pl | 0
.../example_DESeq2_analysis_pipeline/counts.matrix | 0
.../example_DESeq2_analysis_pipeline/run_DESeq2.sh | 0
.../example_DESeq2_analysis_pipeline/samples.txt | 0
.../example_edgeR_analysis_pipeline/Makefile | 0
.../Trinity.fa.seqLens | 0
.../__example_edgeR_output_dir/TMM_info.txt | 0
.../__example_edgeR_output_dir/__tmp_runTMM.R | 0
.../__tmp_run_edgeR.1820.R | 0
.../__tmp_targets.1820.dat | 0
.../__example_edgeR_output_dir/all_data_files.list | 0
.../__example_edgeR_output_dir/cysts.dat | 0
.../example.matrix.normalized.FPKM | 0
.../__example_edgeR_output_dir/myc.dat | 0
.../__example_edgeR_output_dir/myc_vs_cysts.eps | 0
.../myc_vs_cysts.results.txt | 0
.../example_edgeR_analysis_pipeline/cleanMe.sh | 0
.../example_edgeR_analysis_pipeline/example.matrix | 0
.../example_edgeR_analysis_pipeline/runMe.sh | 0
.../deprecated}/testEdgeRfuncs/Makefile | 0
.../deprecated}/testEdgeRfuncs/cleanMe.sh | 0
.../deprecated}/testEdgeRfuncs/dataA.dat | 0
.../deprecated}/testEdgeRfuncs/dataB.dat | 0
.../deprecated}/testEdgeRfuncs/runMe.sh | 0
.../testEdgeRfuncs/run_edgeR_on_sample_data.R | 0
.../deprecated}/testEdgeRfuncs/targets.dat | 0
sample_data/test_DE_analysis/notes | 1 +
sample_data/test_DE_analysis/samples.txt | 14 +
...nome-guided_Trinity_use_existing_bam.use_LSF.sh | 0
...nome-guided_Trinity_use_existing_bam.use_PBS.sh | 0
...nome-guided_Trinity_use_existing_bam.use_SGE.sh | 0
.../{ => old}/run_Schizo_TrinityGG.SE.sh | 0
.../{ => old}/run_Schizo_TrinityGG.sh | 0
.../{ => old}/run_genome-guided_Trinity.sh | 0
.../{ => old}/run_mouse_TrinityGG.sh | 0
sample_data/test_Trinity_Assembly/Makefile | 23 +-
sample_data/test_Trinity_Assembly/README | 4 +-
sample_data/test_Trinity_Assembly/cleanme.pl | 6 +
.../misc_run_tests/__runMe_include_long_reads.sh | 2 +-
..._qual_trimming_and_normalize_libs_separately.sh | 15 +-
sample_data/test_Trinity_Assembly/runMe.sh | 16 +-
.../test_Trinity_Coding_Extraction/Makefile | 6 -
.../Trinity.fasta.gz | Bin 39206 -> 0 bytes
.../test_Trinity_Coding_Extraction/cleanme.pl | 39 -
.../test_Trinity_Coding_Extraction/runMe.sh | 17 -
.../test_align_and_estimate_abundance/Makefile | 15 +-
.../Trinity.fasta.gene_trans_map | 124 -
.../Trinity.fasta.gz | Bin 54372 -> 0 bytes
.../align_and_estimate_tester.pl | 93 +
.../test_align_and_estimate_abundance/cleanme.pl | 27 +-
.../plot_paired_comparisons.Rscript | 14 +
.../reads.left.fq.gz | 1 -
.../reads.right.fq.gz | 1 -
.../run_eXpress.sh | 1 -
.../test_align_and_estimate_abundance/run_rsem.sh | 14 -
.../test_align_and_estimate_abundance/samples.txt | 4 +
sample_data/test_edgeR_diff_expr/Makefile | 17 -
sample_data/test_full_edgeR_pipeline/cleanme.pl | 1 -
.../samples_n_reads_decribed.txt | 8 +-
trinity-plugins/BIN/README | 2 +
trinity-plugins/Makefile | 47 +-
.../fstrozzi-Fastool-7c3e034f05/fastool.c | 7 +-
trinity-plugins/scaffold_iworm_contigs/Makefile | 10 +
.../ScaffoldIwormContigs.cpp | 216 +
.../scaffold_iworm_contigs/error_checker.cpp | 40 +
.../scaffold_iworm_contigs/error_checker.h | 24 +
trinity-plugins/slclust/Makefile.bak | 10 -
util/abundance_estimates_to_matrix.pl | 117 +-
util/align_and_estimate_abundance.pl | 262 +-
util/filter_fasta_by_rsem_values.pl | 6 +-
util/insilico_read_normalization.pl | 6 +
util/misc/blast_outfmt6_group_segments.pl | 165 +
..._outfmt6_group_segments.to_Markov_Clustering.pl | 167 +
...blast_outfmt6_group_segments.tophit_coverage.pl | 110 +
...ig_E_statistic.pl => contig_ExN50_statistic.pl} | 72 +-
.../count_features_given_MIN_FPKM_threshold.pl | 2 +-
...unt_matrix_features_given_MIN_FPKM_threshold.pl | 52 -
...ount_matrix_features_given_MIN_TPM_threshold.pl | 52 +
.../get_longest_isoform_seq_per_trinity_gene.pl | 62 +
util/misc/gmap_gff3_to_percent_length_stats.pl | 1 +
util/misc/merge_RSEM_output_to_matrix.pl | 142 +
util/misc/pair_up_fastq_files_1_2.pl | 30 +
util/misc/pair_up_fastq_files_LeftRight.pl | 32 +
util/misc/pair_up_fastq_files_R1_R2.pl | 30 +
util/misc/run_GSNAP.pl | 2 +-
util/misc/run_HISAT.pl | 29 +-
util/misc/run_STAR.pl | 186 +
util/misc/run_trimmomatic_qual_trimming.pl | 24 +-
util/misc/simulate_illuminaPE_from_transcripts.pl | 239 +-
util/misc/sixFrameTranslation.pl | 38 +
...ine.pl => run_DE_analysis_from_samples_file.pl} | 195 +-
...R_pipeline.pl => run_RSEM_from_samples_file.pl} | 151 +-
util/run_Trinity_edgeR_pipeline.pl | 6 +-
...ipeline.pl => run_Trinity_from_samples_file.pl} | 139 +-
...tor.pl => GG_partitioned_trinity_aggregator.pl} | 2 +-
.../eXpress_trans_to_gene_results.pl | 18 +-
util/support_scripts/fastQ_to_tab.pl | 15 +-
...esults.pl => kallisto_trans_to_gene_results.pl} | 36 +-
.../merge_left_right_nameSorted_SAMs.pl | 6 +-
.../partitioned_trinity_aggregator.pl | 12 +-
util/support_scripts/plugin_install_tests.sh | 7 -
util/support_scripts/run_TMM_scale_matrix.pl | 1 +
util/support_scripts/{tests.py => tests/test.py} | 42 +-
util/support_scripts/tests/test_prep.py | 122 +
util/support_scripts/{ => tests}/tests.py | 38 +-
util/support_scripts/trinity_install_tests.sh | 6 +
...y_cmds.pl => write_partitioned_trinity_cmds.pl} | 0
199 files changed, 31802 insertions(+), 3613 deletions(-)
diff --git a/Analysis/DifferentialExpression/DE_graph_to_dot.pl b/Analysis/DifferentialExpression/DE_graph_to_dot.pl
new file mode 100755
index 0000000..2b43948
--- /dev/null
+++ b/Analysis/DifferentialExpression/DE_graph_to_dot.pl
@@ -0,0 +1,55 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+my $usage = "usage: $0 DE.graph\n\n";
+
+my $DE_graph = $ARGV[0] or die $usage;
+
+
+=color_panel
+
+> colorpanel(10, 'black', 'purple', 'red')
+ [1] "#000000" "#28083C" "#501078" "#7818B4" "#A020F0" "#A020F0" "#B818B4"
+ [8] "#D01078" "#E7083C" "#FF0000"
+
+=cut
+
+
+my @colors = (
+ "#000000", "#28083C", "#501078", "#7818B4", "#A020F0", "#A020F0", "#B818B4",
+ "#D01078", "#E7083C", "#FF0000"
+ );
+
+
+main: {
+
+ print "digraph G {\n";
+
+ open (my $fh, $DE_graph) or die "Error, cannot open file $DE_graph";
+ my $line = <$fh>;
+ chomp $line;
+ close $fh;
+
+ my @x = split(/\t/, $line);
+ shift @x;
+ foreach my $pair (@x) {
+ my ($from, $to, $logFC) = split(/,/, $pair);
+
+ my $color_index = int($logFC + 0.5);
+ if ($color_index > $#colors) {
+ $color_index = $#colors;
+ }
+ my $color = $colors[$color_index];
+
+ print " $from->$to\[color=\"$color\"]\n";
+ }
+
+ print "}\n";
+
+ exit(0);
+}
+
+
+
diff --git a/Analysis/DifferentialExpression/PtR b/Analysis/DifferentialExpression/PtR
index 65d57db..88539fb 100755
--- a/Analysis/DifferentialExpression/PtR
+++ b/Analysis/DifferentialExpression/PtR
@@ -151,6 +151,8 @@ my $usage = <<__EOUSAGE__;
#
# --CPM convert to counts per million (uses sum of totals before filtering)
#
+# --binary all values > 0 are set to 1. All values < 0 are set to zero.
+#
# --log2
#
# --center_rows subtract row mean from each data point. (only used under '--heatmap' )
@@ -284,6 +286,8 @@ my $gene_grep;
my $ZSCALE_ROWS = 0;
+my $MAKE_BINARY_FLAG = 0;
+
my $gene_factors_file;
my $var_vs_count_hist_plot;
@@ -366,6 +370,8 @@ my $NO_REUSE = 0;
'top_rows=i' => \$top_rows,
'min_colSums=i' => \$min_colSums,
'min_rowSums=i' => \$min_rowSums,
+
+ 'binary' => \$MAKE_BINARY_FLAG,
'gene_grep=s' => \$gene_grep,
@@ -543,7 +549,10 @@ main: {
if ($samples_file) {
- $Rscript .= "samples_data = read.table(\"$samples_file\", header=F, check.names=F)\n";
+ $Rscript .= "samples_data = read.table(\"$samples_file\", header=F, check.names=F, fill=T)\n";
+ $Rscript .= "samples_data = samples_data[samples_data[,2] != '',]\n"; # require the rep column to be filled, also enable compatibility with full-trinity-edgeR-pipe samples file
+
+
#$Rscript .= "sample_types = as.factor(unique(samples_data[,1]))\n";
$Rscript .= "sample_types = as.character(unique(samples_data[,1]))\n";
@@ -710,6 +719,11 @@ main: {
$Rscript .= "dev.off()\n";
}
+
+
+ #################
+ ## Filtering data
+ #################
if ($min_expressed_genes && $min_gene_expr_val) {
@@ -759,6 +773,13 @@ main: {
}
+ $Rscript .= "initial_matrix = data # store before doing various data transformations\n";
+
+
+ #############################################
+ ## Now doing data transformations as needed:
+ #############################################
+
if ($CPM) {
$Rscript .= "cs = colSums(data)\n";
@@ -772,6 +793,11 @@ main: {
$output_prefix .= ".log2";
$Rscript .= "write.table(data, file=\"$output_prefix.dat\", quote=F, sep=\"\t\")\n" if $write_intermediate_data_tables_flag;
}
+
+ if ($MAKE_BINARY_FLAG) {
+ $output_prefix .= ".binary";
+ $Rscript .= "data[data<0] = 0; data[data>0] = 1;\n";
+ }
if (defined $minValAltNA) {
@@ -1367,13 +1393,22 @@ main: {
if ($lexical_column_ordering) {
$Rscript .= "heatmap_data = heatmap_data[,order(colnames(heatmap_data))]\n";
+ if ($samples_file) {
+ # sample annotations must continue to match column ordering of data matrix
+ $Rscript .= "sampleAnnotations = sampleAnnotations[,order(colnames(heatmap_data))]\n";
+ }
}
elsif ($specified_column_ordering) {
$Rscript .= "heatmap_data = heatmap_data[,$specified_column_ordering]\n";
+ if ($samples_file) {
+ # sample annotations must continue to match column ordering of data matrix
+ $Rscript .= "sampleAnnotations = sampleAnnotations[,$specified_column_ordering]\n";
+ }
}
}
+
my $Rowv = "as.dendrogram(hc_genes)";
if ($gene_clust eq 'none' || ($gene_factors_file && $order_by_gene_factor)) {
if ($Colv eq 'F') {
@@ -1618,15 +1653,12 @@ sub add_sample_QC_analysis_R {
$Rscript .= " d = data[,samples_want]\n"
+ . " initial_matrix_samples_want = initial_matrix[,samples_want]\n"
. " op <- par(mar = c(10,10,10,10))\n";
- if ($LOG2) {
- $Rscript .= " barplot(colSums(2^(d-1)), las=2, main=paste(\"Sum of Frags for replicates of:\", sample_name), ylab='', cex.names=0.7)\n";
- }
- else {
-
- $Rscript .= " barplot(colSums(d), las=2, main=paste(\"Sum of Frags for replicates of:\", sample_name), ylab='', cex.names=0.7)\n"
- }
+
+ $Rscript .= " barplot(colSums(initial_matrix_samples_want), las=2, main=paste(\"Sum of Frags for replicates of:\", sample_name), ylab='', cex.names=0.7)\n";
+
$Rscript .= " par(op)\n"
. " pairs3(d, pch='.', CustomColorFun=Scatter_color_fun, main=paste('Replicate Scatter:', sample_name)) # scatter plots\n"
diff --git a/Analysis/DifferentialExpression/TissueEnrichment/group_isoforms_by_tissue_enrichment.pl b/Analysis/DifferentialExpression/TissueEnrichment/group_isoforms_by_tissue_enrichment.pl
new file mode 100755
index 0000000..445d1eb
--- /dev/null
+++ b/Analysis/DifferentialExpression/TissueEnrichment/group_isoforms_by_tissue_enrichment.pl
@@ -0,0 +1,54 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+my $usage = "usage: $0 up_cats.counts\n\n";
+
+my $counts_file = $ARGV[0] or die $usage;
+
+
+main: {
+
+ my %data;
+
+ open (my $fh, "$counts_file") or die $!;
+ while (<$fh>) {
+ chomp;
+ my @x = split(/\t/);
+ my $trans = $x[0];
+ my $category = $x[5];
+
+ my $gene = $trans;
+ $gene =~ s/\_i\d+$//;
+
+ $data{$gene}->{$trans} = $category;
+ }
+ close $fh;
+
+
+ foreach my $gene (keys %data) {
+
+ my @trans = keys %{$data{$gene}};
+
+ if (scalar @trans < 2) { next; }
+
+
+ my %categories;
+
+ foreach my $trans (@trans) {
+
+ my $category = $data{$gene}->{$trans};
+
+ $categories{$category}++;
+ }
+
+ my @cats = keys %categories;
+
+ print join("\t", $gene, scalar(@trans), scalar @cats, join("__", sort @cats) ) . "\n";
+ }
+
+
+ exit(0);
+}
+
diff --git a/Analysis/DifferentialExpression/add_blastx_hit_to_trinity_id.pl b/Analysis/DifferentialExpression/add_blastx_hit_to_trinity_id.pl
index 94a0585..eadb6b2 100755
--- a/Analysis/DifferentialExpression/add_blastx_hit_to_trinity_id.pl
+++ b/Analysis/DifferentialExpression/add_blastx_hit_to_trinity_id.pl
@@ -15,13 +15,12 @@ main: {
{
open (my $fh, $blastx_file) or die $!;
while (<$fh>) {
- if (/^comp/) {
- /^(comp\d+_c\d+)(_seq\d+)/ or die "Error, cannot parse trinity accession";
+ if (/^(.*|c\d+)_/) {
+
my $comp_id = $1;
- my $trans_id = $2;
- $trans_id = $comp_id . $trans_id;
-
+
my @x = split(/\t/);
+ my $trans_id = $x[0];
my $hit = $x[1];
$blastx_top_hit{$comp_id} = $hit;
$blastx_top_hit{$trans_id} = $hit;
@@ -30,7 +29,7 @@ main: {
close $fh;
}
-
+
open (my $fh, $trinity_matrix) or die "Error, cannot open file $trinity_matrix";
while (<$fh>) {
chomp;
diff --git a/Analysis/DifferentialExpression/analyze_diff_expr.pl b/Analysis/DifferentialExpression/analyze_diff_expr.pl
index 0c8672c..e451265 100755
--- a/Analysis/DifferentialExpression/analyze_diff_expr.pl
+++ b/Analysis/DifferentialExpression/analyze_diff_expr.pl
@@ -3,7 +3,7 @@
use strict;
use warnings;
use Carp;
-use Getopt::Long qw(:config no_ignore_case bundling);
+use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use FindBin;
use Data::Dumper;
@@ -13,7 +13,7 @@ my $usage = <<__EOUSAGE__;
#
# Required:
#
-# --matrix <string> matrix.normalized.FPKM
+# --matrix <string> TMM.EXPR.matrix
#
# Optional:
#
@@ -150,7 +150,7 @@ main: {
my $matrix_header;
{
- # not counts, but FPKM values!
+ # not counts, but TPM values!
open (my $fh, $matrix_file) or die "Error, cannot read file $matrix_file";
$matrix_header = <$fh>;
chomp $matrix_header;
@@ -284,7 +284,7 @@ sub parse_result_files_find_diffExp {
foreach my $result_file (@$result_files_aref) {
- $result_file =~ /\.([^\.]+)_vs_([^\.]+)\./ or die "Error, cannot extract condition names from $result_file";
+ $result_file =~ /matrix\.(\S+)_vs_(\S+)\.[^\.]+\.DE_results$/ or die "Error, cannot extract condition names from $result_file";
my ($condA, $condB) = ($1, $2);
my $pairwise_samples_file = "$result_file.samples";
diff --git a/Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl b/Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl
index ba49652..c40f19d 100755
--- a/Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl
+++ b/Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl
@@ -123,6 +123,9 @@ main: {
# make another heatmap:
print $ofh "partition_colors = rainbow(length(unique(gene_partition_assignments)), start=0.4, end=0.95)\n";
+ print $ofh "gene_colors_dframe = data.frame(clusters=gene_partition_assignments, colors=partition_colors[gene_partition_assignments])\n";
+ print $ofh "write.table(gene_colors_dframe, file=\"$core_filename.gene_cluster_colors.dat\", quote=F, sep='\t')\n";
+
print $ofh "gene_colors = as.matrix(partition_colors[gene_partition_assignments])\n";
print $ofh "pdf(\"$core_filename.heatmap.pdf\")\n";
diff --git a/Analysis/DifferentialExpression/run_DE_analysis.pl b/Analysis/DifferentialExpression/run_DE_analysis.pl
index 10b1cff..0a7fd4a 100755
--- a/Analysis/DifferentialExpression/run_DE_analysis.pl
+++ b/Analysis/DifferentialExpression/run_DE_analysis.pl
@@ -12,6 +12,10 @@ use Fasta_reader;
use Data::Dumper;
+my $ROTS_B = 500;
+my $ROTS_K = 5000;
+
+
my $usage = <<__EOUSAGE__;
@@ -21,8 +25,10 @@ my $usage = <<__EOUSAGE__;
#
# --matrix|m <string> matrix of raw read counts (not normalized!)
#
-# --method <string> edgeR|DESeq|DESeq2 (DESeq(2?) only supported here w/ bio replicates)
-#
+# --method <string> edgeR|DESeq2|voom|ROTS
+# note: you should have biological replicates.
+# edgeR will support having no bio replicates with
+# a fixed dispersion setting.
#
# Optional:
#
@@ -54,24 +60,24 @@ my $usage = <<__EOUSAGE__;
# ## EdgeR-related parameters
# ## (no biological replicates)
#
-# --dispersion <float> edgeR dispersion value (default: 0.1) set to 0 for poisson (sometimes breaks...)
+# --dispersion <float> edgeR dispersion value (Read edgeR manual to guide your value choice)
+# http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
+# ## ROTS parameters
+# --ROTS_B <int> : number of bootstraps and permutation resampling (default: $ROTS_B)
+# --ROTS_K <int> : largest top genes size (default: $ROTS_K)
#
-# http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
#
###############################################################################################
#
-# ## DE-Seq related parameters
-#
-# --DESEQ_method <string> "pooled", "pooled-CR", "per-condition", "blind"
-# --DESEQ_sharingMode <string> "maximum", "fit-only", "gene-est-only"
-# --DESEQ_fitType <string> fitType = c("parametric", "local")
+# Documentation and manuals for various DE methods. Please read for more advanced and more
+# fine-tuned DE analysis than provided by this helper script.
#
-# ## (no biological replicates)
-# note: FIXED as: method=blind, sharingMode=fit-only
-#
-# http://www.bioconductor.org/packages/release/bioc/html/DESeq.html
+# edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
+# DESeq2: http://bioconductor.org/packages/release/bioc/html/DESeq2.html
+# voom/limma: http://bioconductor.org/packages/release/bioc/html/limma.html
+# ROTS: http://www.btk.fi/research/research-groups/elo/software/rots/
#
-################################################################################################
+###############################################################################################
@@ -87,15 +93,14 @@ my $samples_file;
my $min_rowSum_counts = 2;
my $help_flag;
my $output_dir;
-my $dispersion = 0.1;
+my $dispersion; # I've used 0.1 myself - but read the manual to guide your choice.
+
my $contrasts_file;
my $reference_sample;
my $make_tar_gz_file = 0;
-my ($DESEQ_method, $DESEQ_sharingMode, $DESEQ_fitType);
-
&GetOptions ( 'h' => \$help_flag,
'matrix|m=s' => \$matrix_file,
@@ -108,13 +113,11 @@ my ($DESEQ_method, $DESEQ_sharingMode, $DESEQ_fitType);
'reference_sample=s' => \$reference_sample,
'contrasts=s' => \$contrasts_file,
-
- 'DESEQ_method=s' => \$DESEQ_method,
- 'DESEQ_sharingMode=s' => \$DESEQ_sharingMode,
- 'DESEQ_fitType=s' => \$DESEQ_fitType,
-
'tar_gz_outdir' => \$make_tar_gz_file,
+
+ 'ROTS_B=i' => \$ROTS_B,
+ 'ROTS_K=i' => \$ROTS_K,
);
@@ -142,8 +145,8 @@ if ($matrix_file =~ /fpkm/i) {
}
-unless ($method =~ /^(edgeR|DESeq2?|GLM)$/) {
- die "Error, do not recognize method: [$method], only edgeR or DESeq currently.";
+unless ($method =~ /^(edgeR|DESeq2|voom|ROTS|GLM)$/) {
+ die "Error, do not recognize --method [$method]";
}
@@ -182,7 +185,9 @@ main: {
$output_dir = "$method.$$.dir";
}
- mkdir($output_dir) or die "Error, cannot mkdir $output_dir";
+ unless (-d $output_dir) {
+ mkdir($output_dir) or die "Error, cannot mkdir $output_dir";
+ }
chdir $output_dir or die "Error, cannot cd to $output_dir";
@@ -257,13 +262,15 @@ main: {
&run_edgeR_sample_pair($matrix_file, \%samples, \%sample_name_to_column, $sample_a, $sample_b);
}
- elsif ($method eq "DESeq") {
- &run_DESeq_sample_pair($matrix_file, \%samples, \%sample_name_to_column, $sample_a, $sample_b);
- }
elsif ($method eq "DESeq2") {
&run_DESeq2_sample_pair($matrix_file, \%samples, \%sample_name_to_column, $sample_a, $sample_b);
}
-
+ elsif ($method eq 'voom') {
+ &run_limma_voom_sample_pair($matrix_file, \%samples, \%sample_name_to_column, $sample_a, $sample_b);
+ }
+ elsif ($method eq 'ROTS') {
+ &run_ROTS_sample_pair($matrix_file, \%samples, \%sample_name_to_column, $sample_a, $sample_b);
+ }
}
}
@@ -390,10 +397,17 @@ sub run_edgeR_sample_pair {
if ($num_rep_A > 1 && $num_rep_B > 1) {
print $ofh "exp_study = estimateCommonDisp(exp_study)\n";
print $ofh "exp_study = estimateTagwiseDisp(exp_study)\n";
- print $ofh "et = exactTest(exp_study)\n";
+ print $ofh "et = exactTest(exp_study, pair=c(\"$sample_A\", \"$sample_B\"))\n";
+ }
+ elsif (!$dispersion) {
+ die "Error, cannot calculate dispersions due to lack of replicates. Specify a dispersion parameter --dispersion <float>. See help for details\n";
}
else {
- print $ofh "et = exactTest(exp_study, dispersion=$dispersion)\n";
+ unless (defined $dispersion) {
+ confess "Error, must set --dispersion <float> when using edgeR w/o bio replicates";
+
+ }
+ print $ofh "et = exactTest(exp_study, pair=c(\"$sample_A\", \"$sample_B\"), dispersion=$dispersion)\n";
}
print $ofh "tTags = topTags(et,n=NULL)\n";
print $ofh "write.table(tTags, file=\'$output_prefix.edgeR.DE_results\', sep='\t', quote=F, row.names=T)\n";
@@ -423,13 +437,13 @@ sub run_edgeR_sample_pair {
return;
}
-
-sub run_DESeq_sample_pair {
+
+sub run_DESeq2_sample_pair {
my ($matrix_file, $samples_href, $sample_name_to_column_index_href, $sample_A, $sample_B) = @_;
my $output_prefix = basename($matrix_file) . "." . join("_vs_", ($sample_A, $sample_B));
- my $Rscript_name = "$output_prefix.DESeq.Rscript";
+ my $Rscript_name = "$output_prefix.DESeq2.Rscript";
my @reps_A = @{$samples_href->{$sample_A}};
my @reps_B = @{$samples_href->{$sample_B}};
@@ -437,6 +451,11 @@ sub run_DESeq_sample_pair {
my $num_rep_A = scalar(@reps_A);
my $num_rep_B = scalar(@reps_B);
+
+ if ($num_rep_A < 2 || $num_rep_B < 2) {
+ print STDERR "DESeq2 only supported here with biological replicates for each condition. Skipping: $sample_A vs. $sample_B *** \n\n";
+ return;
+ }
my @rep_column_indices;
foreach my $rep_name (@reps_A, @reps_B) {
@@ -445,10 +464,10 @@ sub run_DESeq_sample_pair {
}
- ## write R-script to run edgeR
+ ## write R-script to run DESeq
open (my $ofh, ">$Rscript_name") or die "Error, cannot write to $Rscript_name";
- print $ofh "library(DESeq)\n";
+ print $ofh "library(DESeq2)\n";
print $ofh "\n";
print $ofh "data = read.table(\"$matrix_file\", header=T, row.names=1, com='')\n";
@@ -456,73 +475,56 @@ sub run_DESeq_sample_pair {
print $ofh "rnaseqMatrix = data[,col_ordering]\n";
print $ofh "rnaseqMatrix = round(rnaseqMatrix)\n";
print $ofh "rnaseqMatrix = rnaseqMatrix[rowSums(rnaseqMatrix)>=$min_rowSum_counts,]\n";
- print $ofh "conditions = factor(c(rep(\"$sample_A\", $num_rep_A), rep(\"$sample_B\", $num_rep_B)))\n";
- print $ofh "\n";
- print $ofh "exp_study = newCountDataSet(rnaseqMatrix, conditions)\n";
- print $ofh "exp_study = estimateSizeFactors(exp_study)\n";
- #print $ofh "sizeFactors(exp_study)\n";
- #print $ofh "exp_study = estimateVarianceFunctions(exp_study)\n";
-
- if ($num_rep_A == 1 && $num_rep_B == 1) {
-
- print STDERR "\n\n** Note, no replicates, setting method='blind', sharingMode='fit-only'\n\n";
-
- $DESEQ_method = "blind";
- $DESEQ_sharingMode = "fit-only";
-
- }
+ print $ofh "conditions = data.frame(conditions=factor(c(rep(\"$sample_A\", $num_rep_A), rep(\"$sample_B\", $num_rep_B))))\n";
+ print $ofh "rownames(conditions) = colnames(rnaseqMatrix)\n";
+ print $ofh "ddsFullCountTable <- DESeqDataSetFromMatrix(\n"
+ . " countData = rnaseqMatrix,\n"
+ . " colData = conditions,\n"
+ . " design = ~ conditions)\n";
+ print $ofh "dds = DESeq(ddsFullCountTable)\n";
+ print $ofh "res = results(dds)\n";
- # got bio replicates
- my $est_disp_cmd = "exp_study = estimateDispersions(exp_study";
-
- if ($DESEQ_method) {
- $est_disp_cmd .= ", method=\"$DESEQ_method\"";
- }
-
- if ($DESEQ_sharingMode) {
- $est_disp_cmd .= ", sharingMode=\"$DESEQ_sharingMode\"";
- }
-
- if ($DESEQ_fitType) {
- $est_disp_cmd .= ", fitType=\"$DESEQ_fitType\"";
- }
-
- $est_disp_cmd .= ")\n";
-
- print $ofh $est_disp_cmd;
-
+
+ # adj from: Carsten Kuenne, thx!
+ ##recreates baseMeanA and baseMeanB columns that are not created by default DESeq2 anymore
+ print $ofh "baseMeanA <- rowMeans(counts(dds, normalized=TRUE)[,colData(dds)\$condition == \"$sample_A\"])\n";
+ print $ofh "baseMeanB <- rowMeans(counts(dds, normalized=TRUE)[,colData(dds)\$condition == \"$sample_B\"])\n";
+ print $ofh "res = cbind(baseMeanA, baseMeanB, as.data.frame(res))\n";
+
+ ##adds an “id” column headline for column 0
+ print $ofh "res = cbind(id=rownames(res), as.data.frame(res))\n";
+
+ print $ofh "res\$padj[is.na(res\$padj)] <- 1\n"; # Carsten Kuenne
- #print $ofh "str(fitInfo(exp_study))\n";
- #print $ofh "plotDispEsts(exp_study)\n";
- print $ofh "\n";
- print $ofh "res = nbinomTest(exp_study, \"$sample_A\", \"$sample_B\")\n";
- print $ofh "\n";
-## output results
- print $ofh "write.table(res[order(res\$pval),], file=\'$output_prefix.DESeq.DE_results\', sep='\t', quote=FALSE, row.names=FALSE)\n";
+ ##set row.names to false to accomodate change above
+
+ ## output results
+ print $ofh "write.table(as.data.frame(res[order(res\$pvalue),]), file=\'$output_prefix.DESeq2.DE_results\', sep='\t', quote=FALSE, row.names=F)\n";
## generate MA and Volcano plots
print $ofh "source(\"$FindBin::Bin/R/rnaseq_plot_funcs.R\")\n";
- print $ofh "pdf(\"$output_prefix.DESeq.DE_results.MA_n_Volcano.pdf\")\n";
+ print $ofh "pdf(\"$output_prefix.DESeq2.DE_results.MA_n_Volcano.pdf\")\n";
print $ofh "plot_MA_and_Volcano(log2(res\$baseMean+1), res\$log2FoldChange, res\$padj)\n";
print $ofh "dev.off()\n";
-
+
+
close $ofh;
-
-
## Run R-script
my $cmd = "R --vanilla -q < $Rscript_name";
&process_cmd($cmd);
return;
}
-
-sub run_DESeq2_sample_pair {
+
+
+####
+sub run_limma_voom_sample_pair {
my ($matrix_file, $samples_href, $sample_name_to_column_index_href, $sample_A, $sample_B) = @_;
-
+
my $output_prefix = basename($matrix_file) . "." . join("_vs_", ($sample_A, $sample_B));
- my $Rscript_name = "$output_prefix.DESeq2.Rscript";
+ my $Rscript_name = "$output_prefix.$sample_A.vs.$sample_B.voom.Rscript";
my @reps_A = @{$samples_href->{$sample_A}};
my @reps_B = @{$samples_href->{$sample_B}};
@@ -530,69 +532,169 @@ sub run_DESeq2_sample_pair {
my $num_rep_A = scalar(@reps_A);
my $num_rep_B = scalar(@reps_B);
-
- if ($num_rep_A < 2 || $num_rep_B < 2) {
- print STDERR "DESeq2 only supported here with biological replicates for each condition. Skipping: $sample_A vs. $sample_B *** \n\n";
- return;
+ unless ($num_rep_A > 1 && $num_rep_B > 1) {
+ die "Error, need multiple biological replicates for each sample in order to run voom";
}
-
+
my @rep_column_indices;
foreach my $rep_name (@reps_A, @reps_B) {
my $column_index = $sample_name_to_column_index_href->{$rep_name} or die "Error, cannot determine column index for replicate name [$rep_name]" . Dumper($sample_name_to_column_index_href);
push (@rep_column_indices, $column_index);
}
-
+
## write R-script to run edgeR
open (my $ofh, ">$Rscript_name") or die "Error, cannot write to $Rscript_name";
- print $ofh "library(DESeq2)\n";
+ print $ofh "library(edgeR)\n";
+ print $ofh "library(limma)\n";
+
print $ofh "\n";
-
+
print $ofh "data = read.table(\"$matrix_file\", header=T, row.names=1, com='')\n";
print $ofh "col_ordering = c(" . join(",", @rep_column_indices) . ")\n";
print $ofh "rnaseqMatrix = data[,col_ordering]\n";
print $ofh "rnaseqMatrix = round(rnaseqMatrix)\n";
print $ofh "rnaseqMatrix = rnaseqMatrix[rowSums(rnaseqMatrix)>=$min_rowSum_counts,]\n";
- print $ofh "conditions = data.frame(conditions=factor(c(rep(\"$sample_A\", $num_rep_A), rep(\"$sample_B\", $num_rep_B))))\n";
- print $ofh "rownames(conditions) = colnames(rnaseqMatrix)\n";
- print $ofh "ddsFullCountTable <- DESeqDataSetFromMatrix(\n"
- . " countData = rnaseqMatrix,\n"
- . " colData = conditions,\n"
- . " design = ~ conditions)\n";
- print $ofh "dds = DESeq(ddsFullCountTable)\n";
- print $ofh "res = results(dds)\n";
+ print $ofh "conditions = factor(c(rep(\"$sample_A\", $num_rep_A), rep(\"$sample_B\", $num_rep_B)))\n";
+ print $ofh "\n";
+ print $ofh "design = model.matrix(~conditions)\n";
+ print $ofh "## TMM normalize data\n";
+ print $ofh "lib_sizes = colSums(rnaseqMatrix)\n";
+ print $ofh "tmm_norm_factors = calcNormFactors(rnaseqMatrix, method='TMM')\n";
+ print $ofh "x = DGEList(counts=rnaseqMatrix)\n";
+ print $ofh "# voom transformation\n";
+ print $ofh "y = voom(x, design, lib.size=lib_sizes*tmm_norm_factors, plot=F)\n";
+ print $ofh "fit = eBayes(lmFit(y,design))\n";
+ print $ofh "tTags = topTable(fit,coef=2,number=Inf)\n";
+ print $ofh "# output results, including average expression val for each feature\n";
+ print $ofh "c = cpm(x)\n";
+ print $ofh "m = apply(c, 1, mean)\n";
+ print $ofh "tTags2 = cbind(tTags, logCPM=log2(m[rownames(tTags)]))\n";
+ print $ofh "DE_matrix = data.frame(logFC=tTags\$logFC, logCPM=tTags2\$logCPM, PValue=tTags\$'P.Value', FDR=tTags\$'adj.P.Val')\n";
+ print $ofh "rownames(DE_matrix) = rownames(tTags)\n";
+ print $ofh "write.table(DE_matrix, file=\'$output_prefix.voom.DE_results\', sep='\t', quote=F, row.names=T)\n";
+
+ ## generate MA and Volcano plots
+ print $ofh "# MA and volcano plots\n";
+ print $ofh "source(\"$FindBin::Bin/R/rnaseq_plot_funcs.R\")\n";
+ print $ofh "pdf(\"$output_prefix.voom.DE_results.MA_n_Volcano.pdf\")\n";
+ print $ofh "plot_MA_and_Volcano(tTags2\$logCPM, tTags\$logFC, tTags\$'adj.P.Val')\n";
+ print $ofh "dev.off()\n";
+
+ close $ofh;
+ ## Run R-script
+ my $cmd = "R --vanilla -q < $Rscript_name";
- # adj from: Carsten Kuenne, thx!
- ##recreates baseMeanA and baseMeanB columns that are not created by default DESeq2 anymore
- print $ofh "baseMeanA <- rowMeans(counts(dds, normalized=TRUE)[,colData(dds)\$condition == \"$sample_A\"])\n";
- print $ofh "baseMeanB <- rowMeans(counts(dds, normalized=TRUE)[,colData(dds)\$condition == \"$sample_B\"])\n";
- print $ofh "res = cbind(baseMeanA, baseMeanB, as.data.frame(res))\n";
-
- ##adds an “id” column headline for column 0
- print $ofh "res = cbind(id=rownames(res), as.data.frame(res))\n";
- print $ofh "res\$padj[is.na(res\$padj)] <- 1\n"; # Carsten Kuenne
+ eval {
+ &process_cmd($cmd);
+ };
+ if ($@) {
+ print STDERR "$@\n\n";
+ print STDERR "\n\nWARNING: This voom comparison failed...\n\n";
+ ## if this is due to data paucity, such as in small sample data sets, then ignore for now.
+ }
- ##set row.names to false to accomodate change above
- ## output results
- print $ofh "write.table(as.data.frame(res[order(res\$pvalue),]), file=\'$output_prefix.DESeq2.DE_results\', sep='\t', quote=FALSE, row.names=F)\n";
+ return;
+}
+
+
+####
+sub run_ROTS_sample_pair {
+ my ($matrix_file, $samples_href, $sample_name_to_column_index_href, $sample_A, $sample_B) = @_;
+
+ my $output_prefix = basename($matrix_file) . "." . join("_vs_", ($sample_A, $sample_B));
+
+ my $Rscript_name = "$output_prefix.$sample_A.vs.$sample_B.ROTS.Rscript";
+
+ my @reps_A = @{$samples_href->{$sample_A}};
+ my @reps_B = @{$samples_href->{$sample_B}};
+
+ my $num_rep_A = scalar(@reps_A);
+ my $num_rep_B = scalar(@reps_B);
+
+ unless ($num_rep_A > 1 && $num_rep_B > 1) {
+ die "Error, need multiple biological replicates for each sample in order to run ROTS";
+ }
+
+ my @rep_column_indices;
+ foreach my $rep_name (@reps_A, @reps_B) {
+ my $column_index = $sample_name_to_column_index_href->{$rep_name} or die "Error, cannot determine column index for replicate name [$rep_name]" . Dumper($sample_name_to_column_index_href);
+ push (@rep_column_indices, $column_index);
+ }
+
+
+ ## write R-script to run DESeq2
+ open (my $ofh, ">$Rscript_name") or die "Error, cannot write to $Rscript_name";
+
+ print $ofh "library(edgeR)\n";
+ print $ofh "library(limma)\n";
+ print $ofh "library(ROTS)\n";
+ print $ofh "\n";
+
+ print $ofh "data = read.table(\"$matrix_file\", header=T, row.names=1, com='')\n";
+ print $ofh "col_ordering = c(" . join(",", @rep_column_indices) . ")\n";
+ print $ofh "rnaseqMatrix = data[,col_ordering]\n";
+ print $ofh "rnaseqMatrix = round(rnaseqMatrix)\n";
+ print $ofh "rnaseqMatrix = rnaseqMatrix[rowSums(rnaseqMatrix)>=$min_rowSum_counts,]\n";
+ print $ofh "conditions = factor(c(rep(\"$sample_A\", $num_rep_A), rep(\"$sample_B\", $num_rep_B)))\n";
+ print $ofh "\n";
+ print $ofh "design = model.matrix(~conditions)\n";
+ print $ofh "## TMM normalize data\n";
+ print $ofh "lib_sizes = colSums(rnaseqMatrix)\n";
+ print $ofh "tmm_norm_factors = calcNormFactors(rnaseqMatrix, method='TMM')\n";
+ print $ofh "x = DGEList(counts=rnaseqMatrix)\n";
+ print $ofh "# voom transformation and ROTS (code derived from ROTS paper supp R code)\n";
+ print $ofh "voom.data = voom(x, design, lib.size=lib_sizes*tmm_norm_factors, plot=F)\n";
+ print $ofh "input_voom = voom.data\$E\n";
+ print $ofh "# run ROTS for DE analysis\n";
+ print $ofh "res_voom <- ROTS(data=input_voom,groups=conditions,B=$ROTS_B, K=$ROTS_K)\n";
+ print $ofh "results = summary(res_voom, fdr=0.1)\n";
+
+ print $ofh "# add logFC and logCPM to result table.\n";
+ print $ofh "c = cpm(x)\n";
+ print $ofh "m = apply(c, 1, mean)\n";
+ print $ofh "sampleA_cpm_matrix = c[,conditions \%in% \"$sample_A\"]\n";
+ print $ofh "mean_sampleA_cpm = apply(sampleA_cpm_matrix, 1, mean)\n";
+ print $ofh "sampleB_cpm_matrix = c[,conditions \%in% \"$sample_B\"]\n";
+ print $ofh "mean_sampleB_cpm = apply(sampleB_cpm_matrix, 1, mean)\n";
+ print $ofh "pseudocount_cpm = 1\n";
+ print $ofh "FC = (mean_sampleA_cpm + pseudocount_cpm) / (mean_sampleB_cpm + pseudocount_cpm)\n";
+ print $ofh "logFC = log2(FC)\n";
+ print $ofh "results = summary(res_voom, fdr=0.1)\n";
+ print $ofh "feature_order = rownames(results)\n";
+ print $ofh "final_table = data.frame(logCPM=log2(m+1)[feature_order], CPM_A=mean_sampleA_cpm[feature_order], CPM_B=mean_sampleB_cpm[feature_order], logFC=logFC[feature_order], results)\n";
+
+ print $ofh "write.table(final_table, file=\"$output_prefix.ROTS.DE_results\", quote=F, sep='\t')\n";
+
## generate MA and Volcano plots
+ print $ofh "# MA and volcano plots\n";
print $ofh "source(\"$FindBin::Bin/R/rnaseq_plot_funcs.R\")\n";
- print $ofh "pdf(\"$output_prefix.DESeq2.DE_results.MA_n_Volcano.pdf\")\n";
- print $ofh "plot_MA_and_Volcano(log2(res\$baseMean+1), res\$log2FoldChange, res\$padj)\n";
+ print $ofh "pdf(\"$output_prefix.voom.DE_results.MA_n_Volcano.pdf\")\n";
+ print $ofh "plot_MA_and_Volcano(final_table\$logCPM, final_table\$logFC, final_table\$FDR)\n";
print $ofh "dev.off()\n";
-
- close $ofh;
+ close $ofh;
+
## Run R-script
my $cmd = "R --vanilla -q < $Rscript_name";
- &process_cmd($cmd);
+
+
+ eval {
+ &process_cmd($cmd);
+ };
+ if ($@) {
+ print STDERR "$@\n\n";
+ print STDERR "\n\nWARNING: This ROTS comparison failed...\n\n";
+ ## if this is due to data paucity, such as in small sample data sets, then ignore for now.
+ }
+
return;
}
@@ -619,15 +721,14 @@ sub run_GLM {
my $output_prefix = basename($matrix_file);
-
-
+
my $Rscript_name = "$output_prefix.GLM.Rscript";
## write R-script to run edgeR
open (my $ofh, ">$Rscript_name") or die "Error, cannot write to $Rscript_name";
print $ofh "library(edgeR)\n";
-
+
print $ofh "\n";
print $ofh "design_matrix = read.table(\"$samples_file\", header=T, row.names=1)\n";
diff --git a/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl b/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
index 699f73a..7e939e0 100755
--- a/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
+++ b/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
@@ -36,6 +36,7 @@ my $usage = <<__EOUSAGE__;
# --allow_non_unique_mappings a single query transcript counts towards all transcripts encapsulated
#
# --reuse no prompting to reuse any existing blat output files, just use them.
+# --no_reuse no prompting, and do NOT reuse any existing files.
#
# --out_prefix prefix for output files generated.
#
@@ -54,7 +55,7 @@ my $query;
my $forward_orient = 0;
my $include_tiers = 0;
my $reuse_flag = 0;
-
+my $no_reuse_flag = 0;
my $allow_non_unique_mappings = 0;
@@ -72,6 +73,7 @@ my $out_prefix;
'min_per_length=f' => \$min_per_length,
'reuse' => \$reuse_flag,
+ 'no_reuse' => \$no_reuse_flag,
'out_prefix=s' => \$out_prefix,
);
@@ -119,7 +121,11 @@ main: {
if ($reuse_flag) {
$cmd .= " --reuse ";
}
+ elsif ($no_reuse_flag) {
+ $cmd .= " --no_reuse ";
+ }
+
$cmd .= " --out_prefix $out_prefix ";
$cmd .= " > $out_prefix.pslx.maps";
diff --git a/Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl b/Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl
index d4d1273..78c5dbb 100755
--- a/Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl
+++ b/Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl
@@ -29,6 +29,7 @@ my $usage = <<__EOUSAGE__;
# transcripts encapsulated
#
# --reuse don't prompt for reusing blat if the output already exists.
+# --no_reuse dont prompt and do NOT reuse existing outputs
#
# --out_prefix <string> output prefix
#
@@ -52,6 +53,7 @@ my $help_flag;
my $allow_non_unique_mappings = 0;
my $reuse_flag = 0;
+my $no_reuse_flag = 0;
my $out_prefix = "";
@@ -62,10 +64,11 @@ my $out_prefix = "";
'forward_orient' => \$forward_orient,
'max_per_gap=i' => \$max_per_gap,
'allow_non_unique_mappings' => \$allow_non_unique_mappings,
- 'min_per_length=f' => \$min_per_length,
+ 'min_per_length=f' => \$min_per_length,
'reuse' => \$reuse_flag,
-
+ 'no_reuse' => \$no_reuse_flag,
+
'out_prefix=s' => \$out_prefix,
);
@@ -102,7 +105,11 @@ main: {
my $run_blat = 0;
if (-s $blat_output) {
- if (! $reuse_flag) {
+
+ if ($no_reuse_flag) {
+ $run_blat = 1;
+ }
+ elsif (! $reuse_flag) {
print STDERR "Regenerate blat output file?";
my $response = <STDIN>;
if ($response =~ /^y/i) {
diff --git a/Butterfly/src/src/TransAssembly_allProbPaths.java b/Butterfly/src/src/TransAssembly_allProbPaths.java
index 5a3bc09..33b2e44 100644
--- a/Butterfly/src/src/TransAssembly_allProbPaths.java
+++ b/Butterfly/src/src/TransAssembly_allProbPaths.java
@@ -11231,11 +11231,18 @@ HashMap<List<Integer>, Pair<Integer>> transcripts = new HashMap<List<Integer>,Pa
*/
private static int getSeqPathLength(
DirectedSparseGraph<SeqVertex, SimpleEdge> graph, List<Integer> path) {
+
+ /*
int len = 0;
for (Integer vid : path)
if (vid>=0)
len +=getSeqVertex(graph, vid).getNameKmerAdj().length();
return len;
+ */
+
+ String pathSeq = getPathSeq(graph, path);
+ return(pathSeq.length());
+
}
/**
diff --git a/Chrysalis/GraphFromFasta_MPI.cc b/Chrysalis/GraphFromFasta_MPI.cc
index c949e63..21fe5d3 100644
--- a/Chrysalis/GraphFromFasta_MPI.cc
+++ b/Chrysalis/GraphFromFasta_MPI.cc
@@ -876,7 +876,7 @@ svec<Pool> sl_cluster_pools(map<int,Pool>& pool, map<int,bool>& ignore) {
// init entries to loweset pool index they're found in.
map<int,int> mapped;
- for (int i = 0; i < pool_vec.size(); i++) {
+ for (size_t i = 0; i < pool_vec.size(); i++) {
Pool p = pool_vec[i];
@@ -1141,7 +1141,7 @@ void add_unclustered_iworm_contigs (svec<Pool>& clustered_pools, vecDNAVector& d
Pool& p = *it;
- for (int i = 0; i < p.size(); i++) {
+ for (size_t i = 0; i < p.size(); i++) {
int id = p[i];
found[id] = true;
if (DEBUG)
@@ -1151,7 +1151,7 @@ void add_unclustered_iworm_contigs (svec<Pool>& clustered_pools, vecDNAVector& d
// add in the missing entries
- for (int i = 0; i < dna.size(); i++) {
+ for (size_t i = 0; i < dna.size(); i++) {
if (found.find(i) == found.end()) {
Pool p;
p.add(i);
@@ -1284,7 +1284,7 @@ int main(int argc,char** argv)
cerr << "done!" << endl;
- int i, j; //TODO: remove this, use local vars instead
+ size_t i, j; //TODO: remove this, use local vars instead
if (k != 24) {
cerr << "The only size of k supported is 24! Exiting!" << endl;
@@ -1331,14 +1331,14 @@ int main(int argc,char** argv)
Welder weld(k, kk); // decides if read support exists to weld two inchworm contigs together into the same component.
#ifdef MPI_ENABLED
- int schedule_chunksize = dna.isize() / (numranks) / 100;
+ int schedule_chunksize = dna.size() / (numranks) / 100;
#else
- int schedule_chunksize = dna.isize() / (real_num_threads) / 100;
+ int schedule_chunksize = dna.size() / (real_num_threads) / 100;
#endif
if(schedule_chunksize<1) schedule_chunksize=1;
- cerr << "-setting omp for schedule chunksize to " << schedule_chunksize << " for " << dna.isize() << " iworm contigs" << endl;
+ cerr << "-setting omp for schedule chunksize to " << schedule_chunksize << " for " << dna.size() << " iworm contigs" << endl;
int counter = 0;
@@ -1444,15 +1444,15 @@ int main(int argc,char** argv)
}
#else
#pragma omp parallel for schedule(dynamic, schedule_chunksize) private(j)
- for (i=0; i<dna.isize(); i++) {
+ for (i=0; i<dna.size(); i++) {
DNAVector & d = dna[i]; // inchworm contig [i]
#pragma omp atomic
iworm_counter++;
- if (iworm_counter % 1000 == 0 || iworm_counter == dna.isize()-1) {
+ if (iworm_counter % 1000 == 0 || iworm_counter == dna.size()-1) {
#pragma omp critical
- cerr << "\rProcessed: " << iworm_counter/(double)dna.isize()*100 << " % of iworm contigs. ";
+ cerr << "\rProcessed: " << iworm_counter/(double)dna.size()*100 << " % of iworm contigs. ";
}
for (j=0; j<=d.isize()-k; j++) {
@@ -1528,7 +1528,7 @@ int main(int argc,char** argv)
cerr << endl << endl << "...done Phase 1. (" << end_time - start_time << " seconds)" << endl;
cerr<< endl << endl << "done Phase 1 with my timers "<<timer_stop()<<" on rank "<<rank<<" (in milliseconds)"<<endl;
- cerr<<"Crossover size on rank "<<rank<<" is "<<crossover.isize()<<std::endl;
+ cerr<<"Crossover size on rank "<<rank<<" is "<<crossover.size()<<std::endl;
//crossover.resize(counter);
@@ -2207,7 +2207,7 @@ if(rank==0)
#else
#pragma omp parallel for schedule(dynamic, schedule_chunksize) private(j)
- for (i=0; i<dna.isize(); i++) {
+ for (i=0; i<dna.size(); i++) {
#pragma omp atomic
@@ -2215,7 +2215,7 @@ if(rank==0)
if (i % 100 == 0) {
#pragma omp critical
- cerr << "\r[" << (iworm_counter/(float)dna.isize()*100) << "% done] ";
+ cerr << "\r[" << (iworm_counter/(float)dna.size()*100) << "% done] ";
}
@@ -2480,7 +2480,7 @@ if(rank==0)
p.sortvec();
int sum_iworm_length = 0;
- for (unsigned int j = 0; j < p.size(); j++) {
+ for (size_t j = 0; j < p.size(); j++) {
int z = p.get(j);
sum_iworm_length += dna[z].isize();
}
@@ -2493,7 +2493,7 @@ if(rank==0)
pool_info << "#POOL_INFO\t" << component_count << ":" << "\t";
cout << "COMPONENT " << component_count << "\t" << p.size() << endl;
- for (unsigned int j = 0; j < p.size(); j++) {
+ for (size_t j = 0; j < p.size(); j++) {
int z = p.get(j);
pool_info << z << " ";
diff --git a/Chrysalis/MakeDepend.dSYM/Contents/Resources/DWARF/MakeDepend b/Chrysalis/MakeDepend.dSYM/Contents/Resources/DWARF/MakeDepend
index 7917515..39c6a29 100644
Binary files a/Chrysalis/MakeDepend.dSYM/Contents/Resources/DWARF/MakeDepend and b/Chrysalis/MakeDepend.dSYM/Contents/Resources/DWARF/MakeDepend differ
diff --git a/Chrysalis/Makefile b/Chrysalis/Makefile
index 448b2d1..61f7cff 100644
--- a/Chrysalis/Makefile
+++ b/Chrysalis/Makefile
@@ -302,6 +302,9 @@ ifeq ($(COMPILER),g++)
ifeq ($(GPP_MAJOR_VERSION),4)
SYS_INCS = -iquote . $(XERCES_INC)
endif
+ ifeq ($(GPP_MAJOR_VERSION),5)
+ SYS_INCS = -iquote . $(XERCES_INC)
+ endif
endif
# Linking control (e.g. to link templates):
diff --git a/Chrysalis/ReadsToTranscripts_MPI.cc b/Chrysalis/ReadsToTranscripts_MPI.cc
index 8216efe..ba61480 100644
--- a/Chrysalis/ReadsToTranscripts_MPI.cc
+++ b/Chrysalis/ReadsToTranscripts_MPI.cc
@@ -185,7 +185,7 @@ int main(int argc,char** argv)
cerr << "Assigning kmers to Iworm bundles ... ";
#pragma omp parallel for schedule(guided,100)
- for (int i=0; i< dna.isize(); i++) {
+ for (size_t i=0; i< dna.size(); i++) {
const DNAVector & d = dna[i];
string bundle_acc = dna.Name(i);
string component_no_string = bundle_acc.substr(3); // remove >s_ prefix
diff --git a/Chrysalis/ReadsToTranscripts_MPI_chang.cc b/Chrysalis/ReadsToTranscripts_MPI_chang.cc
index 1d292d8..709ef59 100644
--- a/Chrysalis/ReadsToTranscripts_MPI_chang.cc
+++ b/Chrysalis/ReadsToTranscripts_MPI_chang.cc
@@ -170,7 +170,7 @@ int main(int argc,char** argv)
cerr << "Assigning kmers to Iworm bundles ... on rank " << rank << endl;
#pragma omp parallel for schedule(guided,100)
- for (int i=0; i< dna.isize(); i++) {
+ for (size_t i=0; i< dna.size(); i++) {
const DNAVector & d = dna[i];
string bundle_acc = dna.Name(i);
string component_no_string = bundle_acc.substr(3); // remove >s_ prefix
diff --git a/Chrysalis/analysis/BreakTransByPairs.cc b/Chrysalis/analysis/BreakTransByPairs.cc
index 7383239..78142a0 100644
--- a/Chrysalis/analysis/BreakTransByPairs.cc
+++ b/Chrysalis/analysis/BreakTransByPairs.cc
@@ -94,7 +94,7 @@ int main(int argc,char** argv)
//dna.Read(fString);
svec<int> used;
- used.resize(seq.isize(), 0);
+ used.resize(seq.size(), 0);
int offset = seq[0].isize();
@@ -102,7 +102,7 @@ int main(int argc,char** argv)
int extra = 25;
- for (i=0; i<dna.isize(); i++) {
+ for (i=0; i<dna.size(); i++) {
DNAVector one = dna[i];
double all = 0.;
broken = 0;
diff --git a/Chrysalis/analysis/Chrysalis.cc b/Chrysalis/analysis/Chrysalis.cc
index a847f26..66cd5bb 100644
--- a/Chrysalis/analysis/Chrysalis.cc
+++ b/Chrysalis/analysis/Chrysalis.cc
@@ -98,7 +98,7 @@ void write_deBruijn_graphs(string iwormBundleFasta, string execDir, bool sStrand
-void write_deBruijn_graphs(vector<string_vec>& bundled, vector<int>& component_ids, ComponentFileMgr& mgr, string outDir, string execDir, bool sStrand, map<int,bool>& pursue_component) {
+void write_deBruijn_graphs(vector<string_vec>& bundled, vector<int>& component_ids, ComponentFileMgr& mgr, string, string execDir, bool sStrand, map<int,bool>& pursue_component) {
string cpp_graph_writer = execDir + "/../Inchworm/bin/FastaToDeBruijn";
@@ -106,7 +106,7 @@ void write_deBruijn_graphs(vector<string_vec>& bundled, vector<int>& component_i
int num_components = bundled.size();
#pragma omp parallel for schedule(dynamic)
- for (int i = 0; i < bundled.size(); i++) {
+ for (size_t i = 0; i < bundled.size(); i++) {
int component_id = component_ids[i];
@@ -174,7 +174,7 @@ void write_deBruijn_graphs(vector<string_vec>& bundled, vector<int>& component_i
-void write_iworm_bundle (string filename, vector<string_vec>& bundled, vector<int>& component_ids, ComponentFileMgr& mgr) {
+void write_iworm_bundle (string filename, vector<string_vec>& bundled, vector<int>& component_ids, ComponentFileMgr&) {
ofstream ofh;
ofh.open(filename.c_str());
@@ -183,7 +183,7 @@ void write_iworm_bundle (string filename, vector<string_vec>& bundled, vector<in
//bundle_listing_ofh.open("iworm_bundle_file_listing.txt");
- for (int i = 0; i < bundled.size(); i++) {
+ for (size_t i = 0; i < bundled.size(); i++) {
int component_id = component_ids[i];
string_vec bundled_iworms = bundled[i];
@@ -607,19 +607,19 @@ int main(int argc,char** argv)
DNAVector app;
app.SetFromBases(parser.AsString(0));
//cerr << "adding: " << parser.AsString(0) << endl;
- tmpSeq[tmpSeq.isize()-1] += app; // adding the iworm sequence to that iworm entry
+ tmpSeq[tmpSeq.size()-1] += app; // adding the iworm sequence to that iworm entry
//fprintf(p, "%s\n", parser.Line().c_str());
}
//fclose(p);
- if (tmpSeq.isize() == 1 && tmpSeq[0].isize() < minLen) {
+ if (tmpSeq.size() == 1 && tmpSeq[0].isize() < minLen) {
//cerr << "-discarding entry, too short." << endl;
continue;
}
bool bGood = false;
- for (int x=0; x<tmpSeq.isize(); x++) {
+ for (size_t x=0; x<tmpSeq.size(); x++) {
if (tmpSeq[x].isize() > minDumpLen) {
bGood = true;
break;
@@ -629,7 +629,7 @@ int main(int argc,char** argv)
if (bGood) {
vector<string> iworm_bundle;
- for (int x = 0; x < tmpSeq.isize(); x++) {
+ for (size_t x = 0; x < tmpSeq.size(); x++) {
iworm_bundle.push_back(get_seq_string(tmpSeq[x]));
}
diff --git a/Chrysalis/analysis/CreateIwormFastaBundle.cc b/Chrysalis/analysis/CreateIwormFastaBundle.cc
index 8a862ff..48c44f9 100644
--- a/Chrysalis/analysis/CreateIwormFastaBundle.cc
+++ b/Chrysalis/analysis/CreateIwormFastaBundle.cc
@@ -47,7 +47,7 @@ void write_iworm_bundle (string filename, vector<string_vec>& bundled, vector<in
ofh.open(filename.c_str());
- for (int i = 0; i < bundled.size(); i++) {
+ for (size_t i = 0; i < bundled.size(); i++) {
int component_id = component_ids[i];
string_vec bundled_iworms = bundled[i];
@@ -177,13 +177,13 @@ int main(int argc,char** argv)
DNAVector app;
app.SetFromBases(parser.AsString(0));
//cerr << "adding: " << parser.AsString(0) << endl;
- tmpSeq[tmpSeq.isize()-1] += app; // adding the iworm sequence to that iworm entry
+ tmpSeq[tmpSeq.size()-1] += app; // adding the iworm sequence to that iworm entry
//fprintf(p, "%s\n", parser.Line().c_str());
}
//fclose(p);
- if (tmpSeq.isize() == 1 && tmpSeq[0].isize() < minLen) {
+ if (tmpSeq.size() == 1 && tmpSeq[0].size() < minLen) {
//cerr << "-discarding entry, too short." << endl;
continue;
}
@@ -192,7 +192,7 @@ int main(int argc,char** argv)
vector<string> iworm_bundle;
int sum_len = 0;
- for (int x = 0; x < tmpSeq.isize(); x++) {
+ for (size_t x = 0; x < tmpSeq.size(); x++) {
iworm_bundle.push_back(get_seq_string(tmpSeq[x]));
sum_len += tmpSeq[x].isize();
}
diff --git a/Chrysalis/analysis/DNAVector.cc b/Chrysalis/analysis/DNAVector.cc
index 1a327d2..8568f1a 100644
--- a/Chrysalis/analysis/DNAVector.cc
+++ b/Chrysalis/analysis/DNAVector.cc
@@ -620,16 +620,16 @@ int vecDNAVector::NameIndex(const string & name) const {
return mIter->second;
}
-const string & vecDNAVector::Name(int i) const {
+const string & vecDNAVector::Name(size_t i) const {
return m_names[i];
}
-const char * vecDNAVector::NameClean(int i) const {
+const char * vecDNAVector::NameClean(size_t i) const {
const char * p = m_names[i].c_str();
return &p[1];
}
-void vecDNAVector::SetName(int i, const string & s) {
+void vecDNAVector::SetName(size_t i, const string & s) {
m_name2index.erase(m_names[i]);
invalidateReferences(m_names[i]);
m_name2index[s] = i;
@@ -651,7 +651,7 @@ void vecDNAVector::push_back(const DNAVector & v, const string & name) {
m_name2index.insert(make_pair(name, m_names.size()-1));
}
-void vecDNAVector::erase(int index) {
+void vecDNAVector::erase(size_t index) {
m_name2index.erase(m_names[index]);
invalidateReferences(m_names[index]);
m_names.erase(m_names.begin() + index);
@@ -669,14 +669,14 @@ bool vecDNAVector::erase(const string &name) {
return false;
}
-void vecDNAVector::fast_erase(int index) {
+void vecDNAVector::fast_erase(size_t index) {
m_name2index.erase(m_names[index]);
invalidateReferences(m_names[index]);
swap(m_names[m_names.size()-1], m_names[index]);
swap(m_data[m_data.size()-1], m_data[index]);
m_names.pop_back();
m_data.pop_back();
- if(index < m_names.isize())
+ if(index < m_names.size())
m_name2index[m_names[index]] = index;
}
@@ -689,16 +689,8 @@ bool vecDNAVector::fast_erase(const string &name) {
return false;
}
-int vecDNAVector::size() const {
- return m_data.isize();
-}
-
-int vecDNAVector::isize() const {
- return m_data.isize();
-}
-
-long long vecDNAVector::lsize() const {
- return m_data.lsize();
+size_t vecDNAVector::size() const {
+ return m_data.size();
}
long long vecDNAVector::totalBases() const {
@@ -739,7 +731,7 @@ void vecDNAVector::DoProteins(bool b)
void vecDNAVector::ReadV(const string & file)
{
int ver = 1;
- int i, j;
+ size_t i, j;
CMReadFileStream s;
s.Open(file.c_str());
@@ -749,13 +741,13 @@ void vecDNAVector::ReadV(const string & file)
s.Read(size);
resize(size);
- for (i=0; i<isize(); i++) {
+ for (i=0; i<this->size(); i++) {
CMString n;
s.Read(n);
m_names[i] = (const char*)n;
DNAVector & d = m_data[i];
m_name2index[m_names[i]] = i;
- int len = 0;
+ size_t len = 0;
s.Read(len);
d.resize(len);
for (j=0; j<len; j++)
@@ -768,18 +760,18 @@ void vecDNAVector::ReadV(const string & file)
void vecDNAVector::WriteV(const string & file) const
{
int ver = 1;
- int i, j;
+ size_t i, j;
CMWriteFileStream s;
s.Open(file.c_str());
s.Write(ver);
- s.Write(isize());
+ s.Write(size());
- for (i=0; i<isize(); i++) {
+ for (i=0; i<size(); i++) {
CMString n = m_names[i].c_str();
s.Write(n);
const DNAVector & d = m_data[i];
- int len = d.isize();
+ size_t len = d.size();
s.Write(len);
for (j=0; j<len; j++)
s.Write(d[j]);
@@ -793,9 +785,8 @@ void vecDNAVector::WriteV(const string & file) const
void vecDNAVector::Write(const string & fileName, bool bSkipEmpty) const
{
FILE * p = fopen(fileName.c_str(), "w");
- int i;
- for (i=0; i<isize(); i++) {
- if (bSkipEmpty && m_data[i].isize() == 0)
+ for (size_t i=0; i<size(); i++) {
+ if (bSkipEmpty && m_data[i].size() == 0)
continue;
//cout << "size: " << m_data[i].isize() << " skip=" << bSkipEmpty << endl;
fprintf(p, "%s\n", m_names[i].c_str());
@@ -807,8 +798,7 @@ void vecDNAVector::Write(const string & fileName, bool bSkipEmpty) const
void vecDNAVector::WriteQuals(const string & fileName) const
{
FILE * p = fopen(fileName.c_str(), "w");
- int i;
- for (i=0; i<isize(); i++) {
+ for (size_t i=0; i<size(); i++) {
fprintf(p, "%s\n", m_names[i].c_str());
m_data[i].WriteQual(p);
}
@@ -1094,13 +1084,13 @@ void vecDNAVector::ReverseComplement() {
void vecDNAVector::UniqueSort() {
map<DNAVector, string> tempNameMap;
- for(int i = 0; i < m_data.isize(); i++)
+ for(size_t i = 0; i < m_data.size(); i++)
tempNameMap[m_data[i]] = m_names[i];
m_name2index.clear();
::UniqueSort(m_data);
- m_names.resize(m_data.isize());
- for(int i = 0; i < m_data.isize(); i++) {
+ m_names.resize(m_data.size());
+ for(size_t i = 0; i < m_data.size(); i++) {
m_name2index[tempNameMap[m_data[i]]] = i;
tempNameMap.erase(m_data[i]);
}
diff --git a/Chrysalis/analysis/DNAVector.h b/Chrysalis/analysis/DNAVector.h
index c236d2d..465c053 100644
--- a/Chrysalis/analysis/DNAVector.h
+++ b/Chrysalis/analysis/DNAVector.h
@@ -429,10 +429,10 @@ class vecDNAVector
void clear();
int NameIndex(const string & name) const;
- const string & Name(int i) const;
- const char * NameClean(int i) const;
+ const string & Name(size_t i) const;
+ const char * NameClean(size_t i) const;
- void SetName(int i, const string & s);
+ void SetName(size_t i, const string & s);
void push_back(const DNAVector & v);
void push_back(const DNAVector & v, const string & name);
@@ -445,7 +445,7 @@ class vecDNAVector
* If you do not care about the element order and n is large,
* fast_erase would be a better choice.
*/
- void erase(int index);
+ void erase(size_t index);
/* erase
* -------------
@@ -463,7 +463,7 @@ class vecDNAVector
* Erases the DNAVector at the index 'index'; as a side effect
* the last element in the vecDNAVector is moved to the vacated index.
*/
- void fast_erase(int index);
+ void fast_erase(size_t index);
/* fast_erase
* -------------
@@ -473,9 +473,7 @@ class vecDNAVector
bool fast_erase(const string &name);
- int size() const;
- int isize() const;
- long long lsize() const;
+ size_t size() const;
long long totalBases() const;
diff --git a/Chrysalis/analysis/GraphFromFasta.cc b/Chrysalis/analysis/GraphFromFasta.cc
index a160668..537d50f 100644
--- a/Chrysalis/analysis/GraphFromFasta.cc
+++ b/Chrysalis/analysis/GraphFromFasta.cc
@@ -90,7 +90,7 @@ public:
void exclude (int i) {
//FIXME: there must be a more efficient way to do this.
svec<int> new_mvec;
- for (int j = 0; j < m_index.size(); j++) {
+ for (size_t j = 0; j < m_index.size(); j++) {
int val = m_index[j];
if (val != i) {
new_mvec.push_back(val);
@@ -153,6 +153,8 @@ bool is_simple_repeat(const DNAVector& kmer) {
int best_right_pos = 0;
float max_repetitive_ratio = 0;
+ stringstream left_kmer;
+ stringstream right_kmer;
int mid_kmer_length = kmer.isize()/2;
@@ -169,8 +171,8 @@ bool is_simple_repeat(const DNAVector& kmer) {
int bases_compared = 0;
int bases_common = 0;
- stringstream left_kmer;
- stringstream right_kmer;
+ left_kmer.clear();
+ right_kmer.clear();
while (internal_kmer_pos <= j + mid_kmer_length - 1) {
@@ -664,7 +666,7 @@ bool sort_pool_sizes_ascendingly(const Pool& a, const Pool& b) {
}
-svec<Pool> bubble_up_cluster_growth(map<int,Pool>& pool, map<int,bool>& ignore) {
+svec<Pool> bubble_up_cluster_growth(map<int,Pool>& pool, map<int,bool>& ) {
vector<Pool> pool_vec;
for (map<int,Pool>::iterator it = pool.begin(); it != pool.end(); it++) {
@@ -682,7 +684,7 @@ svec<Pool> bubble_up_cluster_growth(map<int,Pool>& pool, map<int,bool>& ignore)
map<int,Pool> pool_idx_to_containment;
map<int,int> pool_idx_to_vec_idx;
// init
- for (int i = 0; i < pool_vec.size(); i++) {
+ for (size_t i = 0; i < pool_vec.size(); i++) {
int id = pool_vec[i].get_id();
Pool tmp(id);
pool_idx_to_containment[id] = tmp;
@@ -703,7 +705,7 @@ svec<Pool> bubble_up_cluster_growth(map<int,Pool>& pool, map<int,bool>& ignore)
cerr << "bubbling up graph, round: " << bubble_round << endl;
}
- for (int i = 0; i < pool_vec.size(); i++) {
+ for (size_t i = 0; i < pool_vec.size(); i++) {
@@ -810,7 +812,7 @@ svec<Pool> bubble_up_cluster_growth(map<int,Pool>& pool, map<int,bool>& ignore)
svec<Pool> bubbled_up_pools;
- for (int i = 0; i < pool_vec.size(); i++) {
+ for (size_t i = 0; i < pool_vec.size(); i++) {
Pool& p = pool_vec[i];
int id = p.get_id();
@@ -855,7 +857,7 @@ svec<Pool> sl_cluster_pools(map<int,Pool>& pool, map<int,bool>& ignore) {
// init entries to loweset pool index they're found in.
map<int,int> mapped;
- for (int i = 0; i < pool_vec.size(); i++) {
+ for (size_t i = 0; i < pool_vec.size(); i++) {
Pool p = pool_vec[i];
@@ -1132,7 +1134,7 @@ void add_unclustered_iworm_contigs (svec<Pool>& clustered_pools, vecDNAVector& d
// add in the missing entries
- for (int i = 0; i < dna.size(); i++) {
+ for (size_t i = 0; i < dna.size(); i++) {
if (found.find(i) == found.end()) {
Pool p;
p.add(i);
@@ -1330,9 +1332,9 @@ int main(int argc,char** argv)
//Welder weld(k, kk); // decides if read support exists to weld two inchworm contigs together into the same component.
- int schedule_chunksize = dna.isize() / real_num_threads / 100;
+ int schedule_chunksize = dna.size() / real_num_threads / 100;
if(schedule_chunksize<1) schedule_chunksize=1;
- cerr << "-setting omp for schedule chunksize to " << schedule_chunksize << " for " << dna.isize() << " iworm contigs" << endl;
+ cerr << "-setting omp for schedule chunksize to " << schedule_chunksize << " for " << dna.size() << " iworm contigs" << endl;
int counter = 0;
@@ -1347,7 +1349,7 @@ int main(int argc,char** argv)
Pool p;
- for (int i = 0; i < dna.size(); i++) {
+ for (size_t i = 0; i < dna.size(); i++) {
p.add(i);
}
@@ -1362,15 +1364,15 @@ int main(int argc,char** argv)
iworm_counter = 0;
#pragma omp parallel for schedule(dynamic, schedule_chunksize) private(j)
- for (i=0; i<dna.isize(); i++) {
+ for (i=0; i<dna.size(); i++) {
DNAVector & d = dna[i]; // inchworm contig [i]
#pragma omp atomic
iworm_counter++;
- if (iworm_counter % 1000 == 0 || iworm_counter == dna.isize()-1) {
+ if (iworm_counter % 1000 == 0 || iworm_counter == dna.size()-1) {
#pragma omp critical
- cerr << "\rProcessed: " << iworm_counter/(double)dna.isize()*100 << " % of iworm contigs. ";
+ cerr << "\rProcessed: " << iworm_counter/(double)dna.size()*100 << " % of iworm contigs. ";
}
for (j=0; j<=d.isize()-k; j++) {
@@ -1485,7 +1487,7 @@ int main(int argc,char** argv)
iworm_counter = 0; // reset
#pragma omp parallel for schedule(dynamic, schedule_chunksize) private(j)
- for (i=0; i<dna.isize(); i++) {
+ for (i=0; i<dna.size(); i++) {
#pragma omp atomic
@@ -1493,7 +1495,7 @@ int main(int argc,char** argv)
if (i % 100 == 0) {
#pragma omp critical
- cerr << "\r[" << (iworm_counter/(float)dna.isize()*100) << "% done] ";
+ cerr << "\r[" << (iworm_counter/(float)dna.size()*100) << "% done] ";
}
@@ -1760,7 +1762,7 @@ int main(int argc,char** argv)
p.sortvec();
int sum_iworm_length = 0;
- for (unsigned int j = 0; j < p.size(); j++) {
+ for (size_t j = 0; j < p.size(); j++) {
int z = p.get(j);
sum_iworm_length += dna[z].isize();
}
@@ -1773,7 +1775,7 @@ int main(int argc,char** argv)
pool_info << "#POOL_INFO\t" << component_count << ":" << "\t";
cout << "COMPONENT " << component_count << "\t" << p.size() << endl;
- for (unsigned int j = 0; j < p.size(); j++) {
+ for (size_t j = 0; j < p.size(); j++) {
int z = p.get(j);
pool_info << z << " ";
diff --git a/Chrysalis/analysis/IsoformAugment.cc b/Chrysalis/analysis/IsoformAugment.cc
index 22d7095..15a9b06 100644
--- a/Chrysalis/analysis/IsoformAugment.cc
+++ b/Chrysalis/analysis/IsoformAugment.cc
@@ -46,13 +46,13 @@ int main(int argc,char** argv)
core.AddData(ref);
//core.SortAll();
- int i, j;
+ size_t i, j;
int min = 24;
int k = 24;
- for (i=0; i<iworm.isize(); i++) {
+ for (i=0; i<iworm.size(); i++) {
const DNAVector & d = iworm[i];
//if (d.isize() > 300)
// continue;
diff --git a/Chrysalis/analysis/JoinTransByPairs.cc b/Chrysalis/analysis/JoinTransByPairs.cc
index 994ca16..4e4783f 100644
--- a/Chrysalis/analysis/JoinTransByPairs.cc
+++ b/Chrysalis/analysis/JoinTransByPairs.cc
@@ -274,12 +274,12 @@ int main(int argc,char** argv)
int extra = 100;
svec<int> contigs;
- contigs.resize(seq.isize(), -1);
+ contigs.resize(seq.size(), -1);
svec<ReadPlaces> places;
if (!bCont) {
- places.resize(dna.isize());
+ places.resize(dna.size());
} else {
cout << "Reading placements..." << endl;
ReadThePlaces(places, placementFile);
@@ -290,7 +290,7 @@ int main(int argc,char** argv)
cout << "Assigning contigs to reads." << endl;
- for (i=0; i<dna.isize(); i++) {
+ for (i=0; i<dna.size(); i++) {
const DNAVector & one = dna[i];
double all = 0.;
broken = 0;
@@ -338,7 +338,7 @@ int main(int argc,char** argv)
//if (!bCont)
//WriteThePlaces(places, placementFile);
- for (i=0; i<dna.isize(); i++) {
+ for (i=0; i<dna.size(); i++) {
DNAVector & d = dna[i];
if (d.isize() == 0)
@@ -347,7 +347,7 @@ int main(int argc,char** argv)
continue;
svec<int> possible;
- possible.resize(dna.isize(), 0);
+ possible.resize(dna.size(), 0);
//cout << "Checking contig " << i << endl;
ReadPlaces & pl = places[i];
diff --git a/Chrysalis/analysis/KmerTable.cc b/Chrysalis/analysis/KmerTable.cc
index dbc793e..907519a 100644
--- a/Chrysalis/analysis/KmerTable.cc
+++ b/Chrysalis/analysis/KmerTable.cc
@@ -114,16 +114,16 @@ void KmerSequence::Add(const vecDNAVector & all)
//long long est = (long long)(all[0].isize()-K+1)*(long long)all.isize();
- long long est = 0;
- for (int i=0; i<all.isize(); i++) {
- est += (long long)(all[i].isize()-K+1);
+ size_t est = 0;
+ for (size_t i=0; i<all.size(); i++) {
+ est += (all[i].size()-K+1);
}
// cout << "Estimate space: " << est << endl;
m_kmers.resize(est);
m_count = 0;
- for (int j=0; j<all.isize(); j++) {
+ for (size_t j=0; j<all.size(); j++) {
const DNAVector & d = all[j];
for (int i=0; i<=d.isize()-K; i++) {
if (m_kmers.lsize() <= m_count)
@@ -150,12 +150,12 @@ void KmerSequence::AddRestrict(const vecDNAVector & all, const vecDNAVector & re
nr.SetUp(restrict);
- long long est = (long long)(all[0].isize()-K+1)*(long long)all.isize() / 4;
+ long long est = (long long)(all[0].isize()-K+1)*all.size() / 4;
cout << "Estimate space: " << est << " (" << est * 4 << ")" << endl;
m_kmers.resize(est);
m_count = 0;
int kk = 0;
- for (int j=0; j<all.isize(); j++) {
+ for (size_t j=0; j<all.size(); j++) {
const DNAVector & d = all[j];
for (int i=0; i<=d.isize()-K; i++) {
if (m_kmers.lsize() <= m_count)
diff --git a/Chrysalis/analysis/NonRedKmerTable.cc b/Chrysalis/analysis/NonRedKmerTable.cc
index d74baae..49a856f 100644
--- a/Chrysalis/analysis/NonRedKmerTable.cc
+++ b/Chrysalis/analysis/NonRedKmerTable.cc
@@ -11,15 +11,15 @@ bool Regular(char c) {
// Restricts all k-mers to what's in here.
void NonRedKmerTable::SetUp(const vecDNAVector & templ, bool noNs)
{
- int i, j;
+ size_t i, j;
// cerr << "vecDNAVector length: " << templ.isize() << endl;
- int l = 0;
- for (i=0; i<templ.isize(); i++)
+ long l = 0;
+ for (i=0; i<templ.size(); i++)
l += templ[i].isize()-m_k+1;
- // cerr << "Allocating: " << l << endl;
+ cerr << "Allocating: " << l << endl;
m_data.resize(l);
l = 0;
@@ -27,12 +27,12 @@ void NonRedKmerTable::SetUp(const vecDNAVector & templ, bool noNs)
if (noNs)
{
- for (i=0; i<templ.isize(); i++) {
+ for (i=0; i<templ.size(); i++) {
const DNAVector & d = templ[i];
// first check if sequence contains any irregular chars
bool bGood = true;
- for (int x=0; x<d.isize(); x++) {
+ for (int x=0; x<d.size(); x++) {
if (!Regular(d[x])) {
bGood = false;
break;
@@ -43,7 +43,7 @@ void NonRedKmerTable::SetUp(const vecDNAVector & templ, bool noNs)
{
// good! do not check for irregular chars in each kmer
- for (j=0; j<=d.isize()-m_k; j++) {
+ for (j=0; j<=d.size()-m_k; j++) {
d.Substring(m_data[l], j, m_k);
l++;
}
@@ -53,7 +53,7 @@ void NonRedKmerTable::SetUp(const vecDNAVector & templ, bool noNs)
{
// bad! we need to check for irregular chars in each kmer
- for (j=0; j<=d.isize()-m_k; j++) {
+ for (j=0; j<=d.size()-m_k; j++) {
d.Substring(m_data[l], j, m_k);
bGood = true;
for (int x=0; x<m_k; x++) {
@@ -74,9 +74,9 @@ void NonRedKmerTable::SetUp(const vecDNAVector & templ, bool noNs)
else
{
- for (i=0; i<templ.isize(); i++) {
+ for (i=0; i<templ.size(); i++) {
const DNAVector & d = templ[i];
- for (j=0; j<=d.isize()-m_k; j++) {
+ for (j=0; j<=d.size()-m_k; j++) {
d.Substring(m_data[l], j, m_k);
l++;
}
@@ -84,25 +84,26 @@ void NonRedKmerTable::SetUp(const vecDNAVector & templ, bool noNs)
}
- // cerr << "Resizing: " << l << endl;
+ cerr << "Resizing: " << l << endl;
m_data.resize(l);
+ cerr << "Sorting";
UniqueSort(m_data);
- m_counts.resize(m_data.isize(), 0);
- // cerr << "Done." << endl;
+ m_counts.resize(m_data.size(), 0);
+ cerr << "Done." << endl;
}
void NonRedKmerTable::AddData(const vecDNAVector & data)
{
- int i, j;
+ size_t i, j;
- cerr << "NonRedKmerTable::AddData() - adding Reads: " << data.isize() << endl;
- for (i=0; i<data.isize(); i++) {
+ cerr << "NonRedKmerTable::AddData() - adding Reads: " << data.size() << endl;
+ for (i=0; i<data.size(); i++) {
if (i % 1000 == 0) {
- cerr << 100.*(double)i/(double)data.isize() << " %" << endl;
+ cerr << 100.*(double)i/(double)data.size() << " %" << endl;
}
const DNAVector & d = data[i];
for (j=0; j<= d.isize()-m_k; j++) {
diff --git a/Chrysalis/analysis/NonRedKmerTable.h b/Chrysalis/analysis/NonRedKmerTable.h
index 342a508..32b2f50 100644
--- a/Chrysalis/analysis/NonRedKmerTable.h
+++ b/Chrysalis/analysis/NonRedKmerTable.h
@@ -30,28 +30,28 @@ class NonRedKmerTable
return (i >= 0);
}
- void SetCount(const DNAVector & d, int pos, int count) {
+ void SetCount(const DNAVector & d, size_t pos, int count) {
int i = Index(d, pos);
if (i < 0)
return;
m_counts[i] = count;
}
- int GetCount(const DNAVector & d, int pos) {
+ int GetCount(const DNAVector & d, size_t pos) {
int i = Index(d, pos);;
if (i < 0)
return 0;
return m_counts[i];
}
- int GetCountReal(const DNAVector & d, int pos) {
+ int GetCountReal(const DNAVector & d, size_t pos) {
int i = Index(d, pos);;
if (i < 0)
return -1;
return m_counts[i];
}
- int GetCountReal(const string & seq, int pos) {
+ int GetCountReal(const string & seq, size_t pos) {
string s = seq.substr(pos, m_k);
int i = BinSearch(m_data, s);
if (i < 0)
@@ -60,12 +60,12 @@ class NonRedKmerTable
}
void SetAllCounts(int c) {
- for (int i=0; i<m_counts.isize(); i++)
+ for (size_t i=0; i<m_counts.size(); i++)
m_counts[i] = c;
}
private:
- int Index(const DNAVector & d, int pos) {
+ int Index(const DNAVector & d, size_t pos) {
string s;
d.Substring(s, pos, m_k);
diff --git a/Chrysalis/analysis/QuantifyGraph.cc b/Chrysalis/analysis/QuantifyGraph.cc
index 8b211aa..ff5771f 100644
--- a/Chrysalis/analysis/QuantifyGraph.cc
+++ b/Chrysalis/analysis/QuantifyGraph.cc
@@ -267,7 +267,7 @@ int main(int argc,char** argv)
FILE * pReads = fopen(reads.c_str(), "w"); // output reads in context of graph
svec<IDS> ids;
- ids.reserve(seq.isize());
+ ids.reserve(seq.size());
//string last;
//int lastNode = -1;
diff --git a/Chrysalis/analysis/ReadsToTranscripts.cc b/Chrysalis/analysis/ReadsToTranscripts.cc
index 1b8f0e3..4f5eef7 100644
--- a/Chrysalis/analysis/ReadsToTranscripts.cc
+++ b/Chrysalis/analysis/ReadsToTranscripts.cc
@@ -144,7 +144,7 @@ int main(int argc,char** argv)
cerr << "Assigning kmers to Iworm bundles ... ";
#pragma omp parallel for schedule(guided,100)
- for (int i=0; i< dna.isize(); i++) {
+ for (size_t i=0; i< dna.size(); i++) {
const DNAVector & d = dna[i];
string bundle_acc = dna.Name(i);
string component_no_string = bundle_acc.substr(3); // remove >s_ prefix
@@ -202,6 +202,8 @@ int main(int argc,char** argv)
} else {
// reached EOF
cerr << "finished reading reads" << endl;
+ //MW: If nothing was read leave do loop right away
+ break;
}
componentReadMap.clear();
diff --git a/Chrysalis/analysis/TranscriptomeFromVaryK.cc b/Chrysalis/analysis/TranscriptomeFromVaryK.cc
index 2c0356a..5398748 100644
--- a/Chrysalis/analysis/TranscriptomeFromVaryK.cc
+++ b/Chrysalis/analysis/TranscriptomeFromVaryK.cc
@@ -46,7 +46,7 @@ void Extend(KmerSequence & seq, svec<int> & counts, DNAVector & sub, bool rc, bo
//deep++;
//cout << "Deep=" << deep << endl;
- int i, j;
+ size_t i, j;
vecDNAVector ex;
Right(ex, sub, k);
@@ -72,7 +72,7 @@ void Extend(KmerSequence & seq, svec<int> & counts, DNAVector & sub, bool rc, bo
}
- for (i=0; i<ex.isize(); i++) {
+ for (i=0; i<ex.size(); i++) {
int nFW = 0;
int nRC = 0;
long long iFW = -1;
@@ -154,7 +154,7 @@ int main(int argc,char** argv)
bool bStrand = P.GetBoolValueFor(strandCmmd);
- int i, j;
+ size_t i, j;
//vecbasevector contigBases;
vecDNAVector seq;
@@ -210,7 +210,7 @@ int main(int argc,char** argv)
FILE * pOut = fopen(oString.c_str(), "w");
int cc = 0;
- for (i=0; i<seq.lsize(); i++) {
+ for (i=0; i<seq.size(); i++) {
DNAVector d = seq[i];
for (j=0; j<=d.lsize()-k; j++) {
diff --git a/Chrysalis/analysis/TranscriptomeGraph.cc b/Chrysalis/analysis/TranscriptomeGraph.cc
index 938be1f..174a857 100644
--- a/Chrysalis/analysis/TranscriptomeGraph.cc
+++ b/Chrysalis/analysis/TranscriptomeGraph.cc
@@ -540,10 +540,7 @@ void KmerSearch::Extend(long long last,
m_usedLocal[currNum] = last;
if (!m_connect)
m_local.push_back(currNum);
-
-
- long long j;
-
+
vecDNAVector right;
Shift(right, seq);
@@ -562,7 +559,7 @@ void KmerSearch::Extend(long long last,
long long hi = 0;
long long hi_index = -1;
- for (j=0; j<right.lsize(); j++) {
+ for (size_t j=0; j<right.size(); j++) {
const DNAVector & r = right[j];
long long num = GetGlobalSeq()->BasesToNumber(r, 0);
//long long num = GetFullCount(count, r, 0);
@@ -583,7 +580,7 @@ void KmerSearch::Extend(long long last,
}
- for (j=0; j<right.lsize(); j++) {
+ for (size_t j=0; j<right.size(); j++) {
const DNAVector & r = right[j];
//cout << "r size=" << r.lsize() << endl;
long long num = GetGlobalSeq()->BasesToNumber(r, 0);
@@ -656,9 +653,9 @@ int TranscriptomeGraph(vecDNAVector & seq,
//vecDNAVector seq;
//seq.Read(aString);
- int i;
+ size_t i;
- if (seq.isize() == 1) { // only one sequence, the graph is simple: linear set of overlapping kmers
+ if (seq.size() == 1) { // only one sequence, the graph is simple: linear set of overlapping kmers
/*FILE * pOut = NULL;
if (bAppend)
@@ -671,7 +668,7 @@ int TranscriptomeGraph(vecDNAVector & seq,
for (i=0; i<=d.isize()-k; i++) {
fprintf(pOut, "%d\t%d\t1\t", i, i-1);
//cout << i << "\t" << i-1 << "\t1\t";
- for (int x=i; x<i+k; x++)
+ for (size_t x=i; x<i+k; x++)
fprintf(pOut, "%c", d[x]);
//cout << d[x];
fprintf(pOut, "\t0\n");
@@ -693,10 +690,10 @@ int TranscriptomeGraph(vecDNAVector & seq,
- for (i=0; i<seq.lsize(); i++) {
+ for (i=0; i<seq.size(); i++) {
DNAVector d = seq[i];
//cout << "i=" << i << endl;
- char * tmp = new char[d.lsize()+1];
+ char * tmp = new char[d.size()+1];
for (j=0; j<d.lsize(); j++) {
//cout << j << "\t" << d[j] << endl;
tmp[j] = d[j];
@@ -732,7 +729,7 @@ int TranscriptomeGraph(vecDNAVector & seq,
//cout << "WARNING: no check for left seed extensions!!" << endl;
- for (i=0; i<seq.lsize(); i++) {
+ for (i=0; i<seq.size(); i++) {
DNAVector d = seq[i];
//cout << i << endl;
for (j=0; j<=d.lsize()-k; j++) {
@@ -767,7 +764,7 @@ int TranscriptomeGraph(vecDNAVector & seq,
// examine kmers
- for (i=0; i<seq.lsize(); i++) {
+ for (i=0; i<seq.size(); i++) {
const DNAVector & v = seq[i];
for (j=0; j<=v.lsize()-k; j++) {
diff --git a/Chrysalis/base/SVector.h b/Chrysalis/base/SVector.h
index 5e83045..da789a3 100644
--- a/Chrysalis/base/SVector.h
+++ b/Chrysalis/base/SVector.h
@@ -83,26 +83,26 @@ void UniqueSort(svec<T>& v)
v.resize(k);
}
+template<class Iter, class T>
+Iter binary_find(Iter begin, Iter end, T val)
+{
+ // Finds the lower bound in at most log(last - first) + 1 comparisons
+ Iter i = std::lower_bound(begin, end, val);
+
+ if (i != end && !(val < *i))
+ return i; // found
+ else
+ return end; // not found
+}
+
template<class T>
long long BinSearch(svec<T> & v, const T & item)
{
- typename svec<T>::iterator iter;
- typename svec<T>::iterator begin = v.begin();
- typename svec<T>::iterator end = v.end();
- iter = lower_bound(begin, end, item);
- long long pos = distance(begin, iter);
-
- if (pos < 0)
- return -1;
-
- if (pos == v.isize())
+ typename svec<T>::iterator iter = binary_find(v.begin(), v.end(), item);
+ if (iter == v.end())
return -1;
-
- if (v[pos] < item || item < v[pos])
- return -1;
-
- return pos;
+ return iter - v.begin();
}
template<class T>
diff --git a/Chrysalis/util/mutil.h b/Chrysalis/util/mutil.h
index 66de9b1..730184c 100644
--- a/Chrysalis/util/mutil.h
+++ b/Chrysalis/util/mutil.h
@@ -1201,7 +1201,7 @@ public:
MDLLEXPORT virtual bool IsEnd();
MDLLEXPORT virtual bool WriteLine(const CMString & line);
- virtual IMWriteStream * CloneAndOpen(const CMString &name) {return NULL;}
+ virtual IMWriteStream * CloneAndOpen(const CMString &) {return NULL;}
virtual long BytesProcessed() {return m_bytesProcessed;}
@@ -1238,7 +1238,7 @@ public:
MDLLEXPORT virtual bool Close();
MDLLEXPORT virtual bool IsOpen();
MDLLEXPORT virtual bool IsEnd();
- virtual IMReadStream * CloneAndOpen(const CMString &name) {return NULL;}
+ virtual IMReadStream * CloneAndOpen(const CMString &) {return NULL;}
virtual long BytesProcessed() {return m_bytesProcessed;}
protected:
@@ -1274,7 +1274,7 @@ public:
MDLLEXPORT virtual bool Close();
MDLLEXPORT virtual bool IsOpen();
MDLLEXPORT virtual bool IsEnd();
- virtual IMWriteStream * CloneAndOpen(const CMString &name) {return NULL;}
+ virtual IMWriteStream * CloneAndOpen(const CMString &) {return NULL;}
virtual long BytesProcessed() {return m_bytesProcessed;}
protected:
diff --git a/Inchworm/configure b/Inchworm/configure
index 533ece1..2129f12 100755
--- a/Inchworm/configure
+++ b/Inchworm/configure
@@ -3123,7 +3123,7 @@ fi
AM_CXXFLAGS=-m64
case $CXX in
- g++*) AM_CXXFLAGS="-std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated $AM_CXXFLAGS"
+ g++*) AM_CXXFLAGS="-ansi -pedantic -fopenmp -Wall -Wextra -Wno-deprecated $AM_CXXFLAGS"
;;
sunCC*) AM_CXXFLAGS="-std=c++0x -library=stlport4 -xopenmp -xvpara -fast $AM_CXXFLAGS"
;;
diff --git a/Inchworm/src/Cigar.hpp b/Inchworm/src/Cigar.hpp
index f71da9d..3ef6b31 100644
--- a/Inchworm/src/Cigar.hpp
+++ b/Inchworm/src/Cigar.hpp
@@ -20,7 +20,7 @@ namespace Cigar {
string construct_cigar(vector<alignment_segment>& segments,
unsigned int read_length,
const string& genome_seq,
- char strand = NULL);
+ char strand = 0);
diff --git a/Inchworm/src/DeBruijnGraph.cpp b/Inchworm/src/DeBruijnGraph.cpp
index 211b813..63ec460 100644
--- a/Inchworm/src/DeBruijnGraph.cpp
+++ b/Inchworm/src/DeBruijnGraph.cpp
@@ -427,7 +427,6 @@ vector<DeBruijnKmer> DeBruijnGraph::deconvolute_DS_mirror_graph() {
vector<kmer_int_type_t> collected_kmers;
kmer_int_type_t rk = root_kmers[r];
- DeBruijnKmer rdk = _kmer_map.find(rk)->second;
// cerr << "Got root node ID: " << rdk.getID() << endl;
@@ -575,10 +574,10 @@ vector<string> DeBruijnGraph::get_candidate_weldmers(kmer_int_type_t kmer_val, i
vector<string> weldmers;
- for (int i = 0; i < left_extensions.size(); i++) {
+ for (size_t i = 0; i < left_extensions.size(); i++) {
- for (int j = 0; j < right_extensions.size(); j++) {
+ for (size_t j = 0; j < right_extensions.size(); j++) {
string weldmer = left_extensions[i] + kmer_string + right_extensions[j];
@@ -615,7 +614,7 @@ void DeBruijnGraph::recursively_construct_kmer_extensions(kmer_int_type_t kmer_v
adjacent_kmers = kmer_node.get_prev_kmers(get_kmer_length());
}
- for (int i = 0; i < adjacent_kmers.size(); i++) {
+ for (size_t i = 0; i < adjacent_kmers.size(); i++) {
kmer_int_type_t adjacent_kmer = adjacent_kmers[i];
if (kmer_seen.find(adjacent_kmer) != kmer_seen.end()) {
@@ -629,7 +628,7 @@ void DeBruijnGraph::recursively_construct_kmer_extensions(kmer_int_type_t kmer_v
kmer_extension_chars.push_back(char_extend);
- if (kmer_extension_chars.size() == flank_extension_length) {
+ if (kmer_extension_chars.size() == (size_t)flank_extension_length) {
// reached maximal extension.
string kmer_extension_string = get_kmer_from_char_vector(kmer_extension_chars, direction);
extension_kmer_strings.push_back(kmer_extension_string);
diff --git a/Inchworm/src/FastaToDeBruijn.cpp b/Inchworm/src/FastaToDeBruijn.cpp
index d26f817..e93c9a9 100644
--- a/Inchworm/src/FastaToDeBruijn.cpp
+++ b/Inchworm/src/FastaToDeBruijn.cpp
@@ -39,7 +39,7 @@ DeBruijnGraph constructDeBruijnGraph (vector<string> fasta_filenames, int kmer_l
void createGraphPerRecord(vector<string> fasta_filenames, int kmer_length, bool sStrand, ArgProcessor args);
-string usage (ArgProcessor args) {
+string usage (ArgProcessor) {
stringstream usage_info;
@@ -152,7 +152,7 @@ int fastaToDeBruijn (int argc, char* argv[]) {
void createGraphPerRecord(vector<string> fasta_file_names, int kmer_length, bool sStrand, ArgProcessor args) {
- for (int i = 0; i < fasta_file_names.size(); i++) {
+ for (size_t i = 0; i < fasta_file_names.size(); i++) {
string fasta_filename = fasta_file_names[i];
@@ -194,7 +194,7 @@ void createGraphPerRecord(vector<string> fasta_file_names, int kmer_length, bool
vector<string> seq_regions;
string_util::tokenize(sequence, seq_regions, "X"); // inchworm bundles concatenated with 'X' delimiters by Chrysalis
- for (int s = 0; s < seq_regions.size(); s++) {
+ for (size_t s = 0; s < seq_regions.size(); s++) {
string seq_region = seq_regions[s];
@@ -249,7 +249,7 @@ DeBruijnGraph constructDeBruijnGraph (vector<string> fasta_file_names, int kmer_
DeBruijnGraph g(kmer_length);
- for (int i = 0; i < fasta_file_names.size(); i++) {
+ for (size_t i = 0; i < fasta_file_names.size(); i++) {
string fasta_filename = fasta_file_names[i];
@@ -268,7 +268,7 @@ DeBruijnGraph constructDeBruijnGraph (vector<string> fasta_file_names, int kmer_
vector<string> seq_regions;
string_util::tokenize(sequence, seq_regions, "X"); // inchworm bundles concatenated with 'X' delimiters by Chrysalis
- for (int s = 0; s < seq_regions.size(); s++) {
+ for (size_t s = 0; s < seq_regions.size(); s++) {
string seq_region = seq_regions[s];
diff --git a/Inchworm/src/IRKE.cpp b/Inchworm/src/IRKE.cpp
index b79f16b..c3c7ce5 100644
--- a/Inchworm/src/IRKE.cpp
+++ b/Inchworm/src/IRKE.cpp
@@ -26,9 +26,9 @@
#include "irke_common.hpp"
-static int MAX_RECURSION_HARD_STOP = 50;
+const unsigned int MAX_RECURSION_HARD_STOP = 50;
-typedef struct iworm_tmp_file { //FIXME: make a class for this
+struct iworm_tmp_file { //FIXME: make a class for this
ofstream* fh;
char* tmp_filename;
};
@@ -68,7 +68,7 @@ void IRKE::set_prune_singleton_read_interval (unsigned long interval) {
}
-void IRKE::build_graph(const string& fasta_filename, bool reassembleIworm, bool useKmers) {
+void IRKE::build_graph(const string& fasta_filename, bool, bool useKmers) {
if (useKmers)
populate_Kmers_from_kmers(fasta_filename);
@@ -559,7 +559,7 @@ void IRKE::compute_sequence_assemblies(KmerCounter& kcounter, float min_connecti
string sequence = reconstruct_path_sequence(kcounter, joined_path, assembly_base_coverage);
- int avg_cov = static_cast<int> ( (float)total_counts/(sequence.length()-kcounter.get_kmer_length() +1) + 0.5);
+ unsigned int avg_cov = static_cast<unsigned int> ( (float)total_counts/(sequence.length()-kcounter.get_kmer_length() +1) + 0.5);
/*
cout << "Inchworm-reconstructed sequence, length: " << sequence.length()
@@ -567,9 +567,9 @@ void IRKE::compute_sequence_assemblies(KmerCounter& kcounter, float min_connecti
<< " " << sequence << endl;
*/
- unsigned int contig_length = sequence.length();
+ size_t contig_length = sequence.length();
- if (contig_length >= MIN_ASSEMBLY_LENGTH && avg_cov >= MIN_ASSEMBLY_COVERAGE) {
+ if (contig_length >= MIN_ASSEMBLY_LENGTH && avg_cov >= MIN_ASSEMBLY_COVERAGE) {
*(tmpfiles[myTid].fh) << total_counts << endl
@@ -641,7 +641,6 @@ void IRKE::compute_sequence_assemblies(KmerCounter& kcounter, float min_connecti
//cerr << "Read sequence: " << sequence << endl;
- unsigned int contig_length = sequence.length();
unsigned int contig_hash = generateHash(sequence);
if (! seen_contig_already[contig_hash]
@@ -712,7 +711,7 @@ void IRKE::compute_sequence_assemblies(KmerCounter& kcounter, float min_connecti
bool IRKE::is_good_seed_kmer(kmer_int_type_t kmer, unsigned int kmer_count, unsigned int kmer_length,
- float min_connectivity) {
+ float) {
if (kmer_count == 0) {
return(false);
@@ -758,7 +757,7 @@ bool IRKE::is_good_seed_kmer(kmer_int_type_t kmer, unsigned int kmer_count, unsi
vector<kmer_int_type_t> IRKE::build_inchworm_contig_from_seed(kmer_int_type_t kmer, KmerCounter& kcounter,
float min_connectivity, unsigned int& total_counts,
- bool PARALLEL_IWORM) {
+ bool) {
unsigned int kmer_count = kcounter.get_kmer_count(kmer);
@@ -1171,7 +1170,7 @@ string IRKE::reconstruct_path_sequence(KmerCounter& kcounter, vector<kmer_int_ty
}
-bool IRKE::exceeds_min_connectivity (KmerCounter& kcounter, Kmer_Occurence_Pair kmerA, Kmer_Occurence_Pair kmerB, float min_connectivity) {
+bool IRKE::exceeds_min_connectivity (KmerCounter&, Kmer_Occurence_Pair kmerA, Kmer_Occurence_Pair kmerB, float min_connectivity) {
if (min_connectivity < 1e5) {
return(true); // consider test off
@@ -1345,7 +1344,7 @@ kmer_int_type_t IRKE::extract_best_seed(vector<kmer_int_type_t>& kmer_vec, KmerC
unsigned int kmer_length = kcounter.get_kmer_length();
unsigned int best_kmer_count = 0;
- kmer_int_type_t best_seed;
+ kmer_int_type_t best_seed = 0;
for (unsigned int i = 0; i < kmer_vec.size(); i++) {
diff --git a/Inchworm/src/IRKE_run.cpp b/Inchworm/src/IRKE_run.cpp
index db67c7f..38f8806 100644
--- a/Inchworm/src/IRKE_run.cpp
+++ b/Inchworm/src/IRKE_run.cpp
@@ -271,6 +271,7 @@ int run_IRKE(int argc, char* argv[]) {
// multithreading settings:
+ omp_set_dynamic(false);
if (args.isArgSet("--num_threads")) {
IRKE_COMMON::NUM_THREADS = args.getIntVal("--num_threads");
omp_set_num_threads(IRKE_COMMON::NUM_THREADS);
diff --git a/Inchworm/src/fastaToKmerCoverageStats.cpp b/Inchworm/src/fastaToKmerCoverageStats.cpp
index f684fca..1d8e287 100644
--- a/Inchworm/src/fastaToKmerCoverageStats.cpp
+++ b/Inchworm/src/fastaToKmerCoverageStats.cpp
@@ -26,7 +26,7 @@
#include "argProcessor.hpp"
unsigned int IRKE_COMMON::MONITOR = 0;
-int KMER_SIZE = 25;
+size_t KMER_SIZE = 25;
int MAX_THREADS = 6;
// various devel params
@@ -94,8 +94,6 @@ int runMe(int argc, char* argv[]) {
KmerCounter kcounter (KMER_SIZE, is_DS);
populate_kmer_counter(kcounter, kmers_fasta_file);
Fasta_reader fasta_reader(reads_fasta_file);
- ofstream* filewriter = NULL;
- ofstream* covwriter = NULL;
bool write_coverage_info = args.isArgSet("--capture_coverage_info");
int start_time = time(NULL);
@@ -132,7 +130,7 @@ int runMe(int argc, char* argv[]) {
if(write_coverage_info) {
// add the coverage info
stats_text << "\t";
- for (int i = 0; i < kmer_coverage.size(); i++) {
+ for (size_t i = 0; i < kmer_coverage.size(); i++) {
stats_text<< kmer_coverage[i];
if(i != kmer_coverage.size() - 1) {
stats_text<< ",";
@@ -214,11 +212,11 @@ vector<unsigned int> compute_kmer_coverage(string& sequence, KmerCounter& kcount
if(IRKE_COMMON::MONITOR) {
cerr << "processing sequence: " << sequence << endl;
}
- for (int i = 0; i <= (int) sequence.length() - KMER_SIZE; i++) {
+ for (size_t i = 0; i <= sequence.length() - KMER_SIZE; i++) {
// cerr << "i: " << i << ", <= " << sequence.length() - KMER_SIZE << endl;
string kmer = sequence.substr(i, KMER_SIZE);
if(IRKE_COMMON::MONITOR >= 2) {
- for (int j = 0; j <= i; j++) {
+ for (size_t j = 0; j <= i; j++) {
cerr << " ";
}
cerr << kmer << endl;
@@ -252,7 +250,7 @@ unsigned int median_coverage(vector<unsigned int> coverage) {
}
-string usage(ArgProcessor args) {
+string usage(ArgProcessor) {
stringstream usage_info;
usage_info << endl << endl;
usage_info << "Usage: " << endl
diff --git a/Inchworm/src/sequenceUtil.cpp b/Inchworm/src/sequenceUtil.cpp
index 7ba9c1f..4d92909 100644
--- a/Inchworm/src/sequenceUtil.cpp
+++ b/Inchworm/src/sequenceUtil.cpp
@@ -30,7 +30,7 @@ string currAccession;
bool contains_non_gatc (string kmer) {
for (unsigned int i = 0; i < kmer.size(); i++) {
- char c = kmer[i];
+ unsigned char c = kmer[i];
if (_base_to_int[c] > 3)
return(true);
@@ -52,7 +52,7 @@ bool contains_non_gatc (string kmer) {
string read_sequence_from_file (string filename) {
ifstream fileReader (filename.c_str());
- if (fileReader == 0) { // couldn't open file
+ if (!fileReader) { // couldn't open file
throw(stacktrace() + "\n\nCould not open " + filename + "\n");
}
@@ -256,7 +256,7 @@ kmer_int_type_t kmer_to_intval(string kmer) {
kmer_int_type_t kmer_val = 0;
for (unsigned int i = 0; i < kmer.length(); i++) {
- char c = kmer[i];
+ unsigned char c = kmer[i];
int val = _base_to_int[c];
/* ottmi: Don't need this here: the only possible source for non-gatc characters is
the reads file and we already check in add_kmer() */
@@ -398,7 +398,7 @@ string replace_nonGATC_chars_with_A (string& str) {
stringstream newStr;
for (unsigned int i = 0; i < str.size(); i++) {
- char c = str[i];
+ unsigned char c = str[i];
if (_base_to_int[c] > 3)
c = 'A';
diff --git a/PerlLib/Fastq_reader.pm b/PerlLib/Fastq_reader.pm
index 643cda1..e6e9b02 100755
--- a/PerlLib/Fastq_reader.pm
+++ b/PerlLib/Fastq_reader.pm
@@ -23,6 +23,10 @@ sub new {
else {
if ( $fastqFile =~ /\.gz$/ ) {
open ($filehandle, "gunzip -c $fastqFile | ") or die "Error: Couldn't open compressed $fastqFile\n";
+ }
+ elsif ($fastqFile =~ /\.bz2$/) {
+ open ($filehandle, "bunzip2 -c $fastqFile | ") or die "Error, couldn't open compressed $fastqFile $!";
+
} else {
open ($filehandle, $fastqFile) or die "Error: Couldn't open $fastqFile\n";
}
diff --git a/PerlLib/HPC/PBS_handler.pm b/PerlLib/HPC/PBS_handler.pm
index a8c7b98..9b03323 100644
--- a/PerlLib/HPC/PBS_handler.pm
+++ b/PerlLib/HPC/PBS_handler.pm
@@ -36,16 +36,22 @@ sub submit_job_to_grid {
my $cmd = $self->{config}->{cmd} or confess "Error, need cmd from config file";
- $cmd .= "-d . -j oe -N $shell_script ";
+ $cmd .= " -d . -j oe -N $shell_script ";
$cmd .= " $shell_script 2>&1 ";
-
+
+
+ print STDERR "CMD: $cmd\n";
my $job_id_text = `$cmd`;
- #print STDERR "\nSGE: $job_id_text\n";
+
+
+
my $ret = $?;
+ print STDERR "\nPBS job (ret=$ret), text:: $job_id_text\n";
+
if ($ret) {
print STDERR "FARMIT failed to accept job: $cmd\n (ret $ret)\n$job_id_text\n";
@@ -83,8 +89,11 @@ sub job_running_or_pending_on_grid {
foreach my $line (split(/\n/, $response)) {
my @x = split(/\s+/, $line);
-
- if ($x[0] eq $job_id) {
+ my $lcl_job_id = $x[0];
+ if ($x[0] =~ /(\d+)(\.[0-9a-zA-Z])*/) {
+ $lcl_job_id = $1;
+ }
+ if ($lcl_job_id eq $job_id) {
my $state = $x[4];
$self->{job_id_to_submission_time}->{$job_id} = time();
diff --git a/PerlLib/HPC/SGE_handler.pm b/PerlLib/HPC/SGE_handler.pm
index 9712f0d..2d01f53 100644
--- a/PerlLib/HPC/SGE_handler.pm
+++ b/PerlLib/HPC/SGE_handler.pm
@@ -46,7 +46,7 @@ sub submit_job_to_grid {
if ($ret) {
- print STDERR "FARMIT failed to accept job: $cmd\n (ret $ret)\n$job_id_text\n";
+ print STDERR "FARMIT failed to accept job: [$cmd]\n (ret $ret)\n$job_id_text\n";
return(-1);
}
else {
diff --git a/PerlLib/Pipeliner.pm b/PerlLib/Pipeliner.pm
index 285527c..aa1b1d3 100644
--- a/PerlLib/Pipeliner.pm
+++ b/PerlLib/Pipeliner.pm
@@ -3,8 +3,37 @@ package Pipeliner;
use strict;
use warnings;
use Carp;
+use Cwd;
+################################
+## Verbose levels:
+## 1: see CMD string
+## 2: see stderr during process
my $VERBOSE = 0;
+################################
+
+
+####################
+## Static methods:
+####################
+
+####
+sub ensure_full_path {
+ my ($path) = @_;
+
+ unless ($path =~ m|^/|) {
+ $path = cwd() . "/$path";
+ }
+
+ return($path);
+}
+
+
+
+
+################
+## Obj methods:
+################
####
sub new {
@@ -12,12 +41,13 @@ sub new {
my %params = @_;
if ($params{-verbose}) {
- $VERBOSE = 1;
+ $VERBOSE = $params{-verbose};
}
- my $self = { cmd_objs => [],
+ my $self = {
+ cmd_objs => [],
};
-
+
bless ($self, $packagename);
return($self);
@@ -48,20 +78,40 @@ sub run {
my $checkpoint_file = $cmd_obj->get_checkpoint_file();
if (-e $checkpoint_file) {
- print STDERR "--Skipping cmd: $cmdstr, checkpoint exists.\n" if $VERBOSE;
+ print STDERR "-- Skipping CMD: $cmdstr, checkpoint exists.\n" if $VERBOSE;
}
else {
- print STDERR "Running cmd: $cmdstr\n" if $VERBOSE;
+ print STDERR "* Running CMD: $cmdstr\n" if $VERBOSE;
+
+ my $tmp_stderr = "tmp.$$.stderr";
+ if (-e $tmp_stderr) {
+ unlink($tmp_stderr);
+ }
+ unless ($VERBOSE == 2) {
+ $cmdstr .= " 2>$tmp_stderr";
+ }
+
my $ret = system($cmdstr);
if ($ret) {
+
+ if (-e $tmp_stderr) {
+ system("cat $tmp_stderr");
+ unlink($tmp_stderr);
+ }
+
confess "Error, cmd: $cmdstr died with ret $ret";
}
else {
`touch $checkpoint_file`;
if ($?) {
+
confess "Error creating checkpoint file: $checkpoint_file";
}
}
+
+ if (-e $tmp_stderr) {
+ unlink($tmp_stderr);
+ }
}
}
diff --git a/PerlLib/Process_cmd.pm b/PerlLib/Process_cmd.pm
index c064a05..99be5c8 100644
--- a/PerlLib/Process_cmd.pm
+++ b/PerlLib/Process_cmd.pm
@@ -3,10 +3,11 @@ package Process_cmd;
use strict;
use warnings;
use Carp;
+use Cwd;
require Exporter;
our @ISA = qw(Exporter);
-our @EXPORT = qw(process_cmd);
+our @EXPORT = qw(process_cmd ensure_full_path);
sub process_cmd {
@@ -23,5 +24,17 @@ sub process_cmd {
}
+sub ensure_full_path {
+ my ($path) = @_;
+
+ unless ($path =~ m|^/|) {
+ $path = cwd() . "/$path";
+ }
+
+ return($path);
+}
+
+
+
1; #EOM
diff --git a/PerlLib/SAM_entry.pm b/PerlLib/SAM_entry.pm
index cf140be..11bcc5f 100644
--- a/PerlLib/SAM_entry.pm
+++ b/PerlLib/SAM_entry.pm
@@ -96,6 +96,20 @@ sub get_scaffold_position { # preferred
}
+sub get_aligned_start_position {
+ my $self = shift;
+ my ($lend, $rend) = $self->get_genome_span();
+
+ my $strand = $self->get_query_strand();
+ if ($strand eq '+') {
+ return($lend);
+ }
+ else {
+ return($rend);
+ }
+}
+
+
####
sub get_cigar_alignment {
my $self = shift;
diff --git a/Release.Notes b/Release.Notes
index c952654..cc3fa27 100644
--- a/Release.Notes
+++ b/Release.Notes
@@ -1,4 +1,20 @@
+# next release
+
+ -including -XX:ParallelGCThreads=$bflyGCThreads in ExitTester.jar execution.
+ -incorporating samtools-0.1.19 as plugin
+
+
+
+# Release v2.0.6
+ -patch to autoconf for the inchworm build
+
+
+# Release v2.0.5
+ -bugfix to properly fan out read files (they were inadvertently ending up in a single directory)
+
+
+
# Release v2.0.4
-Trimmomatic symlink set w/ capital T
diff --git a/Trinity b/Trinity
index 73f8264..a41d004 100755
--- a/Trinity
+++ b/Trinity
@@ -6,18 +6,18 @@ use threads;
no strict qw(subs refs);
use FindBin;
-use lib ("$FindBin::Bin/PerlLib");
+use lib ("$FindBin::RealBin/PerlLib");
use File::Basename;
use Time::localtime;
use Cwd;
use Carp;
use COMMON;
-use Getopt::Long qw(:config posix_default no_ignore_case pass_through);
+use Getopt::Long qw(:config posix_default no_ignore_case pass_through gnu_compat);
use Pipeliner;
use Fasta_reader;
+use List::Util qw(min max);
-
-my $VERSION = "v2.0.6";
+my $VERSION = "v2.1.0";
BEGIN {
@@ -31,6 +31,9 @@ use HPC::GridRunner;
open (STDERR, ">&STDOUT"); ## capturing stderr and stdout in a single stdout stream
+
+
+
#directory defnintions
my $ROOTDIR = "$FindBin::RealBin";
my $UTILDIR = "$ROOTDIR/util";
@@ -41,11 +44,12 @@ my $BUTTERFLY_DIR = "$ROOTDIR/Butterfly";
my $JELLYFISH_DIR = "$ROOTDIR/trinity-plugins/jellyfish";
my $FASTOOL_DIR = "$ROOTDIR/trinity-plugins/fastool";
my $COLLECTL_DIR = "$ROOTDIR/trinity-plugins/collectl/bin";
-my $COREUTILS_DIR = "$ROOTDIR/trinity-plugins/coreutils/bin";
my $PARAFLY = "$ROOTDIR/trinity-plugins/parafly/bin/ParaFly";
my $TRIMMOMATIC = "$ROOTDIR/trinity-plugins/Trimmomatic/trimmomatic.jar";
my $TRIMMOMATIC_DIR = "$ROOTDIR/trinity-plugins/Trimmomatic";
+$ENV{PATH} = "$ROOTDIR/trinity-plugins/BIN:$ENV{PATH}";
+
# Site specific setup
@@ -126,7 +130,7 @@ my $min_glue = 2;
my $min_iso_ratio = 0.05;
my $glue_factor = 0.05;
my $max_reads_per_graph = 200000;
-my $max_reads_per_loop = 10000000;
+my $max_reads_per_loop = 50000000; #MW: Set default to 50M, still fits into main memory
my $min_pct_read_mapping = 0;
my $chrysalis_output_dir = "chrysalis";
my $component_directory;
@@ -508,8 +512,6 @@ foreach (@ARGV) {
};
-my $sort_exec = &COMMON::get_sort_exec($CPU);
-
my $NO_FASTOOL = 0;
my $NO_CLEANUP = 0;
my $FULL_CLEANUP = 0;
@@ -547,7 +549,7 @@ my $iworm_opts = "";
my $bypass_java_version_check = 0;
-my $SEE = 0;
+my $VERBOSE = 0;
my $ANANAS_DIR = "";
@@ -560,7 +562,7 @@ my $NO_VERSION_CHECK = 0;
'advanced_help' => \$advanced_help_flag,
'show_full_usage_info' => \$full_usage_info_flag,
- 'verbose' => \$SEE,
+ 'verbose' => \$VERBOSE,
'no_version_check' => \$NO_VERSION_CHECK,
@@ -690,11 +692,117 @@ my $NO_VERSION_CHECK = 0;
+my @__ALL_TRINITY_PARAMS = qw(
+h
+help
+advanced_help
+show_full_usage_info
+verbose
+no_version_check
+seqType
+left
+right
+single
+SS_lib_type
+long_reads
+output
+min_contig_length
+jaccard_clip
+cite
+CPU
+np
+mpiexec
+prep
+KMER_SIZE
+trimmomatic
+quality_trimming_params
+normalize_reads
+normalize_max_read_cov
+normalize_by_read_set
+group_pairs_distance
+bfly_opts
+bflyHeapSpaceMax
+bflyHeapSpaceInit
+bflyGCThreads
+bflyCPU
+bflyCalculateCPU
+bfly_jar
+path_reinforcement_distance
+no_path_merging
+min_per_id_same_path
+max_diffs_same_path
+max_internal_gap_same_path
+PasaFly
+CuffFly
+min_kmer_cov
+inchworm_cpu
+FORCE_INCHWORM_KMER_METHOD
+INCHWORM_CUSTOM_PARAMS
+no_run_inchworm
+iworm_opts
+max_memory
+M
+min_glue
+glue_factor
+min_iso_ratio
+min_pcnt_read_iworm_kmers
+max_reads_per_graph
+max_reads_per_loop
+min_pct_read_mapping
+weldmer_size
+no_bowtie
+bowtie_comp
+no_run_chrysalis
+grid_conf
+show_advanced_options
+run_as_paired
+no_fastool
+no_cleanup
+full_cleanup
+version
+monitoring
+no_distributed_trinity_exec
+KMER_SIZE
+jelly_s
+NO_PARALLEL_IWORM
+chrysalis_debug_weld_all
+genome_guided_bam
+genome_guided_max_intron
+genome_guided_min_coverage
+genome_guided_min_reads_per_partition
+genome_guided_just_prep
+trinity_complete
+grid_node_CPU
+grid_node_max_memory
+bypass_java_version_check
+ananas_dir
+
+);
+
+my %ACCEPTABLE_OPTS = map { + $_ => 1} @__ALL_TRINITY_PARAMS;
+
+my $opts_not_recognized_flag = 0;
+for my $opt (@ARGV) {
+ if ($opt =~ /^-+(\S+)/) {
+ my $opt_part = $1;
+ unless ($ACCEPTABLE_OPTS{$opt_part}) {
+ print STDERR "ERROR, don't recognize parameter: $opt\n";
+ $opts_not_recognized_flag = 1;
+ }
+ }
+}
+if ($opts_not_recognized_flag) {
+ die "Please review usage info for accepted parameters.\n";
+}
+
+
if ($SHOW_CITATION_FLAG) {
&show_lit_citation();
exit(0);
}
+my $sort_exec = &COMMON::get_sort_exec($CPU);
+
if ($full_usage_info_flag) {
$usage = $basic_usage . $full_usage . $usage_synopsis;
@@ -813,12 +921,12 @@ else {
## Check Java version:
-unless ($NO_RUN_INCHWORM_FLAG || $NO_RUN_CHRYSALIS_FLAG || $bypass_java_version_check) {
+unless ($NO_RUN_INCHWORM_FLAG || $NO_RUN_CHRYSALIS_FLAG || $bypass_java_version_check || $TRINITY_COMPLETE_FLAG) {
my $java_version = `java -Xmx64m -version 2>&1 `;
if ($java_version =~ /(java|openjdk) version \"1\.(\d)\./) {
my $version_id = $2;
- if ($version_id != 7) {
- die "Error, Trinity requires access to Java version 1.7. Currently installed version is: $java_version";
+ if ($version_id < 7) {
+ die "Error, Trinity requires access to Java version 1.7 or higher. Currently installed version is: $java_version";
}
}
else {
@@ -888,7 +996,7 @@ if ($PAIRED_MODE && (!$NO_RUN_CHRYSALIS_FLAG) && (!$NO_BOWTIE)) {
my $bowtie_path = `which bowtie`;
my $bowtie_build_path = `which bowtie-build`;
if ($bowtie_path =~ /\w/ && $bowtie_build_path =~ /\w/) {
- print "Paired mode requires bowtie. Found bowtie at: $bowtie_path\n and bowtie-build at $bowtie_build_path\n\n" if $SEE;
+ print "Paired mode requires bowtie. Found bowtie at: $bowtie_path\n and bowtie-build at $bowtie_build_path\n\n" if $VERBOSE;
}
else {
die "Error, cannot find path to bowtie ($bowtie_path) or bowtie-build ($bowtie_build_path), which is now needed as part of Chrysalis' read scaffolding step. If you should choose to not run bowtie, include the --no_bowtie in your Trinity command.\n\n";
@@ -896,7 +1004,7 @@ if ($PAIRED_MODE && (!$NO_RUN_CHRYSALIS_FLAG) && (!$NO_BOWTIE)) {
my $samtools_path = `which samtools`;
if ($samtools_path =~ /\w/) {
- print "Found samtools at: $samtools_path\n" if $SEE;
+ print "Found samtools at: $samtools_path\n" if $VERBOSE;
}
else {
die "Error, cannot find samtools. Please be sure samtools is installed and included in your PATH setting.\n";
@@ -945,8 +1053,8 @@ if ($grid_conf_file) {
main: {
$ENV{OMP_NUM_THREADS} = $CPU;
- unless ($NO_RUN_INCHWORM_FLAG || $NO_RUN_CHRYSALIS_FLAG) {
- print STDERR "-since butterfly will eventually be run, lets test for proper execution of java\n" if $SEE;
+ unless ($NO_RUN_INCHWORM_FLAG || $NO_RUN_CHRYSALIS_FLAG || $TRINITY_COMPLETE_FLAG) {
+ print STDERR "-since butterfly will eventually be run, lets test for proper execution of java\n" if $VERBOSE;
&test_java_failure_capture();
}
@@ -1016,8 +1124,8 @@ main: {
chdir ($output_directory) or die "Error, cannot cd to $output_directory";
- collectl_start() unless ($FULL_CLEANUP);
- &perfmon_start() unless ($FULL_CLEANUP);
+ collectl_start() unless ($TRINITY_COMPLETE_FLAG || $FULL_CLEANUP);
+ &perfmon_start() unless ($TRINITY_COMPLETE_FLAG || $FULL_CLEANUP);
unless ($TRINITY_COMPLETE_FLAG) {
print STDERR "\n\n";
@@ -1099,7 +1207,7 @@ main: {
};
if ($@) {
- print STDERR "$@\n" if $SEE;
+ print STDERR "$@\n" if $VERBOSE;
if ($@ !~ /^NON_FATAL_EXCEPTION/) {
die "Trinity run failed. Must investigate error above.\n";
}
@@ -1107,7 +1215,7 @@ main: {
if ($FULL_CLEANUP) {
- print "Fully cleaning up.\n" if $SEE;
+ print "Fully cleaning up.\n" if $VERBOSE;
$output_directory =~ s|/+$||g; # remove any trailing directory slash
if (-s "Trinity.fasta.tmp") {
@@ -1146,12 +1254,13 @@ main: {
print "###################################################################\n\n\n" unless $TRINITY_COMPLETE_FLAG;
}
else {
- die "ERROR, no butterfly assemblies reported.";
+
+ die "ERROR, no butterfly assemblies reported." unless $TRINITY_COMPLETE_FLAG;
}
}
- &perfmon_end() unless ($FULL_CLEANUP);
+ &perfmon_end() unless ($TRINITY_COMPLETE_FLAG || $FULL_CLEANUP);
exit(0);
@@ -1180,7 +1289,7 @@ sub run_Trinity {
print "\n\n#######################################################################\n"
. "Inchworm file: $inchworm_file detected.\n"
. "Skipping Inchworm Step, Using Previous Inchworm Assembly\n"
- . "#######################################################################\n\n" if ($SEE || ! $TRINITY_COMPLETE_FLAG);
+ . "#######################################################################\n\n" if ($VERBOSE || ! $TRINITY_COMPLETE_FLAG);
#sleep(2);
}
else {
@@ -1189,7 +1298,7 @@ sub run_Trinity {
my $count_of_reads;
if (@left_files && @right_files) {
- unless (-s $trinity_target_fa && !-e "left.fa" && !-e "right.fa") {
+ unless (-s $trinity_target_fa && !-e "left.fa.ok" && !-e "right.fa.ok") {
my ($left_SS_type, $right_SS_type);
if ($SS_lib_type) {
@@ -1198,24 +1307,22 @@ sub run_Trinity {
print("Converting input files. (in parallel)");
my $thr1;
my $thr2;
- if (!(-s "left.fa")) {
+ if (!(-s "left.fa.ok")) {
$thr1 = threads->create('prep_seqs', \@left_files, $seqType, "left", $left_SS_type);
- } else {
- $thr1 = threads->create(sub { print ("left file exists, nothing to do");});
}
- if (!(-s "right.fa")) {
+ if (!(-s "right.fa.ok")) {
$thr2 = threads->create('prep_seqs', \@right_files, $seqType, "right", $right_SS_type);
- } else {
- $thr2 = threads->create(sub { print ("right file exists, nothing to do");});
}
- @left_files = @{$thr1->join()};
- @right_files =@{$thr2->join()};
+
+ $thr1->join();
+ $thr2->join();
if ($thr1->error() || $thr2->error()) {
die "Error prepping sequences.";
}
-
- print("Done converting input files.") if $SEE;
+ &process_cmd("touch left.fa.ok right.fa.ok");
+
+ print("Done converting input files.") if $VERBOSE;
## Calculate input file sizes for performance monitoring
# this should be set as the created fasta otherwise results will differ for same data passed as .fq and .fa?
my $pm_temp = -s "left.fa";
@@ -1225,15 +1332,18 @@ sub run_Trinity {
$pm_temp = $pm_temp / 1024 / 1024;
$pm_right_fa_size = sprintf('%.0f', $pm_temp);
- &process_cmd("cat left.fa right.fa > $trinity_target_fa") unless (-s $trinity_target_fa && (-s $trinity_target_fa == ((-s "left.fa") + (-s "right.fa"))));
- unless (-s $trinity_target_fa == ((-s "left.fa") + (-s "right.fa"))){
+ &process_cmd("cat left.fa right.fa > $trinity_target_fa") unless (-e "$trinity_target_fa.ok"
+ && (-s $trinity_target_fa == ((-s "left.fa") + (-s "right.fa"))));
+
+ unless (-s $trinity_target_fa == ((-s "left.fa") + (-s "right.fa"))) {
die "$trinity_target_fa is smaller (".(-s $trinity_target_fa)." bytes) than the combined size of left.fa and right.fa (".((-s "left.fa") + (-s "right.fa"))." bytes)\n";
}
+ &process_cmd("touch $trinity_target_fa.ok") unless (-e "$trinity_target_fa.ok");
# we keep if we have jaccard; delete later
unlink ("left.fa", "right.fa") unless $jaccard_clip; # no longer needed now that we have 'both.fa', which is needed by chryaslis
}
-
+
foreach my $f ((@left_files, at right_files)){
if (-s $f.'.readcount'){
open (IN,$f.'.readcount');
@@ -1247,8 +1357,10 @@ sub run_Trinity {
}
elsif (@single_files) {
-
- @single_files = @{&prep_seqs(\@single_files, $seqType, "single", $SS_lib_type) unless (-s "single.fa")};
+ unless (-e "single.fa.ok") {
+ &prep_seqs(\@single_files, $seqType, "single", $SS_lib_type);
+ &process_cmd("touch single.fa.ok");
+ }
## Calculate input file sizes for performance monitoring
my $pm_temp = -s "single.fa";
$pm_temp = $pm_temp / 1024 / 1024;
@@ -1275,16 +1387,22 @@ sub run_Trinity {
if ($long_reads) {
# adjust the inchworm target, tack on the longer reads.
-
+ open (LONG_READS,$long_reads);
+ if (<LONG_READS>!~/^>/){ #verify if it is fasta.
+ print "The long reads file does not look like FASTA.\n";
+ die;
+ }
+ close (LONG_READS);
$inchworm_target_fa .= ".wLongReads.fa";
- $count_of_reads += `grep -c '^>' $long_reads | wc -l`; #AP we don't know if these will be one single line
-
- &process_cmd("cat $long_reads | sed 's/>/>LR\\\$\\\|/' > $inchworm_target_fa");
-
- ## merge the long reads with the short reads into a new target file.
- &process_cmd("cat $trinity_target_fa >> $inchworm_target_fa");
-
- #&process_cmd("cat $long_reads $trinity_target_fa > $inchworm_target_fa");
+ $count_of_reads += `grep -c '^>' $long_reads`; #AP we don't know if these will be one single line
+ if (!-e "$inchworm_target_fa.LR.ok"){
+ &process_cmd("cat $long_reads | sed 's/>/>LR\\\$\\\|/' > $inchworm_target_fa"); #
+
+ ## merge the long reads with the short reads into target file.
+ &process_cmd("cat $inchworm_target_fa >> $trinity_target_fa "); #TODO: if it dies while doing this then truncate both.fa (truncate -s size both.fa) to its original size and redo;
+ &process_cmd("touch $inchworm_target_fa.LR.ok");
+ }
+ &process_cmd("ln -fs $trinity_target_fa $inchworm_target_fa "); #just to keep the filename .wLongReads.fa and to avoid unnecessary duplication of reads.
}
open (my $ofh, ">$inchworm_target_fa.read_count") or die $!;
@@ -1355,51 +1473,43 @@ sub run_Trinity {
my $butterfly_cmds = &run_chrysalis($inchworm_file, $inchworm_target_fa,
$min_contig_length, $group_pairs_distance, $SS_lib_type,
$trinity_target_fa, $bowtie_reads_fa);
+ $pm_chrysalis_end = `date +%s`;
+
if ($butterfly_cmds eq "RECURSIVE_TRINITY_COMPLETE") {
## stop here. all done! ## FIXME: this is very bad coding style!!! yes, I know.
return;
}
-
- $pm_chrysalis_end = `date +%s`;
-
- print STDERR "Butterfly_cmds: $butterfly_cmds\n" if $SEE;
+ print STDERR "Butterfly_cmds: $butterfly_cmds\n" if $VERBOSE;
if ($butterfly_cmds && -s $butterfly_cmds) {
## Run Butterfly
print STDERR "Inchworm and Chrysalis complete. Butterfly commands to execute are provided here:\n"
- . $butterfly_cmds . "\n\n" if $SEE;
+ . $butterfly_cmds . "\n\n" if $VERBOSE;
print STDERR "---------------------------------------------------------------\n"
. "-------------------- Butterfly --------------------------------\n"
. "-- (Reconstruct transcripts from reads and de Bruijn graphs) --\n"
- . "---------------------------------------------------------------\n\n" if $SEE;
+ . "---------------------------------------------------------------\n\n" if $VERBOSE;
$pm_butterfly_start = `date +%s`;
- if ($grid_conf_file) {
- my @bfly_cmds = `cat $butterfly_cmds`;
- chomp @bfly_cmds;
- my $grid_runner = new HPC::GridRunner($grid_conf_file, "chrysalis/butterfly_on_grid.cacheSuccess");
- my $ret = $grid_runner->run_on_grid(@bfly_cmds);
- if ($ret) {
- die "Error, not all butterfly commands could complete successfully... cannot continue.";
- }
- }
- else {
- my $cmd = "$PARAFLY -c $butterfly_cmds -shuffle -CPU $bflyCPU -failed_cmds failed_butterfly_commands.$$.txt "; # shuffle them since the first ones are usually the longest-running ones.
- &process_cmd($cmd);
- }
+
+ my $pipeliner = new Pipeliner(-verbose => ($TRINITY_COMPLETE_FLAG) ? $VERBOSE : max(1, $VERBOSE));
+ my $cmd = "$PARAFLY -c $butterfly_cmds -shuffle -CPU $bflyCPU -failed_cmds failed_butterfly_commands.$$.txt "; # shuffle them since the first ones are usually the longest-running ones.
+ $pipeliner->add_commands( new Command($cmd, ".butterfly.ok"));
+ $pipeliner->run();
+
$pm_butterfly_end = `date +%s`;
## capture results:
# my $cmd = 'find ./chrysalis -name "*allProbPaths.fasta" -exec cat {} + > Trinity.fasta.tmp';
# no longer scan the file system... we know which files should exist
print STDERR "\n\n** Harvesting all assembled transcripts into a single multi-fasta file...\n" unless ($TRINITY_COMPLETE_FLAG);
- my $cmd = "$UTILDIR/support_scripts/print_butterfly_assemblies.pl $chrysalis_output_dir/component_base_listing.txt > Trinity.fasta.tmp";
+ $cmd = "$UTILDIR/support_scripts/print_butterfly_assemblies.pl $chrysalis_output_dir/component_base_listing.txt > Trinity.fasta.tmp";
&process_cmd($cmd);
@@ -1424,7 +1534,7 @@ sub run_chrysalis {
## Define iworm links via paired-end read mappings:
if ($PAIRED_MODE && ! $NO_BOWTIE) {
- my $pipeliner = new Pipeliner(-verbose => ($TRINITY_COMPLETE_FLAG) ? 0 : 1);
+ my $pipeliner = new Pipeliner(-verbose => ($TRINITY_COMPLETE_FLAG) ? $VERBOSE : max(1, $VERBOSE));
# generate the pair links.
my $iworm_min100_fa_file = "$chrysalis_output_dir/" . basename("$inchworm_file.min100");
@@ -1432,29 +1542,32 @@ sub run_chrysalis {
$pipeliner->add_commands( new Command($cmd, "$iworm_min100_fa_file.ok"));
$pipeliner->run();
- $pipeliner = new Pipeliner(-verbose => $SEE);
- $cmd = "bowtie-build -q $iworm_min100_fa_file $iworm_min100_fa_file";
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
+ $pipeliner = new Pipeliner(-verbose => $VERBOSE);
+ if($long_reads){
+ $cmd = "bowtie2-build -o 3 $iworm_min100_fa_file $iworm_min100_fa_file"; #-o 3 / defaut is 5, less use more ram but is faster when mapping the reads
}
+ else{ #keeping this because some may wish
+ $cmd = "bowtie-build -q $iworm_min100_fa_file $iworm_min100_fa_file";
+ }
+
if (-s "$iworm_min100_fa_file") {
$pipeliner->add_commands( new Command($cmd, "$iworm_min100_fa_file.bowtie_build.ok"));
my $bowtie_sam_file = "$chrysalis_output_dir/iworm.bowtie.nameSorted.bam";
- $cmd = "bash -c \" set -o pipefail; bowtie -a -m 20 --best --strata --threads $CPU --chunkmbs 512 -q -S -f $iworm_min100_fa_file $bowtie_reads_fa | samtools view $PARALLEL_SAMTOOLS_SORT_TOKEN -F4 -Sb - | samtools sort $PARALLEL_SAMTOOLS_SORT_TOKEN -no - - > $bowtie_sam_file\" ";
-
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
+ if ($long_reads){
+ $cmd = "bash -c \" set -o pipefail;bowtie2 --local -a --threads $CPU -f $iworm_min100_fa_file $bowtie_reads_fa | samtools view $PARALLEL_SAMTOOLS_SORT_TOKEN -F4 -Sb - | samtools sort -m $max_memory $PARALLEL_SAMTOOLS_SORT_TOKEN -no - - > $bowtie_sam_file\" ";
+ }
+ else{
+ $cmd = "bash -c \" set -o pipefail; bowtie -a -m 20 --best --strata --threads $CPU --chunkmbs 512 -q -S -f $iworm_min100_fa_file $bowtie_reads_fa | samtools view $PARALLEL_SAMTOOLS_SORT_TOKEN -F4 -Sb - | samtools sort -m $max_memory $PARALLEL_SAMTOOLS_SORT_TOKEN -no - - > $bowtie_sam_file\" ";
}
+
$pipeliner->add_commands( new Command($cmd, "$bowtie_sam_file.ok"));
## generate the scaffold info
+ $ENV{'LD_LIBRARY_PATH'} .= ":$ROOTDIR/trinity-plugins/htslib";
my $iworm_scaffolds_file = "$chrysalis_output_dir/iworm_scaffolds.txt";
- $cmd = "$UTILDIR/support_scripts/scaffold_iworm_contigs.pl $bowtie_sam_file $inchworm_file > $iworm_scaffolds_file"; # important, must use original inchworm file because positions are indexed for later use by GraphFromFasta
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
+ $cmd = "$ROOTDIR/trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs $bowtie_sam_file $inchworm_file > $iworm_scaffolds_file"; # important, must use original inchworm file because positions are indexed for later use by GraphFromFasta
$pipeliner->add_commands( new Command($cmd, "$iworm_scaffolds_file.ok"));
@@ -1467,7 +1580,7 @@ sub run_chrysalis {
- my $chrysalis_pipeliner = new Pipeliner(-verbose => ($TRINITY_COMPLETE_FLAG) ? 0 : 1);
+ my $chrysalis_pipeliner = new Pipeliner(-verbose => ($TRINITY_COMPLETE_FLAG) ? $VERBOSE : max(1, $VERBOSE));
my $graphFromFasta_outfile = "$chrysalis_output_dir/GraphFromIwormFasta.out";
@@ -1494,10 +1607,6 @@ sub run_chrysalis {
$graphFromFasta_cmd .= " > $graphFromFasta_outfile";
- if ($TRINITY_COMPLETE_FLAG) {
- $graphFromFasta_cmd .= " 2>/dev/null";
- }
-
my $checkpoint = "$graphFromFasta_outfile.ok";
$chrysalis_pipeliner->add_commands( new Command($graphFromFasta_cmd, $checkpoint) );
@@ -1511,9 +1620,6 @@ sub run_chrysalis {
my $cmd = "$CHRYSALIS_DIR/CreateIwormFastaBundle -i $graphFromFasta_outfile -o $iworm_bundles_fasta_file -min $min_contig_length";
- unless ($SEE) {
- $cmd .= " 2>/dev/null ";
- }
$chrysalis_pipeliner->add_commands( new Command($cmd, "$iworm_bundles_fasta_file.ok"));
@@ -1540,9 +1646,6 @@ sub run_chrysalis {
$cmd .= " -min_pct_read_mapping $min_pct_read_mapping ";
}
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
$chrysalis_pipeliner->add_commands( new Command($cmd, "$reads_to_components_output_file.ok"));
}
@@ -1554,9 +1657,6 @@ sub run_chrysalis {
my $cmd = "$sort_exec -T . -S $max_memory -k 1,1n $reads_to_components_output_file > $sorted_reads_to_components_file";
- unless ($SEE) {
- $cmd .= " 2>/dev/null ";
- }
$chrysalis_pipeliner->add_commands( new Command($cmd, "$sorted_reads_to_components_file.ok"));
@@ -1586,10 +1686,6 @@ sub run_chrysalis {
$cmd .= " > $deBruijnGraph_outfile";
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
-
$chrysalis_pipeliner->add_commands(new Command($cmd, "$deBruijnGraph_outfile.ok") );
}
$chrysalis_pipeliner->run();
@@ -1608,14 +1704,9 @@ sub run_chrysalis {
my $partitioning_checkpoint_file = "$chrysalis_output_dir/file_partitioning.ok";
my $cmd = "$UTILDIR/support_scripts/partition_chrysalis_graphs_n_reads.pl --deBruijns $chrysalis_output_dir/bundled_iworm_contigs.fasta.deBruijn --componentReads $chrysalis_output_dir/readsToComponents.out.sort -N 1000 -L $min_contig_length ";
-
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
-
- &process_cmd($cmd) unless (-e $partitioning_checkpoint_file);
-
- &process_cmd("touch $partitioning_checkpoint_file") unless (-e $partitioning_checkpoint_file);
+ my $pipeliner = new Pipeliner(-verbose => ($TRINITY_COMPLETE_FLAG) ? $VERBOSE : max(1, $VERBOSE));
+ $pipeliner->add_commands (new Command( $cmd, "$partitioning_checkpoint_file") );
+ $pipeliner->run();
## write the quantifygraph commands and butterfly commands
my $component_base_listing_file = "$chrysalis_output_dir/component_base_listing.txt";
@@ -1653,10 +1744,6 @@ sub run_chrysalis {
$quantify_graph_cmd .= " -no_cleanup ";
}
- unless ($SEE) {
- $quantify_graph_cmd .= " 2>/dev/null";
- }
-
print $qgraph_cmd_ofh $quantify_graph_cmd . "\n";
}
@@ -1717,27 +1804,15 @@ sub run_chrysalis {
print STDERR "---------------------------------------------------\n"
. "----------- Chrysalis: QuantifyGraph --------------\n"
. "-- (Integrate mapped reads into de Bruijn graph) --\n"
- . "---------------------------------------------------\n\n" if $SEE;
+ . "---------------------------------------------------\n\n" if $VERBOSE;
- if ($grid_conf_file) {
- my @quantify_graph_cmds = `cat $quantify_graph_cmds`;
- chomp @quantify_graph_cmds;
-
- my $grid_runner = new HPC::GridRunner($grid_conf_file, "chrysalis/chrysalis_quantify_graph_on_grid.cacheSuccess");
- my $ret = $grid_runner->run_on_grid(@quantify_graph_cmds);
- if ($ret) {
- die "Error, not all Chrysalis quantify_graph commands completed successfully. Cannot continue.";
- }
- }
- else {
-
- my $cmd = "$PARAFLY -c $quantify_graph_cmds -CPU $CPU -failed_cmds failed_quantify_graph_commands.$$.txt -shuffle ";
- &process_cmd($cmd);
- }
+ my $pipeliner = new Pipeliner(-verbose => ($TRINITY_COMPLETE_FLAG) ? $VERBOSE : max(1, $VERBOSE));
+
+ my $cmd = "$PARAFLY -c $quantify_graph_cmds -CPU $CPU -failed_cmds failed_quantify_graph_commands.$$.txt -shuffle ";
+ $pipeliner->add_commands( new Command($cmd, ".quantify_graph.ok"));
+ $pipeliner->run();
- # write checkpoint
- &process_cmd("touch $quantify_graph_cmds_finished");
}
@@ -1806,7 +1881,7 @@ sub run_recursive_trinity {
if (! -e "recursive_trinity.cmds.ok") {
&write_trinity_partitioned_cmds($read_filenames, "recursive_trinity.cmds");
&process_cmd("touch recursive_trinity.cmds.ok");
- print STDERR "Done prepping partitioned cmds." if $SEE;
+ print STDERR "Done prepping partitioned cmds." if $VERBOSE;
}
if ($NO_DISTRIBUTED_TRINITY_EXEC) {
@@ -1820,7 +1895,7 @@ sub run_recursive_trinity {
print STDERR "\n\n** Harvesting all assembled transcripts into a single multi-fasta file...\n\n" unless ($TRINITY_COMPLETE_FLAG);
- my $cmd = "find read_partitions/ -name '*inity.fasta' | $UTILDIR/support_scripts/partitioned_trinity_aggregator.pl TR > Trinity.fasta.tmp";
+ my $cmd = "find read_partitions/ -name '*inity.fasta' | $UTILDIR/support_scripts/partitioned_trinity_aggregator.pl TRINITY_DN > Trinity.fasta.tmp";
&process_cmd($cmd);
return;
@@ -1861,84 +1936,66 @@ sub run_inchworm {
if (! ($FORCE_INCHWORM_KMER_METHOD || $TRINITY_COMPLETE_FLAG) ) {
my $jelly_kmer_fa_file = "jellyfish.kmers.fa";
- my $jelly_finished_checkpoint_file = "jellyfish.$min_kmer_cov.finished";
- unless (-e $jelly_finished_checkpoint_file) {
-
- print STDERR "-------------------------------------------\n"
- . "----------- Jellyfish --------------------\n"
- . "-- (building a k-mer catalog from reads) --\n"
- . "-------------------------------------------\n\n";
-
-
- my $read_file_size = -s $reads;
-
- my $jelly_hash_size = int( ($jellyfish_ram - $read_file_size)/7); # decided upon by Rick Westerman
-
-
- if ($jelly_hash_size < 100e6) {
- $jelly_hash_size = 100e6; # seems reasonable for a min hash size as 100M
- }
-
- ## for testing
- if ($JELLY_S) {
- $jelly_hash_size = $JELLY_S;
- }
-
- my $cmd = "$JELLYFISH_DIR/bin/jellyfish count -t $CPU -m $KMER_SIZE -s $jelly_hash_size ";
-
- unless ($SS_lib_type) {
- ## count both strands
- $cmd .= " --canonical ";
- }
-
- $cmd .= " $reads";
-
- unless ($SEE) {
- $cmd .= " 2> /dev/null ";
- }
-
- &process_cmd($cmd);
-
-
- if (-s $jelly_kmer_fa_file) {
- unlink($jelly_kmer_fa_file) or die "Error, cannot unlink $jelly_kmer_fa_file";
- }
-
- my $jelly_db = "mer_counts.jf";
-
- $cmd = "$JELLYFISH_DIR/bin/jellyfish dump -L $min_kmer_cov $jelly_db > $jelly_kmer_fa_file";
-
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
-
- &process_cmd($cmd);
-
- ## write a histogram of the kmer counts.
- $cmd = "$JELLYFISH_DIR/bin/jellyfish histo -t $CPU -o $jelly_kmer_fa_file.histo $jelly_db";
-
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
- &process_cmd($cmd);
-
+
+ print STDERR "-------------------------------------------\n"
+ . "----------- Jellyfish --------------------\n"
+ . "-- (building a k-mer catalog from reads) --\n"
+ . "-------------------------------------------\n\n";
+
+ my $pipeliner = new Pipeliner(-verbose => ($TRINITY_COMPLETE_FLAG) ? $VERBOSE : max(1, $VERBOSE));
+
+
+ my $read_file_size = -s $reads;
+
+ my $jelly_hash_size = int( ($jellyfish_ram - $read_file_size)/7); # decided upon by Rick Westerman
+
+
+ if ($jelly_hash_size < 100e6) {
+ $jelly_hash_size = 100e6; # seems reasonable for a min hash size as 100M
+ }
+
+ ## for testing
+ if ($JELLY_S) {
+ $jelly_hash_size = $JELLY_S;
+ }
+
+ my $cmd = "$JELLYFISH_DIR/bin/jellyfish count -t $CPU -m $KMER_SIZE -s $jelly_hash_size ";
+
+ unless ($SS_lib_type) {
+ ## count both strands
+ $cmd .= " --canonical ";
+ }
+
+ $cmd .= " $reads";
+
+ $pipeliner->add_commands(new Command($cmd, ".jellyfish_count.ok") );
+
+
+ my $jelly_db = "mer_counts.jf";
+
+ $cmd = "$JELLYFISH_DIR/bin/jellyfish dump -L $min_kmer_cov $jelly_db > $jelly_kmer_fa_file";
+
+ $pipeliner->add_commands(new Command($cmd, ".jellyfish_dump.ok") );
+
+ ## write a histogram of the kmer counts.
+ $cmd = "$JELLYFISH_DIR/bin/jellyfish histo -t $CPU -o $jelly_kmer_fa_file.histo $jelly_db";
+
+ $pipeliner->add_commands( new Command($cmd, ".jellyfish_histo.ok") );
+
+
+ $pipeliner->run();
+ if (-s $jelly_db) {
unlink($jelly_db);
-
- ## if got this far, consider jellyfish done.
- &process_cmd("touch $jelly_finished_checkpoint_file");
-
-
- if ($NO_RUN_INCHWORM_FLAG && ! $TRINITY_COMPLETE_FLAG) {
- print STDERR "WARNING: --no_run_inchworm parameter in effect. Stopping here prior to running inchworm.\n";
- exit(0);
- }
+ }
-
+ if ($NO_RUN_INCHWORM_FLAG && ! $TRINITY_COMPLETE_FLAG) {
+ print STDERR "WARNING: --no_run_inchworm parameter in effect. Stopping here prior to running inchworm.\n";
+ exit(0);
}
-
+
$inchworm_cmd = "$INCHWORM_DIR/inchworm --kmers $jelly_kmer_fa_file --run_inchworm -K $KMER_SIZE -L $MIN_IWORM_LEN --monitor 1 $iworm_opts ";
@@ -1964,12 +2021,12 @@ sub run_inchworm {
$inchworm_cmd .= " --DS ";
}
- unless ($NO_CLEANUP) {
+ if ($NO_CLEANUP) {
$inchworm_cmd .= " --keep_tmp_files ";
}
- my $num_threads = ($inchworm_cpu) ? $inchworm_cpu : $CPU;
+ my $num_threads = $inchworm_cpu;
$inchworm_cmd .= " --num_threads $num_threads ";
if ($PARALLEL_IWORM_FLAG) {
@@ -1988,14 +2045,14 @@ sub run_inchworm {
. "-- (Linear contig construction from k-mers) --\n"
. "----------------------------------------------\n\n" if (! $TRINITY_COMPLETE_FLAG);
- unless ($SEE) {
- $inchworm_cmd .= " 2>/dev/null";
- }
-
eval {
-
- &process_cmd($inchworm_cmd);;
+
+ my $pipeliner = new Pipeliner(-verbose => ($TRINITY_COMPLETE_FLAG) ? $VERBOSE : max(1, $VERBOSE));
+ $pipeliner->add_commands( new Command($inchworm_cmd, ".iworm.ok") );
+ $pipeliner->add_commands( new Command("mv $inchworm_outfile.tmp $inchworm_outfile", ".iworm_renamed.ok") );
+ $pipeliner->run();
+
};
if ($@) {
@@ -2005,10 +2062,7 @@ sub run_inchworm {
print STDERR "\n\nIf it indicates bad_alloc(), then Inchworm ran out of memory. You'll need to either reduce the size of your data set or run Trinity on a server with more memory available.\n\n";
exit(1);
}
-
- rename("$inchworm_outfile.tmp", $inchworm_outfile) or die "Error, cannot rename $inchworm_outfile.tmp to $inchworm_outfile"; # now we know for sure it's done.
-
-
+
return;
}
@@ -2016,38 +2070,27 @@ sub run_inchworm {
####
sub prep_seqs {
my ($initial_files_ref, $seqType, $file_prefix, $SS_lib_type) = @_;
+
my @initial_files = @$initial_files_ref;
+
return if -e "$file_prefix.fa";
- for (my $i=0;$i<scalar(@initial_files);$i++){
- my $f = $initial_files[$i];
- if ($f=~/\.gz$/){
- my $new = $f;
- $new=~s/\.gz$//;
- unlink($new);
- &process_cmd("gunzip -c $f > $new");
- $initial_files[$i] = $new;
- }elsif ($f=~/\.bz2$/){
- my $new = $f;
- $new=~s/\.bz2$//;
- unlink($new);
- &process_cmd("bunzip2 -dkc $f > $new");
- $initial_files[$i] = $new;
- }
- }
- my $initial_file_str = join(" ", at initial_files);
+ my $initial_file_str = join(" ", at initial_files);
if ($seqType eq "fq") {
# make fasta
foreach my $f (@initial_files){
- my $perlcmd = "$UTILDIR/support_scripts/fastQ_to_fastA.pl -I $f ";
- my $fastool_cmd = "$FASTOOL_DIR/fastool";
+ my $fastool_cmd = "cat $f | $FASTOOL_DIR/fastool";
+ if ($f=~/\.gz$/){
+ $fastool_cmd = "gunzip -c $f | $FASTOOL_DIR/fastool";
+ }elsif ($f=~/\.bz2$/){
+ $fastool_cmd = "bunzip2 -dkc $f | $FASTOOL_DIR/fastool";
+ }
+
if ($SS_lib_type && $SS_lib_type eq "R") {
- $perlcmd .= " --rev ";
- $fastool_cmd .= " --rev ";
+ $fastool_cmd .= " --rev";
}
- $fastool_cmd .= " --illumina-trinity --to-fasta $f >> $file_prefix.fa 2> $f.readcount ";
- $perlcmd .= " >> $file_prefix.fa 2> $f.readcount ";
- my $cmd = ($USE_FASTOOL) ? $fastool_cmd : $perlcmd;
+ $fastool_cmd .= " --illumina-trinity --to-fasta >> $file_prefix.fa 2> $f.readcount ";
+ my $cmd = $fastool_cmd;
&process_cmd($cmd);
}
}
@@ -2055,14 +2098,31 @@ sub prep_seqs {
if (scalar(@initial_files) == 1 && (!$SS_lib_type || $SS_lib_type ne "R")) {
## just symlink it here:
my $cmd = "ln -s $initial_file_str $file_prefix.fa";
+ if ($initial_file_str=~/\.gz$/){
+ $cmd = "gunzip -c $initial_file_str >$file_prefix.fa";
+ }elsif ($initial_file_str=~/\.bz2$/){
+ $cmd = "bunzip2 -dkc $initial_file_str >$file_prefix.fa";
+ }
&process_cmd($cmd);
}elsif(scalar(@initial_files) > 1 && (!$SS_lib_type || $SS_lib_type ne "R")){
- my $cmd = "cat $initial_file_str > $file_prefix.fa";
- &process_cmd($cmd);
+ foreach my $f (@initial_files){
+ my $cmd = "cat $f >> $file_prefix.fa";
+ if ($f=~/\.gz$/){
+ $cmd = "gunzip -c $f >> $file_prefix.fa";
+ }elsif ($f=~/\.bz2$/){
+ $cmd = "bunzip2 -dkc $f >> $file_prefix.fa";
+ }
+ &process_cmd($cmd);
+ }
}else {
#if ($SS_lib_type && $SS_lib_type eq "R") {
foreach my $f (@initial_files){
my $cmd = "$UTILDIR/support_scripts/revcomp_fasta.pl $f >> $file_prefix.fa";
+ if ($f=~/\.gz$/){
+ $cmd = "gunzip -c $f | $UTILDIR/support_scripts/revcomp_fasta.pl >> $file_prefix.fa";
+ }elsif ($f=~/\.bz2$/){
+ $cmd = "bunzip2 -dkc $f | $UTILDIR/support_scripts/revcomp_fasta.pl >> $file_prefix.fa";
+ }
&process_cmd($cmd);
}
}
@@ -2113,10 +2173,11 @@ sub process_cmd {
my $end_time = time();
if ($ret) {
+
die "Error, cmd: $cmd died with ret $ret";
}
- print STDERR "CMD finished (" . ($end_time - $start_time) . " seconds)\n" if $SEE;
+ print STDERR "CMD finished (" . ($end_time - $start_time) . " seconds)\n" if $VERBOSE;
return;
}
@@ -2183,7 +2244,7 @@ sub run_jaccard_clip_single_but_really_paired {
####
sub test_java_failure_capture {
- if ($SEE) {
+ if ($VERBOSE) {
print "#######################################\n";
print "Running Java Tests\n";
}
@@ -2194,7 +2255,7 @@ sub test_java_failure_capture {
}
- my $cmd = "java -Xmx64m -jar $UTILDIR/support_scripts/ExitTester.jar 0";
+ my $cmd = "java -Xmx64m -XX:ParallelGCThreads=$bflyGCThreads -jar $UTILDIR/support_scripts/ExitTester.jar 0";
eval {
&process_cmd($cmd);
};
@@ -2206,21 +2267,21 @@ sub test_java_failure_capture {
}
- $cmd = "java -Xmx64m -jar $UTILDIR/support_scripts/ExitTester.jar 1";
+ $cmd = "java -Xmx64m -XX:ParallelGCThreads=$bflyGCThreads -jar $UTILDIR/support_scripts/ExitTester.jar 1";
eval {
&process_cmd($cmd);
};
if ($@) {
- print "-we properly captured the java failure status, as needed. Looking good.\n" if $SEE;
+ print "-we properly captured the java failure status, as needed. Looking good.\n" if $VERBOSE;
}
else {
print STDERR "-we are unable to properly capture java failure status. Please be sure that java (or any wrapper around java that's being used) can properly capture and propagate failure status before proceeding.\n";
exit(1);
}
- print "Java tests succeeded.\n" if $SEE;
- print "###################################\n\n" if $SEE;
+ print "Java tests succeeded.\n" if $VERBOSE;
+ print "###################################\n\n" if $VERBOSE;
return;
}
@@ -2448,12 +2509,9 @@ sub collectl_stop {
kill("INT", $collectl_pid);
kill("TERM", $collectl_pid);
waitpid($collectl_pid,0);
- chdir($collectl_output_directory) or return;
- system("python $COLLECTL_DIR/make_data_files.py");
- system("python $COLLECTL_DIR/timetable.py");
- $collectl_titlename = "${VERSION} ${CPU} @{left_files}@{single_files}";
- system("python $COLLECTL_DIR/plot.py \"$collectl_titlename\" ${CPU}");
- }
+ chdir($collectl_output_directory) or return;
+ system("$COLLECTL_DIR/collectl2html ${VERSION}");
+ }
}
####
@@ -2634,7 +2692,7 @@ sub normalize {
print STDERR "###############################################################################\n"
. "#### Normalization process was previously completed. Skipping it and using existing normalized files: @ret_files\n"
- . "###############################################################################\n" if $SEE;
+ . "###############################################################################\n" if $VERBOSE;
}
else {
@@ -2667,7 +2725,19 @@ sub files_exist {
sub run_genome_guided_Trinity {
## partition the reads according to coverage piles:
- my $cmd = "$UTILDIR/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM $genome_guided_bam -I $genome_guided_max_intron --sort_buffer $max_memory --CPU $CPU ";
+ ## Be sure that the bam file is coordinate sorted.
+ ## Simply index it using samtools. If it's not coord sorted, samtools will error
+
+ my $cmd = "samtools index $genome_guided_bam";
+ eval {
+ &process_cmd($cmd);
+ };
+ if ($@) {
+ die "$@\n\nPlease be sure that your bam file: $genome_guided_bam is coordinate-sorted before running genome-guided Trinity.\n";
+ }
+
+
+ $cmd = "$UTILDIR/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM $genome_guided_bam -I $genome_guided_max_intron --sort_buffer $max_memory --CPU $CPU ";
if ($SS_lib_type) {
$cmd .= " --SS_lib_type $SS_lib_type ";
@@ -2706,7 +2776,7 @@ sub run_genome_guided_Trinity {
## pull together the final outputs:
- $cmd = "find Dir_* -name '*inity.fasta' | $UTILDIR/support_scripts/partitioned_trinity_aggregator.pl GG > Trinity-GG.fasta.tmp";
+ $cmd = "find Dir_* -name '*inity.fasta' | $UTILDIR/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > Trinity-GG.fasta.tmp";
&process_cmd($cmd);
rename("Trinity-GG.fasta.tmp", "Trinity-GG.fasta"); # now that it's done.
@@ -2760,7 +2830,7 @@ sub write_trinity_partitioned_cmds {
## write Trinity assembly commands for partitions:
##################################################
- my $cmd = "$UTILDIR/support_scripts/GG_write_trinity_cmds.pl --reads_list_file $reads_list_file --CPU $grid_node_CPU --max_memory $grid_node_max_memory ";
+ my $cmd = "$UTILDIR/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file $reads_list_file --CPU $grid_node_CPU --max_memory $grid_node_max_memory ";
if ($run_as_paired_flag) {
$cmd .= " --run_as_paired ";
}
@@ -2768,8 +2838,15 @@ sub write_trinity_partitioned_cmds {
$cmd .= " --SS_lib_type F "; # all sequences already reoriented
}
- $cmd .= " --full_cleanup --seqType fa --trinity_complete";
-
+ $cmd .= " --seqType fa --trinity_complete";
+
+ if ($NO_CLEANUP) {
+ $cmd .= " --no_cleanup ";
+ }
+ else {
+ $cmd .= " --full_cleanup ";
+ }
+
my @potential_args = @ORIG_ARGS;
while (@potential_args) {
@@ -2781,7 +2858,7 @@ sub write_trinity_partitioned_cmds {
}
# value specified options that aren't needed
- if ($arg =~ /seqType|left|right|single|genome|SS_lib_type|GMAP|quality_trimming|output|normalize_max_read_cov|grid_conf|max_mem|grid|long_reads/
+ if ($arg =~ /seqType|left|right|single|genome|SS_lib_type|quality_trimming|output|normalize_max_read_cov|grid_conf|max_mem|grid|long_reads|inchworm_cpu/
||
# more precise identification of parameter
$arg =~ /^(--CPU)$/
@@ -2855,15 +2932,18 @@ sub version_check {
print "Trinity version: $VERSION\n";
my $url = "http://rt-trinity.uits.indiana.edu/flask/version/" . $VERSION . "?timestamp=" . time;
- my $content = `curl --connect-timeout 10 -s "$url"`;
+ #print STDERR "curl --connect-timeout 10 -s \"$url\"";
+ my $content = `curl -m 5 --connect-timeout 5 --max-time 5 -s "$url" 2>&1`;
+
+
## get release info from here:
## https://api.github.com/repos/trinityrnaseq/trinityrnaseq/releases
$url = "https://api.github.com/repos/trinityrnaseq/trinityrnaseq/releases";
- $content = `curl --connect-timeout 10 -s "$url"`;
+ $content = `curl -m 5 --connect-timeout 5 --max-time 5 -s "$url" 2>&1 `;
- if ($?) {
+ if ( (! $content) || $?) {
print STDERR "-ERROR: couldn't run the network check to confirm latest Trinity software version.\n\n";
}
diff --git a/galaxy-plugin/EdgeR_differentialExpression.xml b/galaxy-plugin/EdgeR_differentialExpression.xml
index 774a3f4..2636909 100644
--- a/galaxy-plugin/EdgeR_differentialExpression.xml
+++ b/galaxy-plugin/EdgeR_differentialExpression.xml
@@ -6,15 +6,10 @@
</requirements>
<command interpreter="python">
- trinityToolWrapper.py Analysis/DifferentialExpression/run_DE_analysis.pl
- --matrix $counts_matrix
- --method edgeR
- --output edgeR_results
- --dispersion $dispersion
-
- > stdout.txt
-
-
+ EdgeR_differentialExpression_wrapper.py
+ $counts_matrix
+ $dispersion
+
</command>
<inputs>
@@ -25,12 +20,8 @@
</inputs>
<outputs>
- <data format="txt" name="diff_expressed_edgeR_results" label="${tool.name} on ${on_string}: differentially expressed transcripts per pair of conditions" from_work_dir="edgeR_results/all_diff_expression_results.txt" />
-
- <data format="txt" name="matrix_FPKM" label="${tool.name} on ${on_string}: matrix.TMM_normalized.FPKM" from_work_dir="edgeR_results/matrix.TMM_normalized.FPKM" />
-
- <data format="txt" name="TMM_info" label="${tool.name} on ${on_string}: TMM library size estimates" from_work_dir="edgeR_results/TMM_info.txt" />
-
+ <data format="tar.gz" name="EdgeR_Archive" label="${tool.name} on ${on_string}: EdgeR_Results.tar.gz" from_work_dir="edgeR_results.tar.gz" />
+
</outputs>
<tests>
diff --git a/galaxy-plugin/EdgeR_differentialExpression_wrapper.py b/galaxy-plugin/EdgeR_differentialExpression_wrapper.py
new file mode 100644
index 0000000..ff55cd1
--- /dev/null
+++ b/galaxy-plugin/EdgeR_differentialExpression_wrapper.py
@@ -0,0 +1,40 @@
+import sys, os, subprocess
+
+TRINITY_BASE_DIR = ""
+if os.environ.has_key('TRINITY_HOME'):
+ TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
+else:
+ sys.stderr.write("You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this");
+ sys.exit(1)
+
+usage= "usage: " + " $counts_matrix" + " $dispersion"
+
+if len(sys.argv)<2:
+ print "Require atleast two parameters"
+else:
+ print "All good- command going ahead"
+print " "
+
+def run_command(cmd):
+ print "The command used: " + cmd
+ pipe=subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE)
+ pipe.wait()
+ ret= pipe.returncode
+ if ret:
+ print "command died: " + str(ret)
+ print pipe.stderr.readlines()
+ sys.exit(1)
+ else:
+ return
+print " "
+
+countmatrix= "counts_matrix"
+
+cmd= "cp " + sys.argv[1] + " " + countmatrix
+run_command(cmd)
+
+cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/run_DE_analysis.pl "+ " --matrix "+ countmatrix + " --method edgeR " + " --output edgeR_results "+ " --dispersion " + sys.argv[2] + " --tar_gz_outdir"
+
+run_command(cmd)
+
+sys.exit(0)
diff --git a/galaxy-plugin/EdgeR_differentialExpression.xml b/galaxy-plugin/GauravGalaxy/EdgeR_differentialExpression.xml
similarity index 56%
copy from galaxy-plugin/EdgeR_differentialExpression.xml
copy to galaxy-plugin/GauravGalaxy/EdgeR_differentialExpression.xml
index 774a3f4..2636909 100644
--- a/galaxy-plugin/EdgeR_differentialExpression.xml
+++ b/galaxy-plugin/GauravGalaxy/EdgeR_differentialExpression.xml
@@ -6,15 +6,10 @@
</requirements>
<command interpreter="python">
- trinityToolWrapper.py Analysis/DifferentialExpression/run_DE_analysis.pl
- --matrix $counts_matrix
- --method edgeR
- --output edgeR_results
- --dispersion $dispersion
-
- > stdout.txt
-
-
+ EdgeR_differentialExpression_wrapper.py
+ $counts_matrix
+ $dispersion
+
</command>
<inputs>
@@ -25,12 +20,8 @@
</inputs>
<outputs>
- <data format="txt" name="diff_expressed_edgeR_results" label="${tool.name} on ${on_string}: differentially expressed transcripts per pair of conditions" from_work_dir="edgeR_results/all_diff_expression_results.txt" />
-
- <data format="txt" name="matrix_FPKM" label="${tool.name} on ${on_string}: matrix.TMM_normalized.FPKM" from_work_dir="edgeR_results/matrix.TMM_normalized.FPKM" />
-
- <data format="txt" name="TMM_info" label="${tool.name} on ${on_string}: TMM library size estimates" from_work_dir="edgeR_results/TMM_info.txt" />
-
+ <data format="tar.gz" name="EdgeR_Archive" label="${tool.name} on ${on_string}: EdgeR_Results.tar.gz" from_work_dir="edgeR_results.tar.gz" />
+
</outputs>
<tests>
diff --git a/galaxy-plugin/GauravGalaxy/EdgeR_differentialExpression_wrapper.py b/galaxy-plugin/GauravGalaxy/EdgeR_differentialExpression_wrapper.py
new file mode 100644
index 0000000..ff55cd1
--- /dev/null
+++ b/galaxy-plugin/GauravGalaxy/EdgeR_differentialExpression_wrapper.py
@@ -0,0 +1,40 @@
+import sys, os, subprocess
+
+TRINITY_BASE_DIR = ""
+if os.environ.has_key('TRINITY_HOME'):
+ TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
+else:
+ sys.stderr.write("You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this");
+ sys.exit(1)
+
+usage= "usage: " + " $counts_matrix" + " $dispersion"
+
+if len(sys.argv)<2:
+ print "Require atleast two parameters"
+else:
+ print "All good- command going ahead"
+print " "
+
+def run_command(cmd):
+ print "The command used: " + cmd
+ pipe=subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE)
+ pipe.wait()
+ ret= pipe.returncode
+ if ret:
+ print "command died: " + str(ret)
+ print pipe.stderr.readlines()
+ sys.exit(1)
+ else:
+ return
+print " "
+
+countmatrix= "counts_matrix"
+
+cmd= "cp " + sys.argv[1] + " " + countmatrix
+run_command(cmd)
+
+cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/run_DE_analysis.pl "+ " --matrix "+ countmatrix + " --method edgeR " + " --output edgeR_results "+ " --dispersion " + sys.argv[2] + " --tar_gz_outdir"
+
+run_command(cmd)
+
+sys.exit(0)
diff --git a/galaxy-plugin/GauravGalaxy/RSEM_estimates_to_matrix.xml b/galaxy-plugin/GauravGalaxy/RSEM_estimates_to_matrix.xml
new file mode 100644
index 0000000..3057eb0
--- /dev/null
+++ b/galaxy-plugin/GauravGalaxy/RSEM_estimates_to_matrix.xml
@@ -0,0 +1,51 @@
+<tool id="RSEM_estimates_to_matrix" name="RSEM_estimates_to_matrix" version="0.0.1">
+
+ <description>Join RSEM estimates from multiple samples into a single matrix</description>
+ <requirements>
+ <requirement type="package">trinity</requirement>
+ </requirements>
+ <command interpreter="python">
+
+ trinityToolWrapper.py util/RSEM_util/merge_RSEM_counts_and_labels_single_table.pl
+
+ --labels
+ #for $entry in $RSEM_samples:
+ ${entry.column_label}
+ #end for
+
+ --RSEM_counts
+ #for $entry in $RSEM_samples:
+ ${entry.file}
+ #end for
+
+ > RSEM.counts.matrix
+
+ </command>
+ <inputs>
+
+ <repeat name="RSEM_samples" title="RSEM abundance estimates for samples">
+ <param name="file" label="Add file" type="data" format="text"/>
+ <param name="column_label" label="column label" type="text" />
+ </repeat>
+
+ </inputs>
+ <outputs>
+ <data format="text" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="RSEM.counts.matrix"/>
+ </outputs>
+ <tests>
+
+
+ <test>
+ <param name="target" value="trinity/Trinity.fasta" />
+ <param name="aligner" value="bowtie" />
+ <param name="paired_or_single" value="single" />
+ <param name="library_type" value="None" />
+ <param name="input" value="trinity/reads.left.fq" />
+ </test>
+
+
+ </tests>
+ <help>
+ .. _Trinity: http://trinityrnaseq.sourceforge.net
+ </help>
+</tool>
diff --git a/Trinity b/galaxy-plugin/GauravGalaxy/Trinity
similarity index 69%
copy from Trinity
copy to galaxy-plugin/GauravGalaxy/Trinity
index 73f8264..be72d56 100755
--- a/Trinity
+++ b/galaxy-plugin/GauravGalaxy/Trinity
@@ -12,13 +12,7 @@ use Time::localtime;
use Cwd;
use Carp;
use COMMON;
-use Getopt::Long qw(:config posix_default no_ignore_case pass_through);
-use Pipeliner;
-use Fasta_reader;
-
-
-my $VERSION = "v2.0.6";
-
+use Getopt::Long qw(:config no_ignore_case pass_through);
BEGIN {
@@ -26,29 +20,15 @@ BEGIN {
}
-use HPC::GridRunner;
+use HTC::GridRunner;
open (STDERR, ">&STDOUT"); ## capturing stderr and stdout in a single stdout stream
-#directory defnintions
-my $ROOTDIR = "$FindBin::RealBin";
-my $UTILDIR = "$ROOTDIR/util";
-my $MISCDIR = "$UTILDIR/misc";
-my $INCHWORM_DIR = "$ROOTDIR/Inchworm/bin/";
-my $CHRYSALIS_DIR = "$ROOTDIR/Chrysalis";
-my $BUTTERFLY_DIR = "$ROOTDIR/Butterfly";
-my $JELLYFISH_DIR = "$ROOTDIR/trinity-plugins/jellyfish";
-my $FASTOOL_DIR = "$ROOTDIR/trinity-plugins/fastool";
-my $COLLECTL_DIR = "$ROOTDIR/trinity-plugins/collectl/bin";
-my $COREUTILS_DIR = "$ROOTDIR/trinity-plugins/coreutils/bin";
-my $PARAFLY = "$ROOTDIR/trinity-plugins/parafly/bin/ParaFly";
-my $TRIMMOMATIC = "$ROOTDIR/trinity-plugins/Trimmomatic/trimmomatic.jar";
-my $TRIMMOMATIC_DIR = "$ROOTDIR/trinity-plugins/Trimmomatic";
-
-
# Site specific setup
+my $CPU_MAX = 64; # set higher at your own risk. Definitely don't set it higher than the number of cores available on your machine.
+
my $KMER_SIZE = 25;
my $MAX_KMER_SIZE = 32;
@@ -88,8 +68,10 @@ my $path_reinforcement_distance;
my $PE_path_reinforcement_distance = 75;
my $SE_path_reinforcement_distance = 25;
+my $NO_RUN_BUTTERFLY_FLAG = 0;
+my $RERUN_BUTTERFLY_FLAG = 0;
my $bfly_opts = "";
-my $bflyHeapSpaceMax = "4G";
+my $bflyHeapSpaceMax = "10G";
my $bflyHeapSpaceInit = "1G";
my $BFLY_JAR = "";
@@ -109,8 +91,6 @@ my $inchworm_cpu = 6;
my $min_percent_read_iworm_kmers = -1; # experimental, off
my $CPU = 2;
-my $np = 1;
-my $mpiexec = "mpiexec";
my $bflyCPU;
my $bflyCalculateCPU = 0;
my $bflyGCThreads = 2;
@@ -120,6 +100,7 @@ my $long_reads = "";
## ADVANCED OPTIONS:
+my $no_meryl_flag = 0;
## Chrysalis opts
my $min_glue = 2;
@@ -128,16 +109,16 @@ my $glue_factor = 0.05;
my $max_reads_per_graph = 200000;
my $max_reads_per_loop = 10000000;
my $min_pct_read_mapping = 0;
+my $NO_RUN_QUANTIFYGRAPH_FLAG = 0;
+my $NO_RUN_CHRYSALIS_FLAG = 0;
my $chrysalis_output_dir = "chrysalis";
my $component_directory;
-my $NO_RUN_CHRYSALIS_FLAG = 0;
-
-my $NO_DISTRIBUTED_TRINITY_EXEC = 0;
my $help_flag;
my $advanced_help_flag;
my $SHOW_CITATION_FLAG = 0;
+my $VERSION = "trinityrnaseq_r20140717";
my $show_version_flag = 0;
## Kmer methods
@@ -184,23 +165,24 @@ my $run_as_paired_flag = 0; ## in case we have paired reads in single fasta fil
my $weldmer_size = 48;
my $FORCE_INCHWORM_KMER_METHOD = 0;
+my $TRIPLET_LOCK = 1;
+my $EXTENDED_TRIPLET_LOCK = 0;
+
+
+
my $PARALLEL_IWORM_FLAG = 1;
my $NO_PARALLEL_IWORM = 0;
## Quality trimming params
my $RUN_TRIMMOMATIC_FLAG = 0;
-my $trimmomatic_quality_trim_params = "ILLUMINACLIP:$TRIMMOMATIC_DIR/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25";
+my $trimmomatic_quality_trim_params = "LEADING:5 TRAILING:5 MINLEN:36";
## Normalize reads
my $NORMALIZE_READS_FLAG = 0;
my $normalize_max_read_cov = 50;
my $NORMALIZE_BY_READ_SET = 0;
-
-my $grid_node_CPU = 1;
-my $grid_node_max_memory = "1G";
-
# Note: For the Trinity logo below the backslashes are quoted in order to keep
# them from quoting the character than follows them. "\\" keeps "\ " from occuring.
@@ -223,15 +205,15 @@ my $basic_usage = qq^
#
# --seqType <string> :type of reads: ( $allowed{seqType} )
#
-# --max_memory <string> :suggested max memory to use by Trinity where limiting can be enabled. (jellyfish, sorting, etc)
-# provied in Gb of RAM, ie. '--max_memory 10G'
+# --JM <string> :(Jellyfish Memory) number of GB of system memory to use for
+# k-mer counting by jellyfish (eg. 10G) *include the 'G' char
#
# If paired reads:
-# --left <string> :left reads, one or more file names (separated by commas, no spaces)
-# --right <string> :right reads, one or more file names (separated by commas, no spaces)
+# --left <string> :left reads, one or more (separated by space)
+# --right <string> :right reads, one or more (separated by space)
#
# Or, if unpaired reads:
-# --single <string> :single reads, one or more file names, comma-delimited (note, if single file contains pairs, can use flag: --run_as_paired )
+# --single <string> :single reads, one or more (note, if single file contains pairs, can use flag: --run_as_paired )
#
####################################
## Misc: #########################
@@ -245,10 +227,7 @@ my $basic_usage = qq^
# --min_contig_length <int> :minimum assembled contig length to report
# (def=$min_contig_length)
#
-# --long_reads <string> :fasta file containing error-corrected or circular consensus (CCS) pac bio reads
-#
-# --genome_guided_bam <string> :genome guided mode, provide path to coordinate-sorted bam file.
-# (see genome-guided param section under --show_full_usage_info)
+# --genome <string> :genome guided mode, provide path to genome fasta file (see genome-guided param section under --show_full_usage_info)
#
# --jaccard_clip :option, set if you have paired reads and
# you expect high gene density with UTR
@@ -266,34 +245,26 @@ my $basic_usage = qq^
# --normalize_reads :run in silico normalization of reads. Defaults to max. read coverage of $normalize_max_read_cov.
# see '--normalize_max_read_cov' under full usage info for tailored settings.
#
-# --no_distributed_trinity_exec :do not run Trinity phase 2 (assembly of partitioned reads), and stop after generating command list.
-#
#
# --output <string> :name of directory for output (will be
# created if it doesn't already exist)
-# default( your current working directory: "$output_directory"
-# note: must include 'trinity' in the name as a safety precaution! )
+# default( your current working directory: "$output_directory" )
#
# --full_cleanup :only retain the Trinity fasta file, rename as \${output_dir}.Trinity.fasta
#
# --cite :show the Trinity literature citation
#
-# --verbose :provide additional job status info during the run.
-#
# --version :reports Trinity version ($VERSION) and exits.
#
# --show_full_usage_info :show the many many more options available for running Trinity (expert usage).
^;
my $full_usage = qq^
-#
-# --KMER_SIZE <int> :kmer length to use (default: 25) max=32
-#
# --prep :Only prepare files (high I/O usage) and stop before kmer counting.
#
-# --no_cleanup :retain all intermediate input files.
+# --full_cleanup_ET :only retains assembly fasta file, error tolerant (ET)
#
-# --no_version_check :dont run a network check to determine if software updates are available.
+# --no_cleanup :retain all intermediate input files.
#
####################################################
# Inchworm and K-mer counting-related options: #####
@@ -302,7 +273,7 @@ my $full_usage = qq^
# Inchworm (default: $min_kmer_cov)
# --inchworm_cpu <int> :number of CPUs to use for Inchworm, default is min(6, --CPU option)
#
-# --no_run_inchworm :stop after running jellyfish, before inchworm. (phase 1, read clustering only)
+# --no_run_inchworm :stop after running jellyfish, before inchworm.
#
###################################
# Chrysalis-related options: ######
@@ -311,10 +282,18 @@ my $full_usage = qq^
# a single graph (default: $max_reads_per_graph)
# --min_glue <int> :min number of reads needed to glue two inchworm contigs
# together. (default: $min_glue)
+# --no_run_chrysalis :stop Trinity after Inchworm and before
+# running Chrysalis
+# --no_run_quantifygraph :stop Trinity just before running the
+# parallel QuantifyGraph computes, to
+# leverage a compute farm and massively
+# parallel execution..
#
-# --no_bowtie :dont run bowtie to use pair info in chrysalis clustering.
+# --chrysalis_output <string> :name of directory for chrysalis output (will be
+# created if it doesn't already exist)
+# default( "$chrysalis_output_dir" )
#
-# --no_run_chrysalis :stop after running inchworm, before chrysalis. (phase 1, read clustering only)
+# --no_bowtie :dont run bowtie to use pair info in chrysalis clustering.
#
#####################################
### Butterfly-related options: ####
@@ -344,10 +323,19 @@ my $full_usage = qq^
# path (default: PE: $PE_path_reinforcement_distance, SE: $SE_path_reinforcement_distance)
# Set to 1 for the most lenient path extension requirements.
#
+# --no_triplet_lock : (increase stringency of regular butterfly reconstruction (default: on))
+# lock triplet-supported nodes: node 'c' having read path 'A-B-C' disables 'Z-B-C' if no such read support exists.
+#
+# --extended_lock : (further increase the stringency of regular butterfy reconstruction)
+# extend the triplet lock to include longer range read path information.
+# ex. in extending path 'A-B-Z' to 'A-B-Z-D', we only find read support for 'A-B-C-D', that 'A-B-Z' extension to 'D' will be blocked.
+#
#
# /////////////////////////////////////////
# Butterfly transcript reduction settings:
#
+# --NO_EM_REDUCE : do not run the final EM step to rank transcripts and remove lower-ranking entries that lack unique read conent.
+#
# --no_path_merging : all final transcript candidates are output (including SNP variations, however, some SNPs may be unphased)
#
# By default, alternative transcript candidates are merged (in reality, discarded) if they are found to be too similar, according to the following logic:
@@ -356,7 +344,7 @@ my $full_usage = qq^
#
# with parameters as:
#
-# --min_per_id_same_path <int> default: 98 min percent identity for two paths to be merged into single paths
+# --min_per_id_same_path <int> default: 95 min percent identity for two paths to be merged into single paths
# --max_diffs_same_path <int> default: 2 max allowed differences encountered between path sequences to combine them
# --max_internal_gap_same_path <int> default: 10 maximum number of internal consecutive gap characters allowed for paths to be merged into single paths.
#
@@ -379,11 +367,17 @@ my $full_usage = qq^
# number of CPUs; e.g., $CPU)
# --bflyCalculateCPU :Calculate CPUs based on 80% of max_memory
# divided by maxbflyHeapSpaceMax
+# --no_run_butterfly :stops after the Chrysalis stage. You'll
+# need to run the Butterfly computes
+# separately, such as on a computing grid.
+# Then, concatenate all the Butterfly assemblies by running:
+# 'find trinity_out_dir/ -name "\*allProbPaths.fasta" \
+# -exec cat {} + > trinity_out_dir/Trinity.fasta'
#
# --bfly_jar <string> : /path/to/Butterfly.jar, otherwise default
# Trinity-installed version is used.
#
-#
+
#
################################################################################
#### Quality Trimming Options ####
@@ -405,45 +399,54 @@ my $full_usage = qq^
#
# --genome_guided_max_intron <int> :maximum allowed intron length (also maximum fragment span on genome)
#
+# --genome_guided_use_bam <string> :use a provided coord-sorted bam file as starting point. Otherwise, use gmap to align to the genome.
+#
# * optional:
#
# --genome_guided_min_coverage <int> :minimum read coverage for identifying and expressed region of the genome. (default: 1)
#
# --genome_guided_min_reads_per_partition <int> :default min of 10 reads per partition
#
+# --genome_guided_CPU <int> : number of threads for the individual genome-guided Trinity commands to use. (defaults to --CPU setting)
+#
+# --genome_guided_sort_buffer <string> : amount of RAM to dedicate to the initial prep of genome-guided read partitioning (defaults to --JM)
+#
+#
+# --GMAP_CPU <int> :defaults to --CPU setting.
+#
+# --genome_guided_just_prep : process stops after prepping the reads for assembly (prior to submitting to a computing grid for parallel execution)
#
#################################
# Grid-computing options: #######
#
-# --grid_conf <string> :configuration file for supported compute farms
+# --grid_conf_file <string> :configuration file for supported compute farms
# ex. TRINITY_HOME/htc_conf/BroadInst_LSF.conf
# currently supported computing gris: LSF, SGE
#
-# --grid_node_CPU <int> number of threads for each parallel process to leverage. (default: $grid_node_CPU)
-#
-# --grid_node_max_memory <string> max memory targeted for each grid node. (default: $grid_node_max_memory)
-#
#
^;
-my $usage_synopsis = qq^#
-#
+my $usage_synopsis = qq^
###############################################################################
#
# *Note, a typical Trinity command might be:
#
-# Trinity --seqType fq --max_memory 50G --left reads_1.fq --right reads_2.fq --CPU 6
+# Trinity --seqType fq --JM 100G --left reads_1.fq --right reads_2.fq --CPU 6
#
#
# and for Genome-guided Trinity:
#
-# Trinity --genome_guided_bam rnaseq_alignments.csorted.bam --max_memory 50G\
-# --genome_guided_max_intron 10000 --CPU 6
+# Trinity --genome genome.fasta \
+# --genome_guided_max_intron 10000 --genome_guided_sort_buffer 10G \
+# --genome_guided_CPU 4 \
+# --seqType fq --JM 2G --left reads_1.fq --right reads_2.fq --CPU 6
+# (and optionally provide your own bam file: --genome_guided_use_bam rnaseq_alignments.csorted.bam
+# or Trinity will run GSNAP to generate one. )
+#
#
# see: $FindBin::RealBin/sample_data/test_Trinity_Assembly/
# for sample data and 'runMe.sh' for example Trinity execution
-#
-# For more details, visit: http://trinityrnaseq.github.io
+# For more details, visit: http://trinityrnaseq.sf.net
#
###############################################################################
@@ -462,8 +465,8 @@ my $advanced_usage = <<_ADVANCEDUSAGE_;
#
# --INCHWORM_CUSTOM_PARAMS <string> :additional parameters to be passed on to Inchworm
# --FORCE_INCHWORM_KMER_METHOD :uses inchworm built-in kmer cataloger instead of jellyfish (not recommended)
+# --long_reads <string> :fasta file containing corrected pac bio reads
# --NO_PARALLEL_IWORM : turn off parallel iworm assembly
-# --iworm_opts <string> : options for inchworm
#
#
# Chyrsalis-related options:
@@ -486,7 +489,8 @@ my $advanced_usage = <<_ADVANCEDUSAGE_;
# Other:
# --monitoring :use collectl to monitor all steps of Trinity
#
-# --bypass_java_version_check : skip check for required java version 1.7
+# --compdir|component_directory : use a temporary or local directory for Components_bin
+#
#
@@ -495,6 +499,17 @@ _ADVANCEDUSAGE_
;
+my $ROOTDIR = "$FindBin::RealBin";
+my $UTILDIR = "$ROOTDIR/util";
+my $INCHWORM_DIR = "$ROOTDIR/Inchworm";
+my $CHRYSALIS_DIR = "$ROOTDIR/Chrysalis";
+my $BUTTERFLY_DIR = "$ROOTDIR/Butterfly";
+my $JELLYFISH_DIR = "$ROOTDIR/trinity-plugins/jellyfish";
+my $FASTOOL_DIR = "$ROOTDIR/trinity-plugins/fastool";
+my $COLLECTL_DIR = "$ROOTDIR/trinity-plugins/collectl/bin";
+my $COREUTILS_DIR = "$ROOTDIR/trinity-plugins/coreutils/bin";
+my $PARAFLY = "$ROOTDIR/trinity-plugins/parafly/bin/ParaFly";
+my $TRIMMOMATIC = "$ROOTDIR/trinity-plugins/Trimmomatic/trimmomatic.jar";
my $usage = $basic_usage . $usage_synopsis;
@@ -513,6 +528,7 @@ my $sort_exec = &COMMON::get_sort_exec($CPU);
my $NO_FASTOOL = 0;
my $NO_CLEANUP = 0;
my $FULL_CLEANUP = 0;
+my $FULL_CLEANUP_ERROR_TOLERANT = 0; ## NOTE, THIS IS AN AWFUL IDEA... //FIXME: add propper error-handling mechanisms
my $NO_BOWTIE = 0;
@@ -529,41 +545,27 @@ my $CUFFFLY_MODE = 0;
my $full_usage_info_flag;
my $NO_TRIPLET_LOCK;
+my $NO_EM_REDUCE;
## Genome-guided params:
+my $genome_fasta_file;
my $genome_guided_max_intron;
-my $genome_guided_bam;
+my $genome_guided_use_bam;
my $genome_guided_min_coverage = 1;
my $genome_guided_min_reads_per_partition = 10;
+my $GMAP_CPU;
+my $genome_guided_CPU;
+my $genome_guided_sort_buffer;
my $genome_guided_just_prep_flag = 0;
-## trinity complete flag
-my $TRINITY_COMPLETE_FLAG = 0;
-
my @ORIG_ARGS = @ARGV;
-my $CHRYSALIS_DEBUG_WELD_ALL = 0;
-my $iworm_opts = "";
-
-my $bypass_java_version_check = 0;
-
-my $SEE = 0;
-
-my $ANANAS_DIR = "";
-
-my $NO_VERSION_CHECK = 0;
-
-
&GetOptions(
'h|help' => \$help_flag,
'advanced_help' => \$advanced_help_flag,
'show_full_usage_info' => \$full_usage_info_flag,
-
- 'verbose' => \$SEE,
-
- 'no_version_check' => \$NO_VERSION_CHECK,
-
+
## general opts
"seqType=s" => \$seqType,
"left=s{,}" => \@left_files,
@@ -583,8 +585,7 @@ my $NO_VERSION_CHECK = 0;
"cite" => \$SHOW_CITATION_FLAG,
'CPU=i' => \$CPU,
- 'np=i' => \$np,
- 'mpiexec=s' => \$mpiexec,
+
'prep' => \$prep_only,
'KMER_SIZE=i' => \$KMER_SIZE,
@@ -601,6 +602,9 @@ my $NO_VERSION_CHECK = 0;
# Butterfly opts
+ 'no_run_butterfly' => \$NO_RUN_BUTTERFLY_FLAG,
+ 'no_triplet_lock' => \$NO_TRIPLET_LOCK,
+ 'extended_lock' => \$EXTENDED_TRIPLET_LOCK,
"group_pairs_distance=i" => \$group_pairs_distance,
'bfly_opts=s' => \$bfly_opts,
'bflyHeapSpaceMax=s' => \$bflyHeapSpaceMax,
@@ -611,7 +615,9 @@ my $NO_VERSION_CHECK = 0;
'bfly_jar=s' => \$BFLY_JAR,
'path_reinforcement_distance=i' => \$path_reinforcement_distance,
-
+ 'rerun_butterfly' => \$RERUN_BUTTERFLY_FLAG,
+
+ 'NO_EM_REDUCE' => \$NO_EM_REDUCE,
'no_path_merging' => \$NO_PATH_MERGING,
'min_per_id_same_path=i' => \$MIN_PER_ID_SAME_PATH,
'max_diffs_same_path=i' => \$MAX_DIFFS_SAME_PATH,
@@ -628,25 +634,27 @@ my $NO_VERSION_CHECK = 0;
'FORCE_INCHWORM_KMER_METHOD' => \$FORCE_INCHWORM_KMER_METHOD,
'INCHWORM_CUSTOM_PARAMS=s' => \$INCHWORM_CUSTOM_PARAMS,
'no_run_inchworm' => \$NO_RUN_INCHWORM_FLAG,
- 'iworm_opts=s' => \$iworm_opts,
- 'max_memory|M=s' => \$max_memory, # in GB
+ # Jellyfish
+ 'JM=s' => \$max_memory, # in GB
# Chrysalis -related opts
'min_glue=i' => \$min_glue,
'glue_factor=f' => \$glue_factor,
'min_iso_ratio=f' => \$min_iso_ratio,
'min_pcnt_read_iworm_kmers=i' => \$min_percent_read_iworm_kmers,
+ 'no_run_quantifygraph' => \$NO_RUN_QUANTIFYGRAPH_FLAG,
'max_reads_per_graph=i' => \$max_reads_per_graph,
'max_reads_per_loop=i' => \$max_reads_per_loop,
+ 'no_run_chrysalis' => \$NO_RUN_CHRYSALIS_FLAG,
'min_pct_read_mapping=i' => \$min_pct_read_mapping,
'weldmer_size=i' => \$weldmer_size,
+ "chrysalis_output=s" => \$chrysalis_output_dir,
"no_bowtie" => \$NO_BOWTIE,
"bowtie_comp" => \$BOWTIE_COMP,
- "no_run_chrysalis" => \$NO_RUN_CHRYSALIS_FLAG,
# Grid computing options
- 'grid_conf=s' => \$grid_conf_file,
+ 'grid_conf_file=s' => \$grid_conf_file,
"show_advanced_options" => \$show_advanced_options,
@@ -658,35 +666,28 @@ my $NO_VERSION_CHECK = 0;
'full_cleanup' => \$FULL_CLEANUP,
'version' => \$show_version_flag,
'monitoring' => \$run_with_collectl,
- 'no_distributed_trinity_exec' => \$NO_DISTRIBUTED_TRINITY_EXEC,
+ 'full_cleanup_ET' => \$FULL_CLEANUP_ERROR_TOLERANT,
# hidden (don't look here! ;)
'KMER_SIZE=i' => \$KMER_SIZE,
'jelly_s=i' => \$JELLY_S,
-
+ 'compdir|component_directory=s' => \$component_directory,
'NO_PARALLEL_IWORM' => \$NO_PARALLEL_IWORM,
- 'chrysalis_debug_weld_all' => \$CHRYSALIS_DEBUG_WELD_ALL,
-
-
+
+
+
# genome guided
- "genome_guided_bam=s" => \$genome_guided_bam,
+ "genome=s" => \$genome_fasta_file,
"genome_guided_max_intron=i" => \$genome_guided_max_intron,
-
+ "genome_guided_use_bam=s" => \$genome_guided_use_bam,
"genome_guided_min_coverage=i" => \$genome_guided_min_coverage,
"genome_guided_min_reads_per_partition=i" => \$genome_guided_min_reads_per_partition,
+ "genome_guided_CPU=i" => \$genome_guided_CPU,
+ "GMAP_CPU=i" => \$GMAP_CPU,
+ "genome_guided_sort_buffer=s" => \$genome_guided_sort_buffer,
"genome_guided_just_prep" => \$genome_guided_just_prep_flag,
-
- "trinity_complete" => \$TRINITY_COMPLETE_FLAG,
-
- "grid_node_CPU=i" => \$grid_node_CPU,
- "grid_node_max_memory=s" => \$grid_node_max_memory,
-
- "bypass_java_version_check" => \$bypass_java_version_check,
-
- "ananas_dir=s" => \$ANANAS_DIR,
-
- );
+ );
@@ -710,8 +711,7 @@ if ($help_flag) {
}
if ($show_version_flag) {
- &version_check();
-
+ print "Trinity version: $VERSION\n";
exit(1);
}
@@ -725,7 +725,9 @@ if ($KMER_SIZE > $MAX_KMER_SIZE) {
}
-
+if ($NO_TRIPLET_LOCK) {
+ $TRIPLET_LOCK = 0; # turn it off since on by default.
+}
if ($NO_PARALLEL_IWORM) {
# turn it off.
$PARALLEL_IWORM_FLAG = 0;
@@ -734,6 +736,13 @@ if ($NO_PARALLEL_IWORM) {
my $MIN_IWORM_LEN = $KMER_SIZE;
+unless ($GMAP_CPU) {
+ $GMAP_CPU = $CPU;
+}
+unless ($genome_guided_CPU) {
+ $genome_guided_CPU = $CPU;
+}
+
if (@ARGV) {
die "Error, do not understand options: @ARGV\n";
}
@@ -748,6 +757,25 @@ unless ($BFLY_JAR) {
}
+## Check options set:
+
+# Subroutine takes variable *reference* plus name of variable. Lower-cases
+# variable value and checks to see if it one of the allowed ones.
+# 'die' has new-line in order to keep line number from being shown to user.
+
+sub check_option {
+ my ($option, $name) = @_;
+ $$option = lc $$option;
+ if ($$option eq '') {
+ die "Error, option '--$name' is required.\n";
+ }
+ if (!defined $allowed_check{$name}{$$option}) {
+ die "Error, option '--$name' ($$option) not one of $allowed{$name}\n";
+ }
+}
+
+check_option( \$seqType, 'seqType' );
+
my $USE_FASTOOL = 1; # by default, using fastool for fastq to fasta conversion
if ($NO_FASTOOL) {
$USE_FASTOOL = 0;
@@ -757,33 +785,12 @@ if ($SS_lib_type) {
unless ($SS_lib_type =~ /^(R|F|RF|FR)$/) {
die "Error, unrecognized SS_lib_type value of $SS_lib_type. Should be: F, R, RF, or FR\n";
}
-
- if (@single_files) {
- if ($run_as_paired_flag) {
- die "Error, if you have paired-end reads and want to run as strand-specific, then you must specify the --left and --right parameters";
- }
- if (length($SS_lib_type) != 1) {
- die "Error, with --single reads, the --SS_lib_type can be 'F' or 'R' only.\n";
- }
- }
- if (@left_files && @right_files) {
- if (length($SS_lib_type) != 2) {
- die "Error, with paired end reads, the --SS_lib_type can be 'RF' or 'FR' only.\n";
- }
- }
-
}
-unless ($genome_guided_bam || (@left_files && @right_files) || @single_files ) {
- die "Error, need either options 'left' and 'right' or option 'single' or 'genome_guided_bam'\n";
-}
-unless ($genome_guided_bam) {
- unless ($seqType) {
- die "Error, need --seqType specified\n";
- }
+unless ( (@left_files && @right_files) || @single_files ) {
+ die "Error, need either options 'left' and 'right' or option 'single'\n";
}
-
if (@left_files) {
@left_files = split(",", join(",", @left_files));
}
@@ -799,39 +806,41 @@ if ($min_iso_ratio > 1) {
die "Error, --min_iso_ratio should be <= 1 \n";
}
-## keep the original 'xG' format string for the --JM option, then calculate the numerical value for jellyfish_ram
-my $jellyfish_ram = $max_memory; ## this one is used in the Chrysalis exec string
-if ($jellyfish_ram) {
- $jellyfish_ram =~ /^([\d\.]+)G$/ or die "Error, cannot parse jellyfish_ram value of $jellyfish_ram. Set it to 'xG' where x is a numerical value\n";
+## keep the original 'xG' format string for the --JM option, then calculate the numerical value for max_memory
+my $JM_string = $max_memory; ## this one is used in the Chrysalis exec string
+if ($max_memory) {
+ $max_memory =~ /^([\d\.]+)G$/ or die "Error, cannot parse max_memory value of $max_memory. Set it to 'xG' where x is a numerical value\n";
- $jellyfish_ram = $1;
- $jellyfish_ram *= 1024**3; # convert to from gig to bytes
+ $max_memory = $1;
+ $max_memory *= 1024**3; # convert to from gig to bytes
}
else {
- die "Error, must specify max memory for jellyfish to use, eg. --max_memory 10G \n";
+ die "Error, must specify max memory for jellyfish to use, eg. --JM 10G \n";
}
+unless ($genome_guided_sort_buffer) {
+ $genome_guided_sort_buffer = $JM_string;
+}
-## Check Java version:
-unless ($NO_RUN_INCHWORM_FLAG || $NO_RUN_CHRYSALIS_FLAG || $bypass_java_version_check) {
- my $java_version = `java -Xmx64m -version 2>&1 `;
- if ($java_version =~ /(java|openjdk) version \"1\.(\d)\./) {
- my $version_id = $2;
- if ($version_id != 7) {
- die "Error, Trinity requires access to Java version 1.7. Currently installed version is: $java_version";
- }
- }
- else {
- print STDERR "\n\n\n********************************************************************\n"
- . "** Warning, Trinity cannot determine which version of Java is being used. Version 1.7 is required. \n\nAttempting to continue in 30 seconds\n"
- . "********************************************************************\n\n\n";
- sleep(30);
- }
+## Try to remove stack limits
+if ($^O eq "linux") { # cannot set stacksize on newer macs for some reason...
+# &try_unlimit_stacksize();
}
+my $curr_limit_settings = `/bin/sh -c 'ulimit -a' `;
+unless ($curr_limit_settings && $curr_limit_settings =~ /\w/) {
+ $curr_limit_settings = `/bin/csh -c limit`; # backup, probably not needed.
+}
+
+print "Current settings:\n$curr_limit_settings\n\n";
-unless ($NO_VERSION_CHECK || $TRINITY_COMPLETE_FLAG) {
- &version_check();
+
+## Check Java version:
+unless ($NO_RUN_BUTTERFLY_FLAG || $NO_RUN_CHRYSALIS_FLAG) {
+ my $java_version = `java -Xmx64m -version 2>&1 `;
+ unless ($java_version =~ /(java|openjdk) version \"1\.[67]\./) {
+ die "Error, Trinity requires access to Java version 1.6 or 1.7. Currently installed version is: $java_version";
+ }
}
# Give the variable with memory size and a user-oriented name
@@ -853,28 +862,50 @@ if ($bflyHeapSpaceInitBytes > $bflyHeapSpaceMaxBytes) {
}
+if ($CPU > $CPU_MAX) {
+ print STDERR "Warning, --CPU $CPU might be excessive. Limiting it to $CPU_MAX for now.\n";
+ $CPU = $CPU_MAX;
+}
if ($inchworm_cpu > $CPU) {
$inchworm_cpu = $CPU;
}
-if ($bflyCalculateCPU && $jellyfish_ram) {
- $bflyCPU = int ($jellyfish_ram * 0.80 / $bflyHeapSpaceMaxBytes);
+if ($bflyCalculateCPU && $max_memory) {
+ $bflyCPU = int ($max_memory * 0.80 / $bflyHeapSpaceMaxBytes);
}
$bflyCPU = $CPU if !defined $bflyCPU;
+if ($bflyCPU > $CPU_MAX) {
+ print STDERR "Warning, --bflyCPU $bflyCPU might be excessive. Limiting it to $CPU_MAX for now.\n";
+ $bflyCPU = $CPU_MAX;
+}
+
if (defined($bflyGCThreads) && $bflyGCThreads > 32) {
die "Error, you probably want fewer than $bflyGCThreads java garbage collection threads. Try a number less than 32.";
}
-if ($genome_guided_bam) {
+if ($genome_fasta_file) {
## genome-guided mode.
unless ($genome_guided_max_intron) {
die "Error, must specifiy --genome_guided_max_intron <int> for genome-guided mode.\n";
}
+ unless ($genome_guided_use_bam) {
+ ## check for gsnap software
+ my @tools = qw(gmap_build gsnap);
+ foreach my $tool (@tools) {
+ my $path = `which $tool`;
+ if ($path =~ /\w/) {
+ print STDERR "Found $tool at $path\n";
+ }
+ else {
+ die "Error, cannot locate tool: $tool, required for genome-guided pipeline.";
+ }
+ }
+ }
}
@@ -888,7 +919,7 @@ if ($PAIRED_MODE && (!$NO_RUN_CHRYSALIS_FLAG) && (!$NO_BOWTIE)) {
my $bowtie_path = `which bowtie`;
my $bowtie_build_path = `which bowtie-build`;
if ($bowtie_path =~ /\w/ && $bowtie_build_path =~ /\w/) {
- print "Paired mode requires bowtie. Found bowtie at: $bowtie_path\n and bowtie-build at $bowtie_build_path\n\n" if $SEE;
+ print "Paired mode requires bowtie. Found bowtie at: $bowtie_path\n and bowtie-build at $bowtie_build_path\n\n";
}
else {
die "Error, cannot find path to bowtie ($bowtie_path) or bowtie-build ($bowtie_build_path), which is now needed as part of Chrysalis' read scaffolding step. If you should choose to not run bowtie, include the --no_bowtie in your Trinity command.\n\n";
@@ -896,7 +927,7 @@ if ($PAIRED_MODE && (!$NO_RUN_CHRYSALIS_FLAG) && (!$NO_BOWTIE)) {
my $samtools_path = `which samtools`;
if ($samtools_path =~ /\w/) {
- print "Found samtools at: $samtools_path\n" if $SEE;
+ print "Found samtools at: $samtools_path\n";
}
else {
die "Error, cannot find samtools. Please be sure samtools is installed and included in your PATH setting.\n";
@@ -925,32 +956,16 @@ elsif ($CUFFFLY_MODE) {
$butterfly_output_filename = "Trinity.Cufffly.fasta";
}
-
-
-my $PARALLEL_SAMTOOLS_SORT_TOKEN = "-\@ $CPU";
-
-
-unless (basename($output_directory) =~ /trinity/i) {
- die "Error, output directory must contain the word 'trinity' as a safety precaution, given that auto-deletion can take place.\n";
-}
-
-
-if ($grid_conf_file) {
- # Prep for HPC parafly use.
- $ENV{PATH} = dirname($PARAFLY) . ":$ENV{PATH}";
- &HPC::GridRunner::use_parafly();
-}
-
-
main: {
$ENV{OMP_NUM_THREADS} = $CPU;
+
- unless ($NO_RUN_INCHWORM_FLAG || $NO_RUN_CHRYSALIS_FLAG) {
- print STDERR "-since butterfly will eventually be run, lets test for proper execution of java\n" if $SEE;
+ unless ($NO_RUN_BUTTERFLY_FLAG || $NO_RUN_CHRYSALIS_FLAG) {
+ print STDERR "-since butterfly will eventually be run, lets test for proper execution of java\n";
&test_java_failure_capture();
}
- unless ($genome_guided_bam) {
+ unless ($genome_fasta_file) {
if (basename($chrysalis_output_dir) !~ /chrysalis/i) {
die "Error, chrysalis output directory name must include 'chrysalis' in the name."; # lets try to prevent bad things from happening... (security issue)
@@ -960,6 +975,20 @@ main: {
die "Error, working in full-cleanup mode. Specify a named directory for the output. The directory and contents are purged at end of a successful run.";
}
+ if ($FULL_CLEANUP_ERROR_TOLERANT) { # genome-guided mode
+
+ if (basename($output_directory) !~ /trinity/i) {
+ die "Error, in genome-guided mode, the output directory name must include 'trinity' in the name (precautionary measure)";
+ }
+ $FULL_CLEANUP = 1;
+
+ ## purge chrysalis directory from a previously failed run
+ if (-d $output_directory) {
+ print STDERR "WARNING: $output_directory exists. Since under full-cleanup mode, deleting this first before proceeding.\n:";
+ &process_cmd("rm -rf $output_directory");
+ }
+ }
+
if ($chrysalis_output_dir !~ /^\//) {
$chrysalis_output_dir = "$output_directory/$chrysalis_output_dir";
@@ -1000,7 +1029,8 @@ main: {
@single_files = &create_full_path(\@single_files, 1) if @single_files;
$output_directory = &create_full_path($output_directory, 0);
$long_reads = &create_full_path($long_reads, 1) if $long_reads;
- $genome_guided_bam = &create_full_path($genome_guided_bam, 1) if $genome_guided_bam;
+ $genome_fasta_file = &create_full_path($genome_fasta_file, 1) if $genome_fasta_file;
+ $genome_guided_use_bam = &create_full_path($genome_guided_use_bam, 1) if $genome_guided_use_bam;
$grid_conf_file = &create_full_path($grid_conf_file, 1) if $grid_conf_file;
@@ -1010,7 +1040,7 @@ main: {
$MKDIR_OUTDIR_FLAG = 1;
}
- if ((! $genome_guided_bam) && (! -d $chrysalis_output_dir)) {
+ if ((! $genome_fasta_file) && (! -d $chrysalis_output_dir)) {
&process_cmd("mkdir -p $chrysalis_output_dir"); # note, won't be auto-cleaned up if not in the trinity_out_dir/
}
@@ -1018,16 +1048,7 @@ main: {
collectl_start() unless ($FULL_CLEANUP);
&perfmon_start() unless ($FULL_CLEANUP);
-
- unless ($TRINITY_COMPLETE_FLAG) {
- print STDERR "\n\n";
- print STDERR "----------------------------------------------------------------------------------\n"
- . "-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------\n"
- . "----------------------------------------------------------------------------------\n\n";
-
- }
-
##########################
## Run Quality Trimming
##########################
@@ -1052,7 +1073,6 @@ main: {
my $left_file = shift @left_files;
my $right_file = shift @right_files;
- # note: trimmomatic can use gzipped files directly.
my ($left_file_trimmed, $right_file_trimmed) = &run_trimmomatic_PE($left_file, $right_file, $trimmomatic_quality_trim_params);
push (@trimmed_left_files, $left_file_trimmed);
push (@trimmed_right_files, $right_file_trimmed);
@@ -1087,81 +1107,21 @@ main: {
}
}
- if ($genome_guided_bam) {
- &run_genome_guided_Trinity();
-
- exit(0);
- }
-
-
- eval {
- &run_Trinity();
- };
-
- if ($@) {
- print STDERR "$@\n" if $SEE;
- if ($@ !~ /^NON_FATAL_EXCEPTION/) {
- die "Trinity run failed. Must investigate error above.\n";
- }
- }
-
-
- if ($FULL_CLEANUP) {
- print "Fully cleaning up.\n" if $SEE;
- $output_directory =~ s|/+$||g; # remove any trailing directory slash
-
- if (-s "Trinity.fasta.tmp") {
- rename("Trinity.fasta.tmp", "$output_directory.Trinity.fasta") or die "Error, cannot rename Trinity.fasta.tmp to $output_directory.Trinity.fasta";
-
- print "\n\n"
- . "###################################################################\n"
- . "Butterfly assemblies are written to $output_directory.Trinity.fasta\n"
- . "###################################################################\n\n\n" unless $TRINITY_COMPLETE_FLAG;
-
- }
- else {
- print "# No butterfly assemblies to report.\n" unless $TRINITY_COMPLETE_FLAG;
- }
-
- if ($MKDIR_OUTDIR_FLAG && basename($output_directory) =~ /trinity/i) { # ensure outdirectory as trinity in the name, just to be sure we dont delete something non-trinity related!!!
- system("rm -rf $output_directory &"); # ignore filesystem errors on failed cleanup
- }
- else {
- print STDERR "WARNING, cannot remove output directory $output_directory, since not created in this run. (safety precaution)\n";
- }
+ if ($genome_fasta_file) {
- }
- else {
-
-
- if (-s "Trinity.fasta.tmp") {
- rename("Trinity.fasta.tmp", $butterfly_output_filename) or die "Error, cannot rename Trinity.fasta.tmp to $butterfly_output_filename"; # now that process has finished.
- }
-
- if (-s $butterfly_output_filename) {
-
- print "\n\n";
- print "###################################################################\n";
- print "Butterfly assemblies are written to $output_directory/$butterfly_output_filename\n";
- print "###################################################################\n\n\n" unless $TRINITY_COMPLETE_FLAG;
+ if (@left_files && @right_files) {
+ &run_genome_guided_Trinity(\@left_files, \@right_files);
}
else {
- die "ERROR, no butterfly assemblies reported.";
+ &run_genome_guided_Trinity(\@single_files);
}
- }
-
- &perfmon_end() unless ($FULL_CLEANUP);
- exit(0);
+ exit(0);
+ }
-
-}
-####
-sub run_Trinity {
-
## create inchworm file name
my $inchworm_file = "inchworm.K$KMER_SIZE.L$MIN_IWORM_LEN";
unless ($SS_lib_type) {
@@ -1172,15 +1132,15 @@ sub run_Trinity {
my $trinity_target_fa = (@single_files) ? "single.fa" : "both.fa";
my $inchworm_target_fa = $trinity_target_fa; # change this later if we have long_reads
- my $bowtie_reads_fa = $trinity_target_fa; # dont include long reads in this... keep them separate.
+
## Don't prep the inputs if Inchworm already exists.... Resuming earlier operations.
my $inchworm_finished_checkpoint_file = "$inchworm_file.finished";
if (-s $inchworm_file && -e $inchworm_finished_checkpoint_file) {
print "\n\n#######################################################################\n"
. "Inchworm file: $inchworm_file detected.\n"
. "Skipping Inchworm Step, Using Previous Inchworm Assembly\n"
- . "#######################################################################\n\n" if ($SEE || ! $TRINITY_COMPLETE_FLAG);
+ . "#######################################################################\n\n";
#sleep(2);
}
else {
@@ -1215,7 +1175,7 @@ sub run_Trinity {
die "Error prepping sequences.";
}
- print("Done converting input files.") if $SEE;
+ print("Done converting input files.");
## Calculate input file sizes for performance monitoring
# this should be set as the created fasta otherwise results will differ for same data passed as .fq and .fa?
my $pm_temp = -s "left.fa";
@@ -1234,17 +1194,17 @@ sub run_Trinity {
unlink ("left.fa", "right.fa") unless $jaccard_clip; # no longer needed now that we have 'both.fa', which is needed by chryaslis
}
- foreach my $f ((@left_files, at right_files)){
- if (-s $f.'.readcount'){
- open (IN,$f.'.readcount');
- my $s = <IN>;
- close IN;
- $s=~/([0-9]+)$/;
- $count_of_reads += $1 if $1;
- }
- }
-
-
+ foreach my $f ((@left_files, at right_files)){
+ if (-s $f.'.readcount'){
+ open (IN,$f.'.readcount');
+ my $s = <IN>;
+ close IN;
+ $s=~/([0-9]+)$/;
+ $count_of_reads += $1 if $1;
+ }
+ }
+
+
}
elsif (@single_files) {
@@ -1254,13 +1214,13 @@ sub run_Trinity {
$pm_temp = $pm_temp / 1024 / 1024;
$pm_single_fa_size = sprintf('%.0f', $pm_temp);
foreach my $f (@single_files){
- if (-s $f.'.readcount'){
- open (IN,$f.'.readcount');
- my $s = <IN>;
- close IN;
- $s=~/([0-9]+)$/;
- $count_of_reads += $1 if $1;
- }
+ if (-s $f.'.readcount'){
+ open (IN,$f.'.readcount');
+ my $s = <IN>;
+ close IN;
+ $s=~/([0-9]+)$/;
+ $count_of_reads += $1 if $1;
+ }
}
}
@@ -1273,18 +1233,9 @@ sub run_Trinity {
$count_of_reads/=2;
}
if ($long_reads) {
-
- # adjust the inchworm target, tack on the longer reads.
-
$inchworm_target_fa .= ".wLongReads.fa";
$count_of_reads += `grep -c '^>' $long_reads | wc -l`; #AP we don't know if these will be one single line
-
- &process_cmd("cat $long_reads | sed 's/>/>LR\\\$\\\|/' > $inchworm_target_fa");
-
- ## merge the long reads with the short reads into a new target file.
- &process_cmd("cat $trinity_target_fa >> $inchworm_target_fa");
-
- #&process_cmd("cat $long_reads $trinity_target_fa > $inchworm_target_fa");
+ &process_cmd("cat $long_reads $trinity_target_fa > $inchworm_target_fa");
}
open (my $ofh, ">$inchworm_target_fa.read_count") or die $!;
@@ -1310,26 +1261,55 @@ sub run_Trinity {
unless (-s $inchworm_file) {
-
- die "NON_FATAL_EXCEPTION: WARNING, no Inchworm output is detected at: $inchworm_file";
+
+ ## No inchworm output under genome-guided flag, must be sparse data.
+
+ if ($FULL_CLEANUP_ERROR_TOLERANT && $FULL_CLEANUP && -e $inchworm_file && -e $inchworm_finished_checkpoint_file) {
+ ## GG-trinity mode, clean-up gracefully
+ if ($MKDIR_OUTDIR_FLAG) {
+ &process_cmd("rm -rf $component_directory") if $component_directory;
+ &process_cmd("rm -rf $output_directory");
+ }
+ else {
+ print STDERR "WARNING, cannot remove output directory $output_directory, since not created in this run. (safety precaution)\n";
+ }
+ exit(0);
+ }
+ else {
+ die "Error, no Inchworm output is detected at: $inchworm_file";
+ }
}
+
-
-
- if ($jaccard_clip && $TRINITY_COMPLETE_FLAG) {
-
- if ($jaccard_clip && -s 'left.fa' && -s 'right.fa') {
- $inchworm_file = &run_jaccard_clip_left_right($inchworm_file, \@left_files, \@right_files, $seqType, $SS_lib_type);
- #$inchworm_file = &run_jaccard_clip_left_right($inchworm_file, $left_file, $right_file, $seqType, $SS_lib_type);
+ if ($jaccard_clip) {
+
+ eval {
- }
- elsif ($jaccard_clip && -s 'single.fa') {
- $inchworm_file = &run_jaccard_clip_single_but_really_paired($inchworm_file, \@single_files, $seqType, $SS_lib_type);
- #$inchworm_file = &run_jaccard_clip_single_but_really_paired($inchworm_file, $single_file, $seqType, $SS_lib_type);
+ if ($jaccard_clip && -s 'left.fa' && -s 'right.fa') {
+ $inchworm_file = &run_jaccard_clip_left_right($inchworm_file, \@left_files, \@right_files, $seqType, $SS_lib_type);
+ #$inchworm_file = &run_jaccard_clip_left_right($inchworm_file, $left_file, $right_file, $seqType, $SS_lib_type);
+
+ }
+ elsif ($jaccard_clip && -s 'single.fa') {
+ $inchworm_file = &run_jaccard_clip_single_but_really_paired($inchworm_file, \@single_files, $seqType, $SS_lib_type);
+ #$inchworm_file = &run_jaccard_clip_single_but_really_paired($inchworm_file, $single_file, $seqType, $SS_lib_type);
+ }
+ };
+
+ if ($@) {
+ if ($FULL_CLEANUP_ERROR_TOLERANT) {
+ ## GG-trinity mode, clean up gracefully
+ system("rm -rf $output_directory &"); # ignore file system errors on failed cleanup
+ exit(0);
+ }
+ else {
+ die "Error, jaccard-clip failed: $@";
+ }
}
}
-
- if ($NO_RUN_CHRYSALIS_FLAG && ! $TRINITY_COMPLETE_FLAG) {
+
+
+ if ($NO_RUN_CHRYSALIS_FLAG) {
print "\n\n\n";
print "#########################################################################\n";
print "Inchworm is complete. --no_run_chrysalis was specified, so stopping here.\n";
@@ -1353,275 +1333,233 @@ sub run_Trinity {
## chrysalis will just run or resume depending on what's already been processed.
$pm_chrysalis_start = `date +%s`;
my $butterfly_cmds = &run_chrysalis($inchworm_file, $inchworm_target_fa,
- $min_contig_length, $group_pairs_distance, $SS_lib_type,
- $trinity_target_fa, $bowtie_reads_fa);
-
- if ($butterfly_cmds eq "RECURSIVE_TRINITY_COMPLETE") {
- ## stop here. all done! ## FIXME: this is very bad coding style!!! yes, I know.
- return;
- }
-
-
+ $min_contig_length, $group_pairs_distance, $SS_lib_type, $trinity_target_fa);
$pm_chrysalis_end = `date +%s`;
- print STDERR "Butterfly_cmds: $butterfly_cmds\n" if $SEE;
+ print "Butterfly_cmds: $butterfly_cmds\n";
if ($butterfly_cmds && -s $butterfly_cmds) {
+
+ if ($NO_RUN_BUTTERFLY_FLAG) {
- ## Run Butterfly
-
- print STDERR "Inchworm and Chrysalis complete. Butterfly commands to execute are provided here:\n"
- . $butterfly_cmds . "\n\n" if $SEE;
-
-
- print STDERR "---------------------------------------------------------------\n"
- . "-------------------- Butterfly --------------------------------\n"
- . "-- (Reconstruct transcripts from reads and de Bruijn graphs) --\n"
- . "---------------------------------------------------------------\n\n" if $SEE;
-
- $pm_butterfly_start = `date +%s`;
- if ($grid_conf_file) {
- my @bfly_cmds = `cat $butterfly_cmds`;
- chomp @bfly_cmds;
- my $grid_runner = new HPC::GridRunner($grid_conf_file, "chrysalis/butterfly_on_grid.cacheSuccess");
- my $ret = $grid_runner->run_on_grid(@bfly_cmds);
- if ($ret) {
- die "Error, not all butterfly commands could complete successfully... cannot continue.";
- }
+ print "\n\nYou've opted to run butterfly commands independently from this script, such as on a computing grid.\n\n";
+ print "Butterfly commands to execute are available here:\n"
+ . "\t$butterfly_cmds\n\n";
+ print "After executing Butterfly commands, concatenate all Butterfly outputs by running:\n"
+ . "\t\tfind $output_directory/ -name \"\*allProbPaths.fasta\" -exec cat {} + > $output_directory/Trinity.fasta\n\n\n";
+
+ exit(0);
+
}
else {
- my $cmd = "$PARAFLY -c $butterfly_cmds -shuffle -CPU $bflyCPU -failed_cmds failed_butterfly_commands.$$.txt "; # shuffle them since the first ones are usually the longest-running ones.
- &process_cmd($cmd);
- }
- $pm_butterfly_end = `date +%s`;
-
- ## capture results:
- # my $cmd = 'find ./chrysalis -name "*allProbPaths.fasta" -exec cat {} + > Trinity.fasta.tmp';
- # no longer scan the file system... we know which files should exist
- print STDERR "\n\n** Harvesting all assembled transcripts into a single multi-fasta file...\n" unless ($TRINITY_COMPLETE_FLAG);
- my $cmd = "$UTILDIR/support_scripts/print_butterfly_assemblies.pl $chrysalis_output_dir/component_base_listing.txt > Trinity.fasta.tmp";
- &process_cmd($cmd);
-
-
-
- }
-
-}
-
-
-####
-sub run_chrysalis {
- my ($inchworm_file, $reads_file,
- $min_contig_length, $group_pairs_distance, $SS_lib_type, $pairs_fa, $bowtie_reads_fa) = @_;
-
-
- my $butterfly_cmds = &create_full_path("$chrysalis_output_dir/butterfly_commands");
-
- my $quantify_graph_cmds = &create_full_path("$chrysalis_output_dir/quantifyGraph_commands");
-
- my $pair_links_file = "";
-
- ## Define iworm links via paired-end read mappings:
- if ($PAIRED_MODE && ! $NO_BOWTIE) {
-
- my $pipeliner = new Pipeliner(-verbose => ($TRINITY_COMPLETE_FLAG) ? 0 : 1);
-
- # generate the pair links.
- my $iworm_min100_fa_file = "$chrysalis_output_dir/" . basename("$inchworm_file.min100");
- my $cmd = "$MISCDIR/fasta_filter_by_min_length.pl $inchworm_file 100 > $iworm_min100_fa_file";
- $pipeliner->add_commands( new Command($cmd, "$iworm_min100_fa_file.ok"));
- $pipeliner->run();
-
- $pipeliner = new Pipeliner(-verbose => $SEE);
- $cmd = "bowtie-build -q $iworm_min100_fa_file $iworm_min100_fa_file";
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
- if (-s "$iworm_min100_fa_file") {
- $pipeliner->add_commands( new Command($cmd, "$iworm_min100_fa_file.bowtie_build.ok"));
-
- my $bowtie_sam_file = "$chrysalis_output_dir/iworm.bowtie.nameSorted.bam";
- $cmd = "bash -c \" set -o pipefail; bowtie -a -m 20 --best --strata --threads $CPU --chunkmbs 512 -q -S -f $iworm_min100_fa_file $bowtie_reads_fa | samtools view $PARALLEL_SAMTOOLS_SORT_TOKEN -F4 -Sb - | samtools sort $PARALLEL_SAMTOOLS_SORT_TOKEN -no - - > $bowtie_sam_file\" ";
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
-
- $pipeliner->add_commands( new Command($cmd, "$bowtie_sam_file.ok"));
+ ## Run Butterfly
- ## generate the scaffold info
- my $iworm_scaffolds_file = "$chrysalis_output_dir/iworm_scaffolds.txt";
- $cmd = "$UTILDIR/support_scripts/scaffold_iworm_contigs.pl $bowtie_sam_file $inchworm_file > $iworm_scaffolds_file"; # important, must use original inchworm file because positions are indexed for later use by GraphFromFasta
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
+ print "Inchworm and Chrysalis complete. Butterfly commands to execute are provided here:\n"
+ . $butterfly_cmds . "\n\n";
- $pipeliner->add_commands( new Command($cmd, "$iworm_scaffolds_file.ok"));
- $pair_links_file = $iworm_scaffolds_file;
+ print STDERR "---------------------------------------------------------------\n"
+ . "-------------------- Butterfly --------------------------------\n"
+ . "-- (Reconstruct transcripts from reads and de Bruijn graphs) --\n"
+ . "---------------------------------------------------------------\n\n";
- $pipeliner->run();
+ $pm_butterfly_start = `date +%s`;
+ if ($grid_conf_file) {
+ my @bfly_cmds = `cat $butterfly_cmds`;
+ chomp @bfly_cmds;
+ my $grid_runner = new HTC::GridRunner($grid_conf_file, "chrysalis/butterfly_on_grid.cacheSuccess");
+ my $ret = $grid_runner->run_on_grid(@bfly_cmds);
+ if ($ret) {
+ die "Error, not all butterfly commands could complete successfully... cannot continue.";
+ }
+ }
+ else {
+ my $cmd = "$PARAFLY -c $butterfly_cmds -shuffle -CPU $bflyCPU -failed_cmds failed_butterfly_commands.$$.txt -v "; # shuffle them since the first ones are usually the longest-running ones.
+ &process_cmd($cmd);
+ }
+ $pm_butterfly_end = `date +%s`;
+
+ ## capture results:
+ # my $cmd = 'find ./chrysalis -name "*allProbPaths.fasta" -exec cat {} + > Trinity.fasta.tmp';
+ # no longer scan the file system... we know which files should exist
+ my $cmd = "$UTILDIR/support_scripts/print_butterfly_assemblies.pl $chrysalis_output_dir/component_base_listing.txt > Trinity.fasta.tmp";
+ &process_cmd($cmd);
}
- }
-
-
-
- my $chrysalis_pipeliner = new Pipeliner(-verbose => ($TRINITY_COMPLETE_FLAG) ? 0 : 1);
-
- my $graphFromFasta_outfile = "$chrysalis_output_dir/GraphFromIwormFasta.out";
-
- { # GraphFromFasta
+ }
+
+ if ($FULL_CLEANUP) {
+ print "Fully cleaning up.\n";
+ $output_directory =~ s|/+$||g; # remove any trailing directory slash
- my $graphFromFasta_cmd = "-i $inchworm_file -r $reads_file -min_contig_length $min_contig_length -min_glue $min_glue -glue_factor $glue_factor -min_iso_ratio $min_iso_ratio -t $CPU -k " . ($KMER_SIZE-1) . " -kk " . 2*($KMER_SIZE-1) . " ";
- # use MPI if MPI Procs >1
- if ($np > 1) {
- $graphFromFasta_cmd = "$mpiexec -np $np $CHRYSALIS_DIR/GraphFromFasta_MPI $graphFromFasta_cmd"
+ if (-s "Trinity.fasta.tmp") {
+ rename("Trinity.fasta.tmp", "$output_directory.Trinity.fasta") or die "Error, cannot rename Trinity.fasta.tmp to $output_directory.Trinity.fasta";
+
+ print "\n\n";
+ print "###################################################################\n";
+ print "Butterfly assemblies are written to $output_directory.Trinity.fasta\n";
+ print "###################################################################\n\n\n";
+
}
else {
- $graphFromFasta_cmd = "$CHRYSALIS_DIR/GraphFromFasta $graphFromFasta_cmd"
- }
- if ($SS_lib_type) {
- $graphFromFasta_cmd .= " -strand ";
+ print "\n\n";
+ print "####################################\n";
+ print "## No butterfly assemblies to report.\n";
+ print "####################################\n\n\n";
}
- if ($pair_links_file) {
- $graphFromFasta_cmd .= " -scaffolding $pair_links_file ";
+
+ if ($MKDIR_OUTDIR_FLAG) {
+ system("rm -rf $output_directory &"); # ignore filesystem errors on failed cleanup
}
- if ($CHRYSALIS_DEBUG_WELD_ALL) {
- $graphFromFasta_cmd .= " -debug_weld_all ";
+ else {
+ print STDERR "WARNING, cannot remove output directory $output_directory, since not created in this run. (safety precaution)\n";
}
+
+ }
+ else {
- $graphFromFasta_cmd .= " > $graphFromFasta_outfile";
- if ($TRINITY_COMPLETE_FLAG) {
- $graphFromFasta_cmd .= " 2>/dev/null";
+ if (-s "Trinity.fasta.tmp") {
+ rename("Trinity.fasta.tmp", $butterfly_output_filename) or die "Error, cannot rename Trinity.fasta.tmp to $butterfly_output_filename"; # now that process has finished.
+ }
+
+ if (-s $butterfly_output_filename) {
+
+ print "\n\n";
+ print "###################################################################\n";
+ print "Butterfly assemblies are written to $output_directory/$butterfly_output_filename\n";
+ print "###################################################################\n\n\n";
+ }
+ else {
+ die "ERROR, no butterfly assemblies reported.";
}
-
- my $checkpoint = "$graphFromFasta_outfile.ok";
- $chrysalis_pipeliner->add_commands( new Command($graphFromFasta_cmd, $checkpoint) );
}
+ &perfmon_end() unless ($FULL_CLEANUP);
+ exit(0);
+}
- my $iworm_bundles_fasta_file = "$chrysalis_output_dir/bundled_iworm_contigs.fasta";
- {
- ## create iworm bundles
-
+
+####
+sub run_chrysalis {
+ my ($inchworm_file, $reads_file,
+ $min_contig_length, $group_pairs_distance, $SS_lib_type, $pairs_fa) = @_;
+
+
+ my $butterfly_cmds = &create_full_path("$chrysalis_output_dir/butterfly_commands");
+
+ my $quantify_graph_cmds = &create_full_path("$chrysalis_output_dir/quantifyGraph_commands");
- my $cmd = "$CHRYSALIS_DIR/CreateIwormFastaBundle -i $graphFromFasta_outfile -o $iworm_bundles_fasta_file -min $min_contig_length";
+ my $chrysalis_finished_checkpoint = "$chrysalis_output_dir/chrysalis.finished";
+
+ if (-e $chrysalis_finished_checkpoint) {
- unless ($SEE) {
- $cmd .= " 2>/dev/null ";
- }
+ print "###################################################################\n";
+ print "#### Chrysalis results already exist. Not rerunning Chrysalis. ####\n";
+ print "###################################################################\n\n\n";
- $chrysalis_pipeliner->add_commands( new Command($cmd, "$iworm_bundles_fasta_file.ok"));
+ #sleep(2);
}
-
-
- my $reads_to_components_output_file = "$chrysalis_output_dir/readsToComponents.out";
- {
- ## map reads to chrysalis components:
+ else {
+ ## run Chrysalis
+
+ my $cmd = "$CHRYSALIS_DIR/Chrysalis -i $reads_file -iworm $inchworm_file -o $chrysalis_output_dir -cpu $CPU "
+ . " -min_glue $min_glue -min_iso_ratio $min_iso_ratio -glue_factor $glue_factor -kmer_size " . ($KMER_SIZE-1) # chrysalis wants kmer overlap length
+ . " -weldmer_size $weldmer_size "
+ . " -min $min_contig_length -dist $group_pairs_distance -max_reads $max_reads_per_graph "
+ . " -sort_exec \"$sort_exec\" "
+ . " -sort_buffer_size $JM_string -max_mem_reads $max_reads_per_loop ";
+ if ($SS_lib_type) {
+ $cmd .= " -strand 1 ";
+ }
- my $cmd = ($BOWTIE_COMP) ? "$CHRYSALIS_DIR/ReadsToComponents.pl" : "$CHRYSALIS_DIR/ReadsToTranscripts";
- if ("$cmd" eq "$CHRYSALIS_DIR/ReadsToTranscripts" ) {
- if ($np > 1) {
- $cmd = "$mpiexec -np $np $CHRYSALIS_DIR/ReadsToTranscripts_MPI"
+ if ($PAIRED_MODE) {
+ $cmd .= " -paired ";
+ $cmd .= " -reads_for_pairs $pairs_fa ";
+
+ if ($NO_BOWTIE) {
+ $cmd .= " -no_pair_links ";
}
+
}
-
- $cmd .= " -i $reads_file -f $iworm_bundles_fasta_file -o $reads_to_components_output_file -t $CPU -max_mem_reads $max_reads_per_loop ";
- if ($SS_lib_type) {
- $cmd .= " -strand ";
+
+ if ($BOWTIE_COMP) {
+ $cmd .= " -bowtie_comp ";
}
+
if ($min_pct_read_mapping) {
$cmd .= " -min_pct_read_mapping $min_pct_read_mapping ";
}
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
-
- $chrysalis_pipeliner->add_commands( new Command($cmd, "$reads_to_components_output_file.ok"));
- }
-
- my $sorted_reads_to_components_file = "$reads_to_components_output_file.sort";
- {
- ## sort the read mappings:
-
- my $cmd = "$sort_exec -T . -S $max_memory -k 1,1n $reads_to_components_output_file > $sorted_reads_to_components_file";
+ $cmd .= " -butterfly $BFLY_JAR ";
- unless ($SEE) {
- $cmd .= " 2>/dev/null ";
+ if ($NO_CLEANUP) {
+ $cmd .= " -no_cleanup ";
}
- $chrysalis_pipeliner->add_commands( new Command($cmd, "$sorted_reads_to_components_file.ok"));
-
- }
-
- if (! $TRINITY_COMPLETE_FLAG) {
+ $cmd .= " 2>&1 ";
- $chrysalis_pipeliner->run();
+ eval {
+
+ &process_cmd($cmd);
+
+ };
- &run_recursive_trinity($sorted_reads_to_components_file);
- return ("RECURSIVE_TRINITY_COMPLETE"); # indicate to caller that we're in recursive trinity mode.
- }
-
-
-
-
- my $deBruijnGraph_outfile = "$iworm_bundles_fasta_file.deBruijn";
-
- {
- ## write the deBruijn graphs:
+ if ($@) {
+
+ if ($FULL_CLEANUP_ERROR_TOLERANT) {
+ ## Trinity GG mode - OK, not enough data that's worth pursuing.
+ return("");
+
+ }
- my $cmd = "$INCHWORM_DIR/FastaToDeBruijn --fasta $iworm_bundles_fasta_file -K " . ($KMER_SIZE-1) . " --graph_per_record --threads $CPU";
- if ($SS_lib_type) {
- $cmd .= " --SS ";
- }
-
- $cmd .= " > $deBruijnGraph_outfile";
-
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
+ my $errmsg = "$curr_limit_settings\n";
+ $errmsg .= "Error, the Chrysalis process failed:\n$@\n";
+ croak $errmsg;
}
- $chrysalis_pipeliner->add_commands(new Command($cmd, "$deBruijnGraph_outfile.ok") );
+
+ print "Chrysalis initial stage completed successfully.\n";
+ &process_cmd("touch $chrysalis_finished_checkpoint");
}
- $chrysalis_pipeliner->run();
+ ## partition the graphs and reads in prep for quantify graph and butterfly steps.
-
unless (-s "$chrysalis_output_dir/bundled_iworm_contigs.fasta.deBruijn") {
- die "NON_FATAL_EXCEPTION: WARNING, no deBruijn graphs generated based on inchworm contigs: $chrysalis_output_dir/bundled_iworm_contigs.fasta.deBruijn";
+
+ if ($FULL_CLEANUP_ERROR_TOLERANT) {
+ ## Trinity GG mode - OK, not enough data that's worth pursuing.
+ return("");
+ }
+
+ croak "Error, no deBruijn graphs generated based on inchworm contigs: $chrysalis_output_dir/bundled_iworm_contigs.fasta.deBruijn";
}
- #################################################################################
- ## partition the graphs and reads in prep for quantify graph and butterfly steps.
- #################################################################################
-
my $partitioning_checkpoint_file = "$chrysalis_output_dir/file_partitioning.ok";
- my $cmd = "$UTILDIR/support_scripts/partition_chrysalis_graphs_n_reads.pl --deBruijns $chrysalis_output_dir/bundled_iworm_contigs.fasta.deBruijn --componentReads $chrysalis_output_dir/readsToComponents.out.sort -N 1000 -L $min_contig_length ";
-
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
-
+ my $cmd = "$UTILDIR/support_scripts/partition_chrysalis_graphs_n_reads.pl --deBruijns $chrysalis_output_dir/bundled_iworm_contigs.fasta.deBruijn --componentReads $chrysalis_output_dir/readsToComponents.out.sort -N 1000 -L $min_contig_length --compdir $component_directory ";
+
&process_cmd($cmd) unless (-e $partitioning_checkpoint_file);
&process_cmd("touch $partitioning_checkpoint_file") unless (-e $partitioning_checkpoint_file);
-
+
## write the quantifygraph commands and butterfly commands
my $component_base_listing_file = "$chrysalis_output_dir/component_base_listing.txt";
- if (-e $component_base_listing_file && ! -s $component_base_listing_file) {
-
- die "NON_FATAL_EXCEPTION: WARNING, component base listing file: $component_base_listing_file exists and is empty - likely sparse data";
+ unless (-s $component_base_listing_file) {
+
+ if ($FULL_CLEANUP_ERROR_TOLERANT) {
+ ## Trinity GG mode
+ return("");
+ }
+ croak "Error, component base listing file: $component_base_listing_file does not exist";
}
@@ -1652,10 +1590,6 @@ sub run_chrysalis {
$quantify_graph_cmd .= " -no_cleanup ";
}
-
- unless ($SEE) {
- $quantify_graph_cmd .= " 2>/dev/null";
- }
print $qgraph_cmd_ofh $quantify_graph_cmd . "\n";
@@ -1678,6 +1612,17 @@ sub run_chrysalis {
$bfly_cmd .= " --path_reinforcement_distance=$path_reinforcement_distance ";
+ if ($TRIPLET_LOCK) {
+ $bfly_cmd .= " --triplet-lock ";
+ }
+ if ($EXTENDED_TRIPLET_LOCK) {
+ $bfly_cmd .= " --extended_triplet ";
+ }
+
+ unless ($NO_EM_REDUCE) {
+ $bfly_cmd .= " --EM_REDUCE ";
+ }
+
if ($NO_PATH_MERGING) {
$bfly_cmd .= " --no_path_merging ";
}
@@ -1710,126 +1655,70 @@ sub run_chrysalis {
}
- my $quantify_graph_cmds_finished = &create_full_path("$chrysalis_output_dir/quantifyGraph_commands.run.finished");
- if (! -e $quantify_graph_cmds_finished) {
- ## run it
-
- print STDERR "---------------------------------------------------\n"
- . "----------- Chrysalis: QuantifyGraph --------------\n"
- . "-- (Integrate mapped reads into de Bruijn graph) --\n"
- . "---------------------------------------------------\n\n" if $SEE;
-
-
- if ($grid_conf_file) {
- my @quantify_graph_cmds = `cat $quantify_graph_cmds`;
- chomp @quantify_graph_cmds;
-
- my $grid_runner = new HPC::GridRunner($grid_conf_file, "chrysalis/chrysalis_quantify_graph_on_grid.cacheSuccess");
- my $ret = $grid_runner->run_on_grid(@quantify_graph_cmds);
- if ($ret) {
- die "Error, not all Chrysalis quantify_graph commands completed successfully. Cannot continue.";
- }
- }
- else {
-
- my $cmd = "$PARAFLY -c $quantify_graph_cmds -CPU $CPU -failed_cmds failed_quantify_graph_commands.$$.txt -shuffle ";
- &process_cmd($cmd);
- }
+ # see if we need to run the quantifyGraph commands:
+ if ($NO_RUN_QUANTIFYGRAPH_FLAG) {
+
+ print "#############################################################################\n";
+ print "## Ceasing Trinity prior to execution of massively parallel operations.\n";
+ print "##\n";
+ print "## To complete Trinity, execute the following sets of commands:\n";
+ print "##\n";
+ print "## First, run the Chrysalis QuantifyGraph commands in parallel:\n";
+ print "## $quantify_graph_cmds\n";
+ print "##\n";
+ print "## Then, execute all the Butterfly commands:\n";
+ print "## $butterfly_cmds\n";
+ print "##\n";
+ print "## And, finally, concatenate all Butterfly assemblies into a single output file:\n";
+ print "##\n";
+ print "## find $output_directory/ -name \"\*allProbPaths.fasta\" -exec cat {} + > $output_directory/Trinity.fasta\n";
+ print "##\n";
+ print "##############################################################################\n";
+ print "\n\n";
- # write checkpoint
- &process_cmd("touch $quantify_graph_cmds_finished");
+ exit(0);
}
-
-
- return($butterfly_cmds);
-
-
-}
-
-
-####
-sub run_recursive_trinity {
- my ($reads_sorted_by_component_file) = @_;
+ else {
- my $target_files_per_dir = 100; # new Fb_\d/CBin_\d every (#components/100)
- my $file_bins_per_dir = 1000 * $target_files_per_dir; # new Fb_\d dir
-
- my $component_counter = 0;
-
- my $prev_component_id = -1;
- my $ofh = undef;
-
- my $read_filenames = "partitioned_reads.files.list";
- my $read_filenames_ok = "$read_filenames.ok";
- if (! -e $read_filenames_ok) {
-
- open (my $ofh_read_filenames, ">$read_filenames") or die $!;
- my $currdir = cwd();
-
- open (my $fh, $reads_sorted_by_component_file) or die $!;
- while (<$fh>) {
- chomp;
- my ($component_id, $read_name, $pct, $read_seq) = split(/\t/);
+ my $quantify_graph_cmds_finished = &create_full_path("$chrysalis_output_dir/quantifyGraph_commands.run.finished");
+ if (! -e $quantify_graph_cmds_finished) {
+ ## run it
- if ($component_id != $prev_component_id) {
+ print STDERR "---------------------------------------------------\n"
+ . "----------- Chrysalis: QuantifyGraph --------------\n"
+ . "-- (Integrate mapped reads into de Bruijn graph) --\n"
+ . "---------------------------------------------------\n\n";
+
+
+ if ($grid_conf_file) {
+ my @quantify_graph_cmds = `cat $quantify_graph_cmds`;
+ chomp @quantify_graph_cmds;
- $prev_component_id = $component_id;
- close $ofh if $ofh;
- my $base_dir = "read_partitions/Fb_" . (int($component_counter/$file_bins_per_dir)) . "/CBin_" . (int($component_counter/$target_files_per_dir));
- if (! -d $base_dir) {
- &process_cmd("mkdir -p $base_dir");
+ my $grid_runner = new HTC::GridRunner($grid_conf_file, "chrysalis/chrysalis_quantify_graph_on_grid.cacheSuccess");
+ my $ret = $grid_runner->run_on_grid(@quantify_graph_cmds);
+ if ($ret) {
+ die "Error, not all Chrysalis quantify_graph commands completed successfully. Cannot continue.";
}
- my $readsfile = "$currdir/$base_dir/c$component_id.trinity.reads.fa";
+ }
+ else {
- $component_counter++;
-
- open ($ofh, ">$readsfile") or die "Error, cannot write to file $readsfile";
- print $ofh_read_filenames "$readsfile\n";
+ my $cmd = "$PARAFLY -c $quantify_graph_cmds -CPU $CPU -failed_cmds failed_quantify_graph_commands.$$.txt -v -shuffle ";
+ &process_cmd($cmd);
}
- print $ofh "$read_name\n$read_seq\n";
-
+
+ # write checkpoint
+ &process_cmd("touch $quantify_graph_cmds_finished");
}
- close $ofh if $ofh;
- close $ofh_read_filenames;
+
- &process_cmd("touch $read_filenames_ok");
- }
-
+ return($butterfly_cmds);
- if ($ANANAS_DIR) {
- &run_ANANAS($read_filenames, "read_partitions");
- exit(0);
- }
-
-
- if (! -e "recursive_trinity.cmds.ok") {
- &write_trinity_partitioned_cmds($read_filenames, "recursive_trinity.cmds");
- &process_cmd("touch recursive_trinity.cmds.ok");
- print STDERR "Done prepping partitioned cmds." if $SEE;
}
- if ($NO_DISTRIBUTED_TRINITY_EXEC) {
- print STDERR "\n\n###################################################################\n"
- . "## Stopping here due to --no_distributed_trinity_exec in effect ##\n"
- . "###################################################################\n\n";
- exit(0);
- }
-
- &run_partitioned_cmds("recursive_trinity.cmds");
-
- print STDERR "\n\n** Harvesting all assembled transcripts into a single multi-fasta file...\n\n" unless ($TRINITY_COMPLETE_FLAG);
-
- my $cmd = "find read_partitions/ -name '*inity.fasta' | $UTILDIR/support_scripts/partitioned_trinity_aggregator.pl TR > Trinity.fasta.tmp";
- &process_cmd($cmd);
-
- return;
-
-}
-
-
-
+
+}
####
@@ -1855,11 +1744,11 @@ sub run_inchworm {
#####################################################
- ## Using Jellyfish kmer method (if in initial read partitioning phase (1) )
+ ## Using Jellyfish kmer method
#####################################################
- if (! ($FORCE_INCHWORM_KMER_METHOD || $TRINITY_COMPLETE_FLAG) ) {
-
+ if (! $FORCE_INCHWORM_KMER_METHOD) {
+
my $jelly_kmer_fa_file = "jellyfish.kmers.fa";
my $jelly_finished_checkpoint_file = "jellyfish.$min_kmer_cov.finished";
unless (-e $jelly_finished_checkpoint_file) {
@@ -1873,7 +1762,7 @@ sub run_inchworm {
my $read_file_size = -s $reads;
- my $jelly_hash_size = int( ($jellyfish_ram - $read_file_size)/7); # decided upon by Rick Westerman
+ my $jelly_hash_size = int( ($max_memory - $read_file_size)/7); # decided upon by Rick Westerman
if ($jelly_hash_size < 100e6) {
@@ -1894,10 +1783,6 @@ sub run_inchworm {
$cmd .= " $reads";
- unless ($SEE) {
- $cmd .= " 2> /dev/null ";
- }
-
&process_cmd($cmd);
@@ -1908,20 +1793,12 @@ sub run_inchworm {
my $jelly_db = "mer_counts.jf";
$cmd = "$JELLYFISH_DIR/bin/jellyfish dump -L $min_kmer_cov $jelly_db > $jelly_kmer_fa_file";
-
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
&process_cmd($cmd);
## write a histogram of the kmer counts.
$cmd = "$JELLYFISH_DIR/bin/jellyfish histo -t $CPU -o $jelly_kmer_fa_file.histo $jelly_db";
-
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
&process_cmd($cmd);
@@ -1931,7 +1808,7 @@ sub run_inchworm {
&process_cmd("touch $jelly_finished_checkpoint_file");
- if ($NO_RUN_INCHWORM_FLAG && ! $TRINITY_COMPLETE_FLAG) {
+ if ($NO_RUN_INCHWORM_FLAG) {
print STDERR "WARNING: --no_run_inchworm parameter in effect. Stopping here prior to running inchworm.\n";
exit(0);
}
@@ -1940,7 +1817,7 @@ sub run_inchworm {
}
- $inchworm_cmd = "$INCHWORM_DIR/inchworm --kmers $jelly_kmer_fa_file --run_inchworm -K $KMER_SIZE -L $MIN_IWORM_LEN --monitor 1 $iworm_opts ";
+ $inchworm_cmd = "$INCHWORM_DIR/bin/inchworm --kmers $jelly_kmer_fa_file --run_inchworm -K $KMER_SIZE -L $MIN_IWORM_LEN --monitor 1 ";
# hold on to the jellyfish file - we might use it for other applications.
#push (@tmp_files, $jelly_finished_checkpoint_file, $jelly_kmer_fa_file) unless $NO_CLEANUP;
@@ -1949,21 +1826,22 @@ sub run_inchworm {
else {
######################################################
- ## Using Inchworm kmer method (original, slow w/ large data)
+ ## Using Inchworm kmer method (original, slow method)
######################################################
- $inchworm_cmd = "$INCHWORM_DIR/inchworm --reads $reads --run_inchworm -K $KMER_SIZE -L $MIN_IWORM_LEN --monitor 1 ";
+ $inchworm_cmd = "$INCHWORM_DIR/bin/inchworm --reads $reads --run_inchworm -K $KMER_SIZE -L $MIN_IWORM_LEN --monitor 1 ";
if ($min_kmer_cov > 1) {
$inchworm_cmd .= " --minKmerCount $min_kmer_cov ";
}
}
+
## finish constructing the inchworm command to execute
unless ($strand_specific_flag) {
$inchworm_cmd .= " --DS ";
}
-
+
unless ($NO_CLEANUP) {
$inchworm_cmd .= " --keep_tmp_files ";
}
@@ -1986,12 +1864,8 @@ sub run_inchworm {
print STDERR "----------------------------------------------\n"
. "--------------- Inchworm ---------------------\n"
. "-- (Linear contig construction from k-mers) --\n"
- . "----------------------------------------------\n\n" if (! $TRINITY_COMPLETE_FLAG);
+ . "----------------------------------------------\n\n";
- unless ($SEE) {
- $inchworm_cmd .= " 2>/dev/null";
- }
-
eval {
@@ -2106,18 +1980,18 @@ sub create_full_path {
sub process_cmd {
my ($cmd) = @_;
- print STDERR &mytime."CMD: $cmd\n" unless ($TRINITY_COMPLETE_FLAG);
-
+ print &mytime."CMD: $cmd\n";
+
my $start_time = time();
- my $ret = system("bash", "-c", $cmd);
+ my $ret = system($cmd);
my $end_time = time();
if ($ret) {
die "Error, cmd: $cmd died with ret $ret";
}
- print STDERR "CMD finished (" . ($end_time - $start_time) . " seconds)\n" if $SEE;
-
+ print "CMD finished (" . ($end_time - $start_time) . " seconds)\n";
+
return;
}
@@ -2183,10 +2057,8 @@ sub run_jaccard_clip_single_but_really_paired {
####
sub test_java_failure_capture {
- if ($SEE) {
- print "#######################################\n";
- print "Running Java Tests\n";
- }
+ print "#######################################\n";
+ print "Running Java Tests\n";
my $java_prog = `which java`;
unless ($java_prog) {
@@ -2212,15 +2084,15 @@ sub test_java_failure_capture {
};
if ($@) {
- print "-we properly captured the java failure status, as needed. Looking good.\n" if $SEE;
+ print "-we properly captured the java failure status, as needed. Looking good.\n";
}
else {
print STDERR "-we are unable to properly capture java failure status. Please be sure that java (or any wrapper around java that's being used) can properly capture and propagate failure status before proceeding.\n";
exit(1);
}
- print "Java tests succeeded.\n" if $SEE;
- print "###################################\n\n" if $SEE;
+ print "Java tests succeeded.\n";
+ print "###################################\n\n";
return;
}
@@ -2232,7 +2104,7 @@ sub extract_reads_with_iworm_kmers {
my $extracted_reads_file = "$trinity_target_fa." . $min_percent_read_containing_kmers . "pcnt.iworm_extracted";
- my $cmd = "$INCHWORM_DIR/pull_reads_with_kmers "
+ my $cmd = "$INCHWORM_DIR/bin/pull_reads_with_kmers "
. "--target $inchworm_file "
. "--reads $trinity_target_fa "
. "--min_percent_read_containing_kmers $min_percent_read_containing_kmers ";
@@ -2351,7 +2223,7 @@ sub perfmon_start {
print FILE "===========\n";
print FILE "Trinity Version: $VERSION\n";
my $tempp="";
- $tempp=`ldd $INCHWORM_DIR/inchworm 2>/dev/null | grep "libgomp"`;
+ $tempp=`ldd $INCHWORM_DIR/bin/inchworm 2>/dev/null | grep "libgomp"`;
if ($tempp eq "") {
print FILE "Compiler: Intel\n";
} else {
@@ -2449,10 +2321,10 @@ sub collectl_stop {
kill("TERM", $collectl_pid);
waitpid($collectl_pid,0);
chdir($collectl_output_directory) or return;
- system("python $COLLECTL_DIR/make_data_files.py");
- system("python $COLLECTL_DIR/timetable.py");
+ system("$COLLECTL_DIR/make_data_files.sh");
+ system("$COLLECTL_DIR/timetable.sh");
$collectl_titlename = "${VERSION} ${CPU} @{left_files}@{single_files}";
- system("python $COLLECTL_DIR/plot.py \"$collectl_titlename\" ${CPU}");
+ system("$COLLECTL_DIR/plot.sh \"$collectl_titlename\" ${CPU}");
}
}
@@ -2484,18 +2356,10 @@ sub run_trimmomatic_PE {
&process_cmd($cmd);
- if ($NORMALIZE_READS_FLAG) {
- ## can't use the orphans:
- &process_cmd("cp $trimmed_left_file_base.P.qtrim $trimmed_left_fq");
- &process_cmd("cp $trimmed_right_file_base.P.qtrim $trimmed_right_fq");
- }
- else {
-
- ## append the orphans so we can still use them in assembly
- &process_cmd("cat $trimmed_left_file_base.P.qtrim $trimmed_left_file_base.U.qtrim > $trimmed_left_fq");
- &process_cmd("cat $trimmed_right_file_base.P.qtrim $trimmed_right_file_base.U.qtrim > $trimmed_right_fq");
- }
-
+ ## append the orphans so we can still use them in assembly
+ &process_cmd("cat $trimmed_left_file_base.P.qtrim $trimmed_left_file_base.U.qtrim > $trimmed_left_fq");
+ &process_cmd("cat $trimmed_right_file_base.P.qtrim $trimmed_right_file_base.U.qtrim > $trimmed_right_fq");
+
&process_cmd("touch $checkpoint");
# compress the trimmomatic direct outputs to conserve space:
@@ -2600,7 +2464,7 @@ sub normalize {
- my $cmd = "$UTILDIR/insilico_read_normalization.pl --seqType $seqType --JM $max_memory "
+ my $cmd = "$UTILDIR/insilico_read_normalization.pl --seqType $seqType --JM $JM_string "
. " --max_cov $max_read_coverage --CPU $CPU --output $normalize_outdir";
if ($SS_lib_type) {
@@ -2611,8 +2475,6 @@ sub normalize {
$cmd .= " --no_cleanup ";
}
- #@read_files = &add_fifo_for_gzip(@read_files);
-
my @ret_files;
if (scalar @read_files == 2) {
@@ -2632,9 +2494,9 @@ sub normalize {
my $checkpoint = "$normalize_outdir/normalization.ok";
if (&files_exist(@ret_files, $checkpoint)) {
- print STDERR "###############################################################################\n"
- . "#### Normalization process was previously completed. Skipping it and using existing normalized files: @ret_files\n"
- . "###############################################################################\n" if $SEE;
+ print STDERR "###############################################################################\n";
+ print STDERR "#### Normalization process was previously completed. Skipping it and using existing normalized files: @ret_files\n";
+ print STDERR "###############################################################################\n";
}
else {
@@ -2659,16 +2521,74 @@ sub files_exist {
return(0); # not exists
}
}
-
+
return(1); # all exist
}
####
sub run_genome_guided_Trinity {
- ## partition the reads according to coverage piles:
+ my ($left_files_aref, $right_files_aref) = @_;
+
+
+ my $bam_file;
+ if ($genome_guided_use_bam) {
+ $bam_file = $genome_guided_use_bam;
+ }
+ else {
+ ## run gsnap to align reads:
+
+ $bam_file = "gsnap.coordSorted.bam";
+
+ unless (-s "$bam_file" && -e "$bam_file.ok") {
+
+ my @files;
+ if ($left_files_aref && $right_files_aref) {
+ while (@$left_files_aref) {
+ my $left_file = shift @$left_files_aref;
+ my $right_file = shift @$right_files_aref;
+ push (@files, $left_file, $right_file);
+ }
+ }
+ else {
+ @files = @$left_files_aref; # really single files
+ }
+
+ @files = &add_zcat_gz(@files);
+
+
+ ## prep the genome
+ my $cmd = "ln -sf $genome_fasta_file gsnap_target.fa";
+ &process_cmd($cmd);
+
+ if (-s "$genome_fasta_file.gmap") {
+ &process_cmd("ln -sf $genome_fasta_file.gmap gsnap_target.gmap");
+ }
+ else {
+
+ my $cmd = "gmap_build -k 13 -D . -d gsnap_target.gmap gsnap_target.fa ";
+ &process_cmd($cmd) unless (-e "target.gmap");
+ }
+
+ if (-s "$genome_fasta_file.fai") {
+ &process_cmd("ln -sf $genome_fasta_file.fai gsnap_target.fa.fai");
+ }
+ else {
+ my $cmd = "samtools faidx gsnap_target.fa";
+ &process_cmd($cmd);
+ }
+
+ $cmd = "bash -c \"set -o pipefail; gsnap -d gsnap_target.gmap -D . -A sam --nofails -N 1 -t $GMAP_CPU -w $genome_guided_max_intron -n 20 @files | samtools view -bt gsnap_target.fa.fai - | samtools sort -o - - > $bam_file \"";
+ &process_cmd($cmd);
+
+ &process_cmd("touch $bam_file.ok"); # checkpoint
+ }
+
+ }
- my $cmd = "$UTILDIR/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM $genome_guided_bam -I $genome_guided_max_intron --sort_buffer $max_memory --CPU $CPU ";
+ ## partition the reads according to coverage piles:
+ my $cmd = "$UTILDIR/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM $bam_file -I $genome_guided_max_intron --sort_buffer $genome_guided_sort_buffer --CPU $CPU ";
+
if ($SS_lib_type) {
$cmd .= " --SS_lib_type $SS_lib_type ";
}
@@ -2682,85 +2602,11 @@ sub run_genome_guided_Trinity {
&process_cmd($cmd) unless (-s "read_files.list" && -e "read_files.list.ok");
&process_cmd("touch read_files.list.ok") unless (-e "read_files.list.ok"); # checkpoint
-
- if ($ANANAS_DIR) {
- &run_ANANAS("read_files.list", "Dir_\*");
- exit(0);
- }
-
-
-
- unless (-e "trinity_GG.cmds.ok") {
- &write_trinity_partitioned_cmds("read_files.list", "trinity_GG.cmds");
- &process_cmd("touch trinity_GG.cmds.ok");
- }
-
- if ($NO_DISTRIBUTED_TRINITY_EXEC) {
- print STDERR "\n\n###################################################################\n"
- . "## Stopping here due to --no_distributed_trinity_exec in effect ##\n"
- . "###################################################################\n\n";
- exit(0);
- }
-
- &run_partitioned_cmds("trinity_GG.cmds");
-
-
- ## pull together the final outputs:
- $cmd = "find Dir_* -name '*inity.fasta' | $UTILDIR/support_scripts/partitioned_trinity_aggregator.pl GG > Trinity-GG.fasta.tmp";
- &process_cmd($cmd);
-
- rename("Trinity-GG.fasta.tmp", "Trinity-GG.fasta"); # now that it's done.
-
- print STDERR "\n\nFinished. See Trinity-GG.fasta for reconstructed transcripts\n\n";
-
- return;
-}
-
-####
-sub run_partitioned_cmds {
- my ($cmds_file) = @_;
-
-
- print STDERR "\n\n";
- print STDERR "--------------------------------------------------------------------------------\n"
- . "------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------\n"
- . "--------------------------------------------------------------------------------\n\n";
-
-
- if ($ANANAS_DIR) {
- print STDERR " ************ Using Ananas Assembler ***************** \n\n";
- }
-
- ## Execute the commands:
- if ($grid_conf_file) {
- my @cmds = `cat $cmds_file`;
- chomp @cmds;
-
- my $grid_runner = new HPC::GridRunner($grid_conf_file, "$cmds_file.htc_cache_success");
- my $ret = $grid_runner->run_on_grid(@cmds);
- if ($ret) {
- die "Error, not all $cmds_file commands completed successfully. Cannot continue.";
- }
-
- }
- else {
- my $cmd = "$PARAFLY -c $cmds_file -CPU $CPU -v ";
- &process_cmd($cmd);
- }
-
- return;
-}
-
-
-####
-sub write_trinity_partitioned_cmds {
- my ($reads_list_file, $cmds_file) = @_;
-
##################################################
## write Trinity assembly commands for partitions:
##################################################
- my $cmd = "$UTILDIR/support_scripts/GG_write_trinity_cmds.pl --reads_list_file $reads_list_file --CPU $grid_node_CPU --max_memory $grid_node_max_memory ";
+ $cmd = "$UTILDIR/support_scripts/GG_write_trinity_cmds.pl --reads_list_file read_files.list --CPU $genome_guided_CPU ";
if ($run_as_paired_flag) {
$cmd .= " --run_as_paired ";
}
@@ -2768,7 +2614,8 @@ sub write_trinity_partitioned_cmds {
$cmd .= " --SS_lib_type F "; # all sequences already reoriented
}
- $cmd .= " --full_cleanup --seqType fa --trinity_complete";
+ $cmd .= " --full_cleanup_ET --seqType fa ";
+
my @potential_args = @ORIG_ARGS;
@@ -2776,15 +2623,15 @@ sub write_trinity_partitioned_cmds {
my $arg = shift @potential_args;
# single value options that aren't needed:
- if ($arg =~ /run_as_paired|normalize_by_read_set|trimmomatic|normalize_reads|prep|recurs|clean/) {
+ if ($arg =~ /run_as_paired|normalize_by_read_set|trimmomatic|normalize_reads|prep/) {
next;
}
-
+
# value specified options that aren't needed
- if ($arg =~ /seqType|left|right|single|genome|SS_lib_type|GMAP|quality_trimming|output|normalize_max_read_cov|grid_conf|max_mem|grid|long_reads/
+ if ($arg =~ /seqType|left|right|single|genome|SS_lib_type|GMAP|quality_trimming|output|normalize_max_read_cov|grid_conf/
||
# more precise identification of parameter
- $arg =~ /^(--CPU)$/
+ $arg =~ /^(CPU)$/
) {
# skipping these, already represented by opt configuration above.
@@ -2803,16 +2650,44 @@ sub write_trinity_partitioned_cmds {
}
}
- $cmd .= " > $cmds_file";
+ $cmd .= " > trinity_GG.cmds";
+
+ &process_cmd($cmd) unless (-e "trinity_GG.cmds.ok");
+ &process_cmd("touch trinity_GG.cmds.ok") unless (-e "trinity_GG.cmds.ok");
+
+ if ($genome_guided_just_prep_flag) {
+ print STDERR "###### Just prepping data for genome-guided assembly. Stopping here due to --genome_guided_just_prep invocation. #####\n\n";
+ exit(0);
+ }
+
+ ## execute the commands:
+ if ($grid_conf_file) {
+ my @trin_GG_cmds = `cat trinity_GG.cmds`;
+ chomp @trin_GG_cmds;
+
+ my $grid_runner = new HTC::GridRunner($grid_conf_file, "trinity_GG_cmds.htc_cache_success");
+ my $ret = $grid_runner->run_on_grid(@trin_GG_cmds);
+ if ($ret) {
+ die "Error, not all Trinity-GG commands completed successfully. Cannot continue.";
+ }
+
+ }
+ else {
+ my $cmd = "$PARAFLY -c trinity_GG.cmds -CPU $CPU -v ";
+ &process_cmd($cmd);
+ }
- &process_cmd($cmd) unless (-e "$cmds_file.ok");
- &process_cmd("touch $cmds_file.ok") unless (-e "$cmds_file.ok");
+ ## pull together the final outputs:
+ $cmd = "find Dir_* -name '*inity.fasta' | $UTILDIR/support_scripts/GG_trinity_accession_incrementer.pl > Trinity-GG.fasta.tmp";
+ &process_cmd($cmd);
+ rename("Trinity-GG.fasta.tmp", "Trinity-GG.fasta"); # now that it's done.
+ print STDERR "\n\nFinished. See Trinity-GG.fasta for reconstructed transcripts\n\n";
+
return;
}
-
sub add_zcat_gz {
my (@in_files) = @_;
@@ -2830,124 +2705,3 @@ sub add_zcat_gz {
return(@files);
}
-
-
-####
-sub add_fifo_for_gzip {
- my @files = @_;
-
- foreach my $file (@files) {
- if (ref $file eq "ARRAY") {
- my @f = &add_fifo_for_gzip(@{$file});
- $file = [@f];
- }
- elsif ($file =~ /\.gz$/) {
- $file = "<(zcat $file)";
- }
- }
-
- return(@files);
-
-}
-
-sub version_check {
-
- print "Trinity version: $VERSION\n";
-
- my $url = "http://rt-trinity.uits.indiana.edu/flask/version/" . $VERSION . "?timestamp=" . time;
- my $content = `curl --connect-timeout 10 -s "$url"`;
-
- ## get release info from here:
- ## https://api.github.com/repos/trinityrnaseq/trinityrnaseq/releases
-
- $url = "https://api.github.com/repos/trinityrnaseq/trinityrnaseq/releases";
- $content = `curl --connect-timeout 10 -s "$url"`;
-
- if ($?) {
-
- print STDERR "-ERROR: couldn't run the network check to confirm latest Trinity software version.\n\n";
- }
- else {
-
- if ($content =~ /\"tag_name\": \"([^\"]+)\"/) {
- my $latest_version_tag = $1;
- if ($VERSION eq '__TRINITY_VERSION_TAG__') {
- print STDERR "-using Trinity devel version. Note, latest production release is: $latest_version_tag\n\n";
- }
- elsif ($latest_version_tag ne $VERSION) {
- print "** NOTE: Latest version of Trinity is $latest_version_tag, and can be obtained at:\n"
- . "\thttps://github.com/trinityrnaseq/trinityrnaseq/releases\n\n";
- }
- else {
- print STDERR "-currently using the latest production release of Trinity.\n\n";
- }
- }
- else {
- print STDERR "-ERROR: couldn't parse latest version tag info from github: $content\n\n";
- }
- }
-
- return;
-}
-
-
-####
-sub run_ANANAS {
- my ($read_filenames, $base_out_dir) = @_;
-
- ## Create Ananas command set
- my $ananas_cmds_file = "ananas.cmds";
- my $ananas_cmds_checkpoint = "$ananas_cmds_file.ok";
-
- my $ananas_SS = "";
- my $ananas_dir = "na";
- if ($SS_lib_type) {
- $ananas_SS = " -strand 1 ";
- if ($PAIRED_MODE) {
- $ananas_dir = "ff";
- }
- }
- elsif ($PAIRED_MODE) {
- $ananas_dir = "fr";
- }
-
- unless (-e $ananas_cmds_checkpoint) {
- open (my $fh, $read_filenames) or die "Error, cannot open file $read_filenames";
- open (my $ofh, ">$ananas_cmds_file") or die "Error, cannot write to $ananas_cmds_file";
- while (<$fh>) {
- chomp;
- my $reads_file = $_;
-
- my $ananas_cmd = "$ANANAS_DIR/Ananas -i $reads_file -o $reads_file.out_dir -dir $ananas_dir $ananas_SS";
- print $ofh "$ananas_cmd\n";
- }
- close $fh;
- close $ofh;
-
- &process_cmd("touch $ananas_cmds_checkpoint");
- }
-
- if ($NO_DISTRIBUTED_TRINITY_EXEC) {
- print STDERR "\n\n###################################################################\n"
- . "## Stopping here due to --no_distributed_trinity_exec in effect ##\n"
- . "###################################################################\n\n";
- exit(0);
- }
-
-
- &run_partitioned_cmds($ananas_cmds_file);
-
-
- ## capture all outputs into a single output file.
-
- my $cmd = "find $base_out_dir -name \"*final.fa\" | $UTILDIR/support_scripts/partitioned_trinity_aggregator.pl ANANAS > Ananas.fasta.tmp";
- &process_cmd($cmd);
-
- rename("Ananas.fasta.tmp", "Ananas.fasta");
-
- print STDERR "Done. See Ananas.fasta \n\n";
-
-
-
- exit(0);
-}
diff --git a/galaxy-plugin/GauravGalaxy/__add_to_PATH_setting.txt b/galaxy-plugin/GauravGalaxy/__add_to_PATH_setting.txt
new file mode 100644
index 0000000..85feb78
--- /dev/null
+++ b/galaxy-plugin/GauravGalaxy/__add_to_PATH_setting.txt
@@ -0,0 +1 @@
+/usr/local/bin
diff --git a/galaxy-plugin/GauravGalaxy/abundance_estimation_to_matrix.xml b/galaxy-plugin/GauravGalaxy/abundance_estimation_to_matrix.xml
new file mode 100644
index 0000000..46ef57e
--- /dev/null
+++ b/galaxy-plugin/GauravGalaxy/abundance_estimation_to_matrix.xml
@@ -0,0 +1,42 @@
+<tool id="abundance_estimation_to_matrix" name="abundance_estimation_to_matrix" version="0.0.1">
+
+ <description>Join RSEM estimates from multiple samples into a single matrix</description>
+ <requirements>
+ <requirement type="package">trinity</requirement>
+ </requirements>
+ <command interpreter="python">
+
+ abundance_estimation_to_matrix_wrapper.py
+ #for $q in $RSEM_samples
+ ${q.file} "${q.column_label}"
+ #end for
+
+ </command>
+ <inputs>
+
+ <repeat name="RSEM_samples" title="RSEM abundance estimates for samples">
+ <param name="file" label="Add file" type="data" format="text"/>
+ <param name="column_label" label="column label" type="text" />
+ </repeat>
+
+ </inputs>
+ <outputs>
+ <data format="text" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="matrix.counts.matrix"/>
+ </outputs>
+ <tests>
+
+
+ <test>
+ <param name="target" value="trinity/Trinity.fasta" />
+ <param name="aligner" value="bowtie" />
+ <param name="paired_or_single" value="single" />
+ <param name="library_type" value="None" />
+ <param name="input" value="trinity/reads.left.fq" />
+ </test>
+
+
+ </tests>
+ <help>
+ .. _Trinity: http://trinityrnaseq.sourceforge.net
+ </help>
+</tool>
diff --git a/galaxy-plugin/abundance_estimation_to_matrix_wrapper.py b/galaxy-plugin/GauravGalaxy/abundance_estimation_to_matrix_wrapper.py
similarity index 95%
copy from galaxy-plugin/abundance_estimation_to_matrix_wrapper.py
copy to galaxy-plugin/GauravGalaxy/abundance_estimation_to_matrix_wrapper.py
index 33df387..e906e3a 100644
--- a/galaxy-plugin/abundance_estimation_to_matrix_wrapper.py
+++ b/galaxy-plugin/GauravGalaxy/abundance_estimation_to_matrix_wrapper.py
@@ -32,7 +32,7 @@ for i in range(1, len(sys.argv), 2):
# run the abundance estimation script
-cmd = os.path.dirname(sys.argv[0]) + "/trinityToolWrapper.py " + " util/abundance_estimates_to_matrix.pl --est_method RSEM --cross_sample_fpkm_norm none " + " ".join(label_list)
+cmd = os.path.dirname(sys.argv[0]) + "/trinityToolWrapper.py " + " util/abundance_estimates_to_matrix.pl --est_method RSEM --cross_sample_fpkm_norm TMM " + " ".join(label_list)
run_command(cmd)
diff --git a/galaxy-plugin/GauravGalaxy/align_and_estimate_abundance.xml b/galaxy-plugin/GauravGalaxy/align_and_estimate_abundance.xml
new file mode 100644
index 0000000..d102646
--- /dev/null
+++ b/galaxy-plugin/GauravGalaxy/align_and_estimate_abundance.xml
@@ -0,0 +1,90 @@
+<tool id="RSEM_abundance_estimation" name="RSEM_abundance_estimation" version="0.0.1">
+
+ <description>run RSEM to estimate transcript abundances</description>
+ <requirements>
+ <requirement type="package">trinity</requirement>
+ </requirements>
+ <command interpreter="python">
+
+ trinityToolWrapper.py util/align_and_estimate_abundance.pl --transcripts $transcripts --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference
+
+ ## Inputs.
+ #if str($inputs.paired_or_single) == "paired":
+ --left $inputs.left_input --right $inputs.right_input
+ #if $inputs.left_input.ext == 'fa':
+ --seqType fa
+ #else:
+ --seqType fq
+ #end if
+ #if str($inputs.library_type) != "None":
+ --SS_lib_type $inputs.library_type
+ #end if
+
+ #else:
+ --single $inputs.input
+ #if str($inputs.input.ext) == 'fa':
+ --seqType fa
+ #else:
+ --seqType fq
+ #end if
+ #if str($inputs.library_type) != "None":
+ --SS_lib_type $inputs.library_type
+ #end if
+ #end if
+
+
+ </command>
+ <inputs>
+ <param format="fasta" name="transcripts" type="data" label="transcripts_fasta" help="Fasta sequences for which reads are aligned." />
+
+ <conditional name="inputs">
+ <param name="paired_or_single" type="select" label="Paired or Single-end data?">
+ <option value="paired">Paired</option>
+ <option value="single">Single</option>
+ </param>
+ <when value="paired">
+ <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
+ <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
+ <param name="library_type" type="select" label="Strand-specific Library Type">
+ <option value="None">None</option>
+ <option value="FR">FR</option>
+ <option value="RF">RF</option>
+ </param>
+
+ </when>
+ <when value="single">
+ <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
+ <param name="library_type" type="select" label="Strand-specific Library Type">
+ <option value="None">None</option>
+ <option value="F">F</option>
+ <option value="R">R</option>
+ </param>
+
+ </when>
+ </conditional>
+
+
+ </inputs>
+ <outputs>
+ <data format="text" name="transcript_counts" label="${tool.name} on ${on_string}: Isoform Counts" from_work_dir="RSEM.isoforms.results"/>
+ <data format="text" name="gene_counts" label="${tool.name} on ${on_string}: Gene counts" from_work_dir="RSEM.genes.results"/>
+
+
+ </outputs>
+ <tests>
+
+
+ <test>
+ <param name="target" value="trinity/Trinity.fasta" />
+ <param name="aligner" value="bowtie" />
+ <param name="paired_or_single" value="single" />
+ <param name="library_type" value="None" />
+ <param name="input" value="trinity/reads.left.fq" />
+ </test>
+
+
+ </tests>
+ <help>
+ .. _Trinity: http://trinityrnaseq.sourceforge.net
+ </help>
+</tool>
diff --git a/galaxy-plugin/GauravGalaxy/alignreads.xml b/galaxy-plugin/GauravGalaxy/alignreads.xml
new file mode 100644
index 0000000..6347a13
--- /dev/null
+++ b/galaxy-plugin/GauravGalaxy/alignreads.xml
@@ -0,0 +1,138 @@
+<tool id="alignreads" name="alignReads" version="0.0.1">
+
+ <description>alignReads: short read alignment tool wrapper</description>
+ <requirements>
+ <requirement type="package">trinity</requirement>
+ </requirements>
+ <command interpreter="python">
+
+ trinityToolWrapper.py util/alignReads.pl --target $target -o alignment --aligner $aligner_selection.aligner
+
+
+ ## Inputs.
+ #if str($inputs.paired_or_single) == "paired":
+ --left $inputs.left_input --right $inputs.right_input
+ #if $inputs.left_input.ext == 'fa':
+ --seqType fa
+ #else:
+ --seqType fq
+ #end if
+ #if str($inputs.library_type) != "None":
+ --SS_lib_type $inputs.library_type
+ #end if
+ --max_dist_between_pairs $inputs.max_dist_between_pairs
+ #else:
+ --single $inputs.input
+ #if str($inputs.input.ext) == 'fa':
+ --seqType fa
+ #else:
+ --seqType fq
+ #end if
+ #if str($inputs.library_type) != "None":
+ --SS_lib_type $inputs.library_type
+ #end if
+ #end if
+
+ ## Additional parameters.
+ ##if str($inputs.use_additional) == "yes":
+ ## -- $inputs.additional_params
+ ##end if
+
+
+ ## direct to output
+ > outCapture.txt
+
+
+ </command>
+ <inputs>
+ <param format="fasta" name="target" type="data" label="target" help="Fasta sequences targeted for short-read alignment" />
+
+ <conditional name="inputs">
+ <param name="paired_or_single" type="select" label="Paired or Single-end data?">
+ <option value="paired">Paired</option>
+ <option value="single">Single</option>
+ </param>
+ <when value="paired">
+ <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
+ <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
+ <param name="library_type" type="select" label="Strand-specific Library Type">
+ <option value="None">None</option>
+ <option value="FR">FR</option>
+ <option value="RF">RF</option>
+ </param>
+ <param name="max_dist_between_pairs" type="integer" value="2000" min="1" label="max_dist_between_pairs" help="Maximum length expected between fragment pairs as aligned to the target, including introns where relevant."/>
+
+
+ </when>
+ <when value="single">
+ <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
+ <param name="library_type" type="select" label="Strand-specific Library Type">
+ <option value="None">None</option>
+ <option value="F">F</option>
+ <option value="R">R</option>
+ </param>
+ </when>
+ </conditional>
+
+ <conditional name="aligner_selection">
+ <param name="aligner" type="select" label="Select alignment tool to run">
+ <option value="bowtie">bowtie</option>
+ <option value="bwa">bwa</option>
+ <option value="blat">blat</option>
+ </param>
+ <when value="blat">
+ <param name="max_intron_length" type="integer" value="10000" min = "1" label="maximum intron length" help="" />
+ <param name="min_percent_identity" type="integer" value="95" min="1" label="minimum percent identity" help="" />
+ </when>
+ <when value="bwa">
+ </when>
+ <when value="bowtie">
+ </when>
+ </conditional>
+
+
+ <!--
+ <conditional name="use_additional_params">
+ <param name="use_additional" type="select" label="Use Additional Params?">
+ <option value="no">No</option>
+ <option value="yes">Yes</option>
+ </param>
+ <when value="no">
+ </when>
+ <when value="yes">
+ <param name="additional_params" type="text" value="" label="Additional command-line parameters to aligner" help="" />
+ </when>
+ </conditional>
+
+ -->
+
+ </inputs>
+ <outputs>
+ <data format="bam" name="coordSortedBam" label="${tool.name} on ${on_string}: COORD-sorted read alignments" from_work_dir="alignment/alignment.coordSorted.bam"/>
+ <data format="bam" name="nameSortedBam" label="${tool.name} on ${on_string}: NAME-sorted read alignments" from_work_dir="alignment/alignment.nameSorted.bam"/>
+
+ <!-- notes: need to retain:
+ -the sample name for the alignment
+ -coordinate-sorted vs. name-sorted bam file
+ -paired vs. unpaired vs. strictly proper pairs (for RSEM)
+ -strand-specific or not
+ -->
+
+ </outputs>
+ <tests>
+
+
+ <test>
+ <param name="target" value="trinity/Trinity.fasta" />
+ <param name="aligner" value="bowtie" />
+ <param name="paired_or_single" value="single" />
+ <param name="library_type" value="None" />
+ <param name="input" value="trinity/reads.left.fq" />
+ </test>
+
+
+ </tests>
+ <help>
+ .. _Trinity: http://trinityrnaseq.sourceforge.net
+ </help>
+</tool>
diff --git a/galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml b/galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml
new file mode 100644
index 0000000..5e3c6d6
--- /dev/null
+++ b/galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml
@@ -0,0 +1,41 @@
+<tool id="Analyze_Diff_Exp" name="Analyze_Differential_Expression" version="0.0.1">
+
+ <description>Analyze differential expression</description>
+ <requirements>
+ <requirement type="package">trinity</requirement>
+ </requirements>
+ <command interpreter="python">
+
+ analyze_diff_exp_wrapper.py $EdgeRTarGz $TMM_Matrix_FPKM $Pvalue $Cvalue
+
+ </command>
+ <inputs>
+ <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="file"/>
+ <param name="TMM_Matrix_FPKM" label="TMM Normalized FPKM matrix" type="data" format="file" />
+ <param name="Pvalue" label="P-value" value="0.05" type="float" />
+ <param name="Cvalue" label="C-value" value="0" type="float" />
+
+ </inputs>
+ <outputs>
+ <data format="data" name="diffExpr_matrix" label="${tool.name} on ${on_string}: Matrix" from_work_dir="diffExpr.matrix"/>
+ <data format="data" name="diffExpr_correlation_matrix" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix" from_work_dir="diffExpr.matrix.log2.sample_cor.dat"/>
+ <data format="data" name="diffExpr_correlation_matrix_pdf" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix_PDF" from_work_dir="diffExpr.matrix.log2.sample_cor_matrix.pdf"/>
+ <data format="data" name="Heatmap" label="${tool.name} on ${on_string}: Heatmap" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
+ </outputs>
+ <tests>
+
+
+ <test>
+ <param name="target" value="trinity/Trinity.fasta" />
+ <param name="aligner" value="bowtie" />
+ <param name="paired_or_single" value="single" />
+ <param name="library_type" value="None" />
+ <param name="input" value="trinity/reads.left.fq" />
+ </test>
+
+
+ </tests>
+ <help>
+ .. _Trinity: http://trinityrnaseq.sourceforge.net
+ </help>
+</tool>
diff --git a/galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml~ b/galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml~
new file mode 100644
index 0000000..a28907f
--- /dev/null
+++ b/galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml~
@@ -0,0 +1,41 @@
+<tool id="Analyze_Diff_Exp" name="Analyze_Differential_Expression" version="0.0.1">
+
+ <description>Analyze differential expression</description>
+ <requirements>
+ <requirement type="package">trinity</requirement>
+ </requirements>
+ <command interpreter="python">
+
+ analyze_diff_exp_wrapper.py $EdgeRTarGz $TMM_Matrix_FPKM $Pvalue $Cvalue
+
+ </command>
+ <inputs>
+ <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="file"/>
+ <param name="TMM_Matrix_FPKM" label="TMM Normalized FPKM matrix" type="data" format="file" />
+ <param name="Pvalue" label="P-value" value="0.05" type="float" />
+ <param name="Cvalue" label="C-value" value="0" type="float" />
+
+ </inputs>
+ <outputs>
+ <data format="data" name="diffExpr_matrix" label="${tool.name} on ${on_string}: Diffexp" from_work_dir="diffExpr.matrix"/>
+ <data format="data" name="diffExpr_correlation_matrix" label="${tool.name} on ${on_string}: Diffexp" from_work_dir="diffExpr.matrix.log2.sample_cor.dat"/>
+ <data format="data" name="diffExpr_correlation_matrix_pdf" label="${tool.name} on ${on_string}: Diffexp" from_work_dir="diffExpr.matrix.log2.sample_cor_matrix.pdf"/>
+ <data format="data" name="Heatmap" label="${tool.name} on ${on_string}: Diffexp" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
+ </outputs>
+ <tests>
+
+
+ <test>
+ <param name="target" value="trinity/Trinity.fasta" />
+ <param name="aligner" value="bowtie" />
+ <param name="paired_or_single" value="single" />
+ <param name="library_type" value="None" />
+ <param name="input" value="trinity/reads.left.fq" />
+ </test>
+
+
+ </tests>
+ <help>
+ .. _Trinity: http://trinityrnaseq.sourceforge.net
+ </help>
+</tool>
diff --git a/galaxy-plugin/GauravGalaxy/analyze_diff_exp_wrapper.py b/galaxy-plugin/GauravGalaxy/analyze_diff_exp_wrapper.py
new file mode 100644
index 0000000..d4d7fae
--- /dev/null
+++ b/galaxy-plugin/GauravGalaxy/analyze_diff_exp_wrapper.py
@@ -0,0 +1,63 @@
+import sys, os, subprocess
+
+TRINITY_BASE_DIR = ""
+if os.environ.has_key('TRINITY_HOME'):
+ TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
+else:
+ sys.stderr.write("You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this");
+ sys.exit()
+
+usage= "usage: " + sys.argv[0] + " " + "edgeR.tar.gz " + "TMM_normalized_FPKM_matrix " + "P-value " + "C-value"
+print sys.argv
+print usage
+print " "
+
+if len(sys.argv)<5:
+ print "Require atleast two parameters"
+else:
+ print "All good- command going ahead"
+print " "
+
+Normalized_Matrix=sys.argv[2]
+Pvalue=sys.argv[3]
+Cvalue=sys.argv[4]
+
+def run_command(cmd):
+ print "The command used: " + cmd
+ pipe= subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE)
+ pipe.wait()
+ ret= pipe.returncode
+ if ret:
+ print "command died: " + str(ret)
+ print pipe.stderr.readlines()
+ sys.exit(1)
+ else:
+ return
+print " "
+
+Final_tar_gz= "edgeR.tar.gz"
+run_command("cp "+ sys.argv[1] + " " + "Final_tar_gz")
+run_command("tar -xvf " + "Final_tar_gz")
+run_command("mv " + "edgeR_results" + "/* ." )
+
+# run the analyze command
+cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/analyze_diff_expr.pl "+ "--matrix " + Normalized_Matrix + " -P " + Pvalue + " -C " + Cvalue
+run_command(cmd)
+
+origMatrixName= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix"
+# diffExpr.P0.001_C2.0.matrix
+run_command("mv " + origMatrixName + " diffExpr.matrix")
+
+SampleCorName= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.sample_cor.dat"
+# diffExpr.P0.001_C2.0.matrix.log2.sample_cor.dat
+run_command("mv " + SampleCorName + " diffExpr.matrix.log2.sample_cor.dat")
+
+CorMatrix= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.sample_cor_matrix.pdf"
+# diffExpr.P0.001_C2.0.matrix.log2.sample_cor_matrix.pdf
+run_command("mv " + CorMatrix + " diffExpr.matrix.log2.sample_cor_matrix.pdf")
+
+Heatmap= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.centered.genes_vs_samples_heatmap.pdf"
+#diffExpr.P0.001_C2.0.matrix.log2.centered.genes_vs_samples_heatmap.pdf
+run_command("mv " + Heatmap + " diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf")
+
+sys.exit(0)
diff --git a/galaxy-plugin/GauravGalaxy/bash_command_executer.py b/galaxy-plugin/GauravGalaxy/bash_command_executer.py
new file mode 100755
index 0000000..c6ab738
--- /dev/null
+++ b/galaxy-plugin/GauravGalaxy/bash_command_executer.py
@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+
+
+import sys, subprocess, os
+
+def stop_err( msg ):
+ sys.stderr.write( "%s\n" % msg )
+ sys.exit()
+
+def __main__():
+ # Get command-line arguments
+ args = sys.argv
+ # Remove name of calling program, i.e. ./stderr_wrapper.py
+ args.pop(0)
+
+ # If there are no arguments left, we're done
+ if len(args) == 0:
+ return
+
+ # If one needs to silence stdout
+ #args.append( ">" )
+ #args.append( "/dev/null" )
+
+ cmdline = " ".join(args)
+
+
+ try:
+ # Run program
+ err_capture = open("stderr.txt", 'w')
+ proc = subprocess.Popen( args=cmdline, shell=True, stderr=err_capture, stdout=sys.stdout )
+ returncode = proc.wait()
+ err_capture.close()
+
+
+ if returncode != 0:
+ raise Exception
+
+ except Exception:
+ # Running Grinder failed: write error message to stderr
+ err_text = open("stderr.txt").readlines()
+ stop_err( "ERROR:\n" + "\n".join(err_text))
+
+
+if __name__ == "__main__": __main__()
diff --git a/galaxy-plugin/GauravGalaxy/cat.xml b/galaxy-plugin/GauravGalaxy/cat.xml
new file mode 100644
index 0000000..9aeaa50
--- /dev/null
+++ b/galaxy-plugin/GauravGalaxy/cat.xml
@@ -0,0 +1,41 @@
+<tool id="catbash" name="Concatenate datasets">
+ <description>tail-to-head</description>
+ <command interpreter="python">
+ bash_command_executer.py cat
+ $input1
+ #for $q in $queries
+ ${q.input2}
+ #end for
+ > $out_file1
+ </command>
+ <inputs>
+ <param name="input1" type="data" label="Concatenate Dataset"/>
+ <repeat name="queries" title="Dataset">
+ <param name="input2" type="data" label="Select" />
+ </repeat>
+ </inputs>
+ <outputs>
+ <data name="out_file1" format="input" metadata_source="input1"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="input1" value="1.bed"/>
+ <param name="input2" value="2.bed"/>
+ <output name="out_file1" file="cat_wrapper_out1.bed"/>
+ </test>
+ <!--TODO: if possible, enhance the underlying test code to handle this test
+ the problem is multiple params with the same name "input2"
+ <test>
+ <param name="input1" value="1.bed"/>
+ <param name="input2" value="2.bed"/>
+ <param name="input2" value="3.bed"/>
+ <output name="out_file1" file="cat_wrapper_out2.bed"/>
+ </test>
+ -->
+ </tests>
+ <help>
+
+ no help
+
+ </help>
+</tool>
diff --git a/galaxy-plugin/EdgeR_differentialExpression.xml b/galaxy-plugin/GauravGalaxy/diffExpress_edgeR.xml
similarity index 85%
copy from galaxy-plugin/EdgeR_differentialExpression.xml
copy to galaxy-plugin/GauravGalaxy/diffExpress_edgeR.xml
index 774a3f4..1a5b186 100644
--- a/galaxy-plugin/EdgeR_differentialExpression.xml
+++ b/galaxy-plugin/GauravGalaxy/diffExpress_edgeR.xml
@@ -1,14 +1,14 @@
-<tool id="EdgeR_differentialExpression" name="EdgeR_differentialExpression" version="0.0.1">
+<tool id="diffExpress_edgeR" name="diffExpress_edgeR" version="0.0.1">
<description>Identify Differentially Expressed Transcripts Using EdgeR</description>
<requirements>
- <requirement type="package">trinity</requirement>
+ <requirement type="package">edgeR</requirement>
</requirements>
<command interpreter="python">
- trinityToolWrapper.py Analysis/DifferentialExpression/run_DE_analysis.pl
+ trinityToolWrapper.py Analysis/DifferentialExpression/run_EdgeR.pl
--matrix $counts_matrix
- --method edgeR
+ --transcripts $transcripts_fasta_file
--output edgeR_results
--dispersion $dispersion
diff --git a/galaxy-plugin/GauravGalaxy/transcriptsToOrfs.xml b/galaxy-plugin/GauravGalaxy/transcriptsToOrfs.xml
new file mode 100644
index 0000000..2afb8f6
--- /dev/null
+++ b/galaxy-plugin/GauravGalaxy/transcriptsToOrfs.xml
@@ -0,0 +1,53 @@
+<tool id="transcriptsToOrfs" name="transcriptsToOrfs" version="0.0.1">
+
+ <description>Trinity Transcripts to Candidate Peptides</description>
+ <requirements>
+ <requirement type="package">trinity</requirement>
+ </requirements>
+ <command interpreter="python">
+ trinityToolWrapper.py Analysis/Coding/transcripts_to_best_scoring_ORFs.pl
+
+ -t $transcripts
+ -m $min_prot_length
+ --CPU $CPU
+ --search_pfam "${ filter( lambda x: str( x[0] ) == str( $pfam_db ), $__app__.tool_data_tables[ 'pfam_databases' ].get_fields() )[0][-1] }"
+
+ #if str($strand_specificity) == 'SS':
+ -S
+ #end if
+
+ ## direct to output
+ > output
+
+ </command>
+ <inputs>
+
+ <param format="fasta" name="transcripts" type="data" label="Transcripts sequences in fastA format" help="" />
+
+ <param name="min_prot_length" type="integer" label="Minimum peptide length (in amino acids)" value="100" min="50" help="" />
+
+ <param name="strand_specificity" type="select" label="Strand specificity type">
+ <option value="DS">NOT strand specific, examine both strands</option>
+ <option value="SS">Strand specific, examine only top strand</option>
+ </param>
+
+ <param name="pfam_db" type="select" label="Pfam database">
+ <options from_data_table="pfam_databases" />
+ </param>
+
+ <param name="CPU" type="integer" value="2" min="1" label="CPU" help="Number of CPUs to use by hmmscan" />
+
+ </inputs>
+ <outputs>
+ <data format="txt" name="trinity_pep_pfam" label="${tool.name} on ${on_string}: Pfam matches to Candidate Peptide Sequences" from_work_dir="longest_orfs.pep.pfam.dat"/>
+ <data format="fasta" name="trinity_pep_seqs" label="${tool.name} on ${on_string}: Candidate Peptide Sequences" from_work_dir="best_candidates.eclipsed_orfs_removed.pep"/>
+ <data format="bed" name="trinity_pep_coords" label = "${tool.name} on ${on_string} Candidate Peptide Coordinates" from_work_dir="best_candidates.eclipsed_orfs_removed.bed" />
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+ Trinity is a de novo transcript assembler that uses RNA-seq data as input. This tool runs all Trinity_ commands--Inchworm, Chrysalis, and Butterfly--in a single pass.
+
+ .. _Trinity: http://trinityrnaseq.sourceforge.net
+ </help>
+</tool>
diff --git a/galaxy-plugin/trinityToolWrapper.py b/galaxy-plugin/GauravGalaxy/trinityToolWrapper.py
similarity index 92%
copy from galaxy-plugin/trinityToolWrapper.py
copy to galaxy-plugin/GauravGalaxy/trinityToolWrapper.py
index 5d80fbf..957ae12 100755
--- a/galaxy-plugin/trinityToolWrapper.py
+++ b/galaxy-plugin/GauravGalaxy/trinityToolWrapper.py
@@ -17,9 +17,8 @@ TRINITY_BASE_DIR = ""
if os.environ.has_key('TRINITY_HOME'):
TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
else:
- sys.write("You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this");
sys.stderr.write("You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this");
- sys.exit(1)
+ sys.exit()
diff --git a/galaxy-plugin/trinityrnaseq.xml b/galaxy-plugin/GauravGalaxy/trinityrnaseq.xml
similarity index 98%
copy from galaxy-plugin/trinityrnaseq.xml
copy to galaxy-plugin/GauravGalaxy/trinityrnaseq.xml
index b57a9ab..621ff5e 100644
--- a/galaxy-plugin/trinityrnaseq.xml
+++ b/galaxy-plugin/GauravGalaxy/trinityrnaseq.xml
@@ -6,12 +6,12 @@
<requirement type="package">trinity</requirement>
</requirements>
<command interpreter="python">
- trinityToolWrapper.py Trinity --JM $JM --CPU $CPU
+ trinityToolWrapper.py Trinity --max_memory $JM --CPU $CPU
## Inputs.
#if str($inputs.paired_or_single) == "paired":
--left $inputs.left_input --right $inputs.right_input
- #if $inputs.left_input.ext == 'fa':
+ #if $inputs.left_input.ext == 'fa':
--seqType fa
#else:
--seqType fq
diff --git a/galaxy-plugin/trinityrnaseq.xml b/galaxy-plugin/GauravGalaxy/trinityrnaseq.xml.Graham_version_022014
similarity index 94%
copy from galaxy-plugin/trinityrnaseq.xml
copy to galaxy-plugin/GauravGalaxy/trinityrnaseq.xml.Graham_version_022014
index b57a9ab..d92bb13 100644
--- a/galaxy-plugin/trinityrnaseq.xml
+++ b/galaxy-plugin/GauravGalaxy/trinityrnaseq.xml.Graham_version_022014
@@ -5,8 +5,8 @@
<requirements>
<requirement type="package">trinity</requirement>
</requirements>
- <command interpreter="python">
- trinityToolWrapper.py Trinity --JM $JM --CPU $CPU
+ <command>
+ Trinity.pl --JM $JM --CPU $CPU
## Inputs.
#if str($inputs.paired_or_single) == "paired":
@@ -34,15 +34,15 @@
## Additional parameters.
#if str($additional_params.use_additional) == "yes":
- --min_kmer_cov $inputs.min_kmer_cov --max_reads_per_graph $inputs.max_reads_per_graph --bflyHeapSpaceMax $input.bflyHeapSpaceMax
- #if $inputs.bfly_opts != 'None':
- --bfly_opts " $inputs.bfly_opts "
+ --min_kmer_cov $additional_params.min_kmer_cov --max_reads_per_graph $additional_params.max_reads_per_graph --bflyHeapSpaceMax $additional_params.bflyHeapSpaceMax
+ #if $additional_params.bfly_opts != 'None':
+ --bfly_opts " $additional_params.bfly_opts "
#end if
#end if
## direct to output
- > $trinity_log
+ > $trinity_log 2>&1
</command>
<inputs>
diff --git a/galaxy-plugin/GauravGalaxy/trinityrnaseq_norm.xml b/galaxy-plugin/GauravGalaxy/trinityrnaseq_norm.xml
new file mode 100644
index 0000000..8e13024
--- /dev/null
+++ b/galaxy-plugin/GauravGalaxy/trinityrnaseq_norm.xml
@@ -0,0 +1,102 @@
+<tool id="trinityrnaseq_norm" name="Trinity read normalization" version="0.0.1">
+<!--tool id="trinityrnaseq" name="Trinity" version="0.0.1" -->
+
+ <!-- Written by Jeremy Goecks, modified by Josh Bowden for normalization proceedure, now maintained here by bhaas -->
+ <description>Pre-process RNA-seq data to reduce coverage of highly covered areas</description>
+ <requirements>
+ <requirement type="package">trinity</requirement>
+ </requirements>
+ <command interpreter="perl">
+ trinityToolWrapper.py util/normalize_by_kmer_coverage.pl --JM $JM --max_cov $MAXCOV
+
+ ## Inputs.
+ #if str($inputs.paired_or_single) == "paired":
+ --left $inputs.left_input --right $inputs.right_input
+ --outleft $output_left --outright $output_right
+ #if $inputs.left_input.ext == 'fa':
+ --seqType fa
+ #else:
+ --seqType fq
+ #end if
+ #if str($inputs.library_type) != "None":
+ --SS_lib_type $inputs.library_type
+ #end if
+
+ #else:
+ --single $inputs.input
+ #if str($inputs.input.ext) == 'fa':
+ --seqType fa
+ #else:
+ --seqType fq
+ #end if
+ #if str($inputs.library_type) != "None":
+ --SS_lib_type $inputs.library_type
+ #end if
+ --outputsingle $output_single
+ #end if
+ --galaxy
+
+ ## direct to output
+ > $trinity_coverage_normalization_log
+
+ </command>
+ <inputs>
+ <param name="JM" type="select" label="JM" help="Amount of memory to allocate to Jellyfish for Kmer catalog construction">
+ <option value="1G">1G</option>
+ <option value="10G">10G</option>
+ <option value="20G">20G</option>
+ <option value="50G">50G</option>
+ <option value="100G">100G</option>
+ </param>
+
+ <param name="MAXCOV" type="select" label="MAXCOV" help="Read coverage in terms of maximum covarge to keep">
+ <option value="30">30</option>
+ <option value="40">40</option>
+ <option value="50">50</option>
+ <option value="60">60</option>
+ <option value="70">70</option>
+ <option value="100">100</option>
+ </param>
+
+ <conditional name="inputs">
+ <param name="paired_or_single" type="select" label="Paired or Single-end data?">
+ <option value="paired">Paired</option>
+ <option value="single">Single</option>
+ </param>
+ <when value="paired">
+ <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
+ <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
+ <param name="library_type" type="select" label="Strand-specific Library Type">
+ <option value="None">None</option>
+ <option value="FR">FR</option>
+ <option value="RF">RF</option>
+ </param>
+ </when>
+ <when value="single">
+ <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
+ <param name="library_type" type="select" label="Strand-specific Library Type">
+ <option value="None">None</option>
+ <option value="F">F</option>
+ <option value="R">R</option>
+ </param>
+
+ </when>
+ </conditional>
+ </inputs>
+
+ <outputs>
+ <!-- I have not found a way to do condional outputs so all potential output files are specified and some will be empty -->
+ <data format="txt" name="trinity_coverage_normalization_log" label="${tool.name} on ${on_string}: log" />
+ <data format="fasta,fastq" name="output_left" label="${tool.name} on ${on_string}: Normalized left data" />
+ <data format="fasta,fastq" name="output_right" label="${tool.name} on ${on_string}: Normalized right data" />
+ <data format="fasta,fastq" name="output_single" label="${tool.name} on ${on_string}: Normalized data" />
+ <!-- data format="fastq" name="normalized right dataset" label="${tool.name} on ${on_string}: Normalized right data " from_work_dir="${inputs.right_input}.${inputs.input.ext}.normalized_K25_C${MAXCOV}_pctSD100.fq"/-->
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+ Runs script $TRINITY_HOME/util/normalize_by_kmer_coverage.pl which reduces data sizes with minimal impact on recovered transcripts when used by Trinity.pl.
+
+ .. _Trinity: http://trinityrnaseq.sourceforge.net
+ </help>
+</tool>
diff --git a/Trinity b/galaxy-plugin/Trinity
similarity index 69%
copy from Trinity
copy to galaxy-plugin/Trinity
index 73f8264..be72d56 100755
--- a/Trinity
+++ b/galaxy-plugin/Trinity
@@ -12,13 +12,7 @@ use Time::localtime;
use Cwd;
use Carp;
use COMMON;
-use Getopt::Long qw(:config posix_default no_ignore_case pass_through);
-use Pipeliner;
-use Fasta_reader;
-
-
-my $VERSION = "v2.0.6";
-
+use Getopt::Long qw(:config no_ignore_case pass_through);
BEGIN {
@@ -26,29 +20,15 @@ BEGIN {
}
-use HPC::GridRunner;
+use HTC::GridRunner;
open (STDERR, ">&STDOUT"); ## capturing stderr and stdout in a single stdout stream
-#directory defnintions
-my $ROOTDIR = "$FindBin::RealBin";
-my $UTILDIR = "$ROOTDIR/util";
-my $MISCDIR = "$UTILDIR/misc";
-my $INCHWORM_DIR = "$ROOTDIR/Inchworm/bin/";
-my $CHRYSALIS_DIR = "$ROOTDIR/Chrysalis";
-my $BUTTERFLY_DIR = "$ROOTDIR/Butterfly";
-my $JELLYFISH_DIR = "$ROOTDIR/trinity-plugins/jellyfish";
-my $FASTOOL_DIR = "$ROOTDIR/trinity-plugins/fastool";
-my $COLLECTL_DIR = "$ROOTDIR/trinity-plugins/collectl/bin";
-my $COREUTILS_DIR = "$ROOTDIR/trinity-plugins/coreutils/bin";
-my $PARAFLY = "$ROOTDIR/trinity-plugins/parafly/bin/ParaFly";
-my $TRIMMOMATIC = "$ROOTDIR/trinity-plugins/Trimmomatic/trimmomatic.jar";
-my $TRIMMOMATIC_DIR = "$ROOTDIR/trinity-plugins/Trimmomatic";
-
-
# Site specific setup
+my $CPU_MAX = 64; # set higher at your own risk. Definitely don't set it higher than the number of cores available on your machine.
+
my $KMER_SIZE = 25;
my $MAX_KMER_SIZE = 32;
@@ -88,8 +68,10 @@ my $path_reinforcement_distance;
my $PE_path_reinforcement_distance = 75;
my $SE_path_reinforcement_distance = 25;
+my $NO_RUN_BUTTERFLY_FLAG = 0;
+my $RERUN_BUTTERFLY_FLAG = 0;
my $bfly_opts = "";
-my $bflyHeapSpaceMax = "4G";
+my $bflyHeapSpaceMax = "10G";
my $bflyHeapSpaceInit = "1G";
my $BFLY_JAR = "";
@@ -109,8 +91,6 @@ my $inchworm_cpu = 6;
my $min_percent_read_iworm_kmers = -1; # experimental, off
my $CPU = 2;
-my $np = 1;
-my $mpiexec = "mpiexec";
my $bflyCPU;
my $bflyCalculateCPU = 0;
my $bflyGCThreads = 2;
@@ -120,6 +100,7 @@ my $long_reads = "";
## ADVANCED OPTIONS:
+my $no_meryl_flag = 0;
## Chrysalis opts
my $min_glue = 2;
@@ -128,16 +109,16 @@ my $glue_factor = 0.05;
my $max_reads_per_graph = 200000;
my $max_reads_per_loop = 10000000;
my $min_pct_read_mapping = 0;
+my $NO_RUN_QUANTIFYGRAPH_FLAG = 0;
+my $NO_RUN_CHRYSALIS_FLAG = 0;
my $chrysalis_output_dir = "chrysalis";
my $component_directory;
-my $NO_RUN_CHRYSALIS_FLAG = 0;
-
-my $NO_DISTRIBUTED_TRINITY_EXEC = 0;
my $help_flag;
my $advanced_help_flag;
my $SHOW_CITATION_FLAG = 0;
+my $VERSION = "trinityrnaseq_r20140717";
my $show_version_flag = 0;
## Kmer methods
@@ -184,23 +165,24 @@ my $run_as_paired_flag = 0; ## in case we have paired reads in single fasta fil
my $weldmer_size = 48;
my $FORCE_INCHWORM_KMER_METHOD = 0;
+my $TRIPLET_LOCK = 1;
+my $EXTENDED_TRIPLET_LOCK = 0;
+
+
+
my $PARALLEL_IWORM_FLAG = 1;
my $NO_PARALLEL_IWORM = 0;
## Quality trimming params
my $RUN_TRIMMOMATIC_FLAG = 0;
-my $trimmomatic_quality_trim_params = "ILLUMINACLIP:$TRIMMOMATIC_DIR/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25";
+my $trimmomatic_quality_trim_params = "LEADING:5 TRAILING:5 MINLEN:36";
## Normalize reads
my $NORMALIZE_READS_FLAG = 0;
my $normalize_max_read_cov = 50;
my $NORMALIZE_BY_READ_SET = 0;
-
-my $grid_node_CPU = 1;
-my $grid_node_max_memory = "1G";
-
# Note: For the Trinity logo below the backslashes are quoted in order to keep
# them from quoting the character than follows them. "\\" keeps "\ " from occuring.
@@ -223,15 +205,15 @@ my $basic_usage = qq^
#
# --seqType <string> :type of reads: ( $allowed{seqType} )
#
-# --max_memory <string> :suggested max memory to use by Trinity where limiting can be enabled. (jellyfish, sorting, etc)
-# provied in Gb of RAM, ie. '--max_memory 10G'
+# --JM <string> :(Jellyfish Memory) number of GB of system memory to use for
+# k-mer counting by jellyfish (eg. 10G) *include the 'G' char
#
# If paired reads:
-# --left <string> :left reads, one or more file names (separated by commas, no spaces)
-# --right <string> :right reads, one or more file names (separated by commas, no spaces)
+# --left <string> :left reads, one or more (separated by space)
+# --right <string> :right reads, one or more (separated by space)
#
# Or, if unpaired reads:
-# --single <string> :single reads, one or more file names, comma-delimited (note, if single file contains pairs, can use flag: --run_as_paired )
+# --single <string> :single reads, one or more (note, if single file contains pairs, can use flag: --run_as_paired )
#
####################################
## Misc: #########################
@@ -245,10 +227,7 @@ my $basic_usage = qq^
# --min_contig_length <int> :minimum assembled contig length to report
# (def=$min_contig_length)
#
-# --long_reads <string> :fasta file containing error-corrected or circular consensus (CCS) pac bio reads
-#
-# --genome_guided_bam <string> :genome guided mode, provide path to coordinate-sorted bam file.
-# (see genome-guided param section under --show_full_usage_info)
+# --genome <string> :genome guided mode, provide path to genome fasta file (see genome-guided param section under --show_full_usage_info)
#
# --jaccard_clip :option, set if you have paired reads and
# you expect high gene density with UTR
@@ -266,34 +245,26 @@ my $basic_usage = qq^
# --normalize_reads :run in silico normalization of reads. Defaults to max. read coverage of $normalize_max_read_cov.
# see '--normalize_max_read_cov' under full usage info for tailored settings.
#
-# --no_distributed_trinity_exec :do not run Trinity phase 2 (assembly of partitioned reads), and stop after generating command list.
-#
#
# --output <string> :name of directory for output (will be
# created if it doesn't already exist)
-# default( your current working directory: "$output_directory"
-# note: must include 'trinity' in the name as a safety precaution! )
+# default( your current working directory: "$output_directory" )
#
# --full_cleanup :only retain the Trinity fasta file, rename as \${output_dir}.Trinity.fasta
#
# --cite :show the Trinity literature citation
#
-# --verbose :provide additional job status info during the run.
-#
# --version :reports Trinity version ($VERSION) and exits.
#
# --show_full_usage_info :show the many many more options available for running Trinity (expert usage).
^;
my $full_usage = qq^
-#
-# --KMER_SIZE <int> :kmer length to use (default: 25) max=32
-#
# --prep :Only prepare files (high I/O usage) and stop before kmer counting.
#
-# --no_cleanup :retain all intermediate input files.
+# --full_cleanup_ET :only retains assembly fasta file, error tolerant (ET)
#
-# --no_version_check :dont run a network check to determine if software updates are available.
+# --no_cleanup :retain all intermediate input files.
#
####################################################
# Inchworm and K-mer counting-related options: #####
@@ -302,7 +273,7 @@ my $full_usage = qq^
# Inchworm (default: $min_kmer_cov)
# --inchworm_cpu <int> :number of CPUs to use for Inchworm, default is min(6, --CPU option)
#
-# --no_run_inchworm :stop after running jellyfish, before inchworm. (phase 1, read clustering only)
+# --no_run_inchworm :stop after running jellyfish, before inchworm.
#
###################################
# Chrysalis-related options: ######
@@ -311,10 +282,18 @@ my $full_usage = qq^
# a single graph (default: $max_reads_per_graph)
# --min_glue <int> :min number of reads needed to glue two inchworm contigs
# together. (default: $min_glue)
+# --no_run_chrysalis :stop Trinity after Inchworm and before
+# running Chrysalis
+# --no_run_quantifygraph :stop Trinity just before running the
+# parallel QuantifyGraph computes, to
+# leverage a compute farm and massively
+# parallel execution..
#
-# --no_bowtie :dont run bowtie to use pair info in chrysalis clustering.
+# --chrysalis_output <string> :name of directory for chrysalis output (will be
+# created if it doesn't already exist)
+# default( "$chrysalis_output_dir" )
#
-# --no_run_chrysalis :stop after running inchworm, before chrysalis. (phase 1, read clustering only)
+# --no_bowtie :dont run bowtie to use pair info in chrysalis clustering.
#
#####################################
### Butterfly-related options: ####
@@ -344,10 +323,19 @@ my $full_usage = qq^
# path (default: PE: $PE_path_reinforcement_distance, SE: $SE_path_reinforcement_distance)
# Set to 1 for the most lenient path extension requirements.
#
+# --no_triplet_lock : (increase stringency of regular butterfly reconstruction (default: on))
+# lock triplet-supported nodes: node 'c' having read path 'A-B-C' disables 'Z-B-C' if no such read support exists.
+#
+# --extended_lock : (further increase the stringency of regular butterfy reconstruction)
+# extend the triplet lock to include longer range read path information.
+# ex. in extending path 'A-B-Z' to 'A-B-Z-D', we only find read support for 'A-B-C-D', that 'A-B-Z' extension to 'D' will be blocked.
+#
#
# /////////////////////////////////////////
# Butterfly transcript reduction settings:
#
+# --NO_EM_REDUCE : do not run the final EM step to rank transcripts and remove lower-ranking entries that lack unique read conent.
+#
# --no_path_merging : all final transcript candidates are output (including SNP variations, however, some SNPs may be unphased)
#
# By default, alternative transcript candidates are merged (in reality, discarded) if they are found to be too similar, according to the following logic:
@@ -356,7 +344,7 @@ my $full_usage = qq^
#
# with parameters as:
#
-# --min_per_id_same_path <int> default: 98 min percent identity for two paths to be merged into single paths
+# --min_per_id_same_path <int> default: 95 min percent identity for two paths to be merged into single paths
# --max_diffs_same_path <int> default: 2 max allowed differences encountered between path sequences to combine them
# --max_internal_gap_same_path <int> default: 10 maximum number of internal consecutive gap characters allowed for paths to be merged into single paths.
#
@@ -379,11 +367,17 @@ my $full_usage = qq^
# number of CPUs; e.g., $CPU)
# --bflyCalculateCPU :Calculate CPUs based on 80% of max_memory
# divided by maxbflyHeapSpaceMax
+# --no_run_butterfly :stops after the Chrysalis stage. You'll
+# need to run the Butterfly computes
+# separately, such as on a computing grid.
+# Then, concatenate all the Butterfly assemblies by running:
+# 'find trinity_out_dir/ -name "\*allProbPaths.fasta" \
+# -exec cat {} + > trinity_out_dir/Trinity.fasta'
#
# --bfly_jar <string> : /path/to/Butterfly.jar, otherwise default
# Trinity-installed version is used.
#
-#
+
#
################################################################################
#### Quality Trimming Options ####
@@ -405,45 +399,54 @@ my $full_usage = qq^
#
# --genome_guided_max_intron <int> :maximum allowed intron length (also maximum fragment span on genome)
#
+# --genome_guided_use_bam <string> :use a provided coord-sorted bam file as starting point. Otherwise, use gmap to align to the genome.
+#
# * optional:
#
# --genome_guided_min_coverage <int> :minimum read coverage for identifying and expressed region of the genome. (default: 1)
#
# --genome_guided_min_reads_per_partition <int> :default min of 10 reads per partition
#
+# --genome_guided_CPU <int> : number of threads for the individual genome-guided Trinity commands to use. (defaults to --CPU setting)
+#
+# --genome_guided_sort_buffer <string> : amount of RAM to dedicate to the initial prep of genome-guided read partitioning (defaults to --JM)
+#
+#
+# --GMAP_CPU <int> :defaults to --CPU setting.
+#
+# --genome_guided_just_prep : process stops after prepping the reads for assembly (prior to submitting to a computing grid for parallel execution)
#
#################################
# Grid-computing options: #######
#
-# --grid_conf <string> :configuration file for supported compute farms
+# --grid_conf_file <string> :configuration file for supported compute farms
# ex. TRINITY_HOME/htc_conf/BroadInst_LSF.conf
# currently supported computing gris: LSF, SGE
#
-# --grid_node_CPU <int> number of threads for each parallel process to leverage. (default: $grid_node_CPU)
-#
-# --grid_node_max_memory <string> max memory targeted for each grid node. (default: $grid_node_max_memory)
-#
#
^;
-my $usage_synopsis = qq^#
-#
+my $usage_synopsis = qq^
###############################################################################
#
# *Note, a typical Trinity command might be:
#
-# Trinity --seqType fq --max_memory 50G --left reads_1.fq --right reads_2.fq --CPU 6
+# Trinity --seqType fq --JM 100G --left reads_1.fq --right reads_2.fq --CPU 6
#
#
# and for Genome-guided Trinity:
#
-# Trinity --genome_guided_bam rnaseq_alignments.csorted.bam --max_memory 50G\
-# --genome_guided_max_intron 10000 --CPU 6
+# Trinity --genome genome.fasta \
+# --genome_guided_max_intron 10000 --genome_guided_sort_buffer 10G \
+# --genome_guided_CPU 4 \
+# --seqType fq --JM 2G --left reads_1.fq --right reads_2.fq --CPU 6
+# (and optionally provide your own bam file: --genome_guided_use_bam rnaseq_alignments.csorted.bam
+# or Trinity will run GSNAP to generate one. )
+#
#
# see: $FindBin::RealBin/sample_data/test_Trinity_Assembly/
# for sample data and 'runMe.sh' for example Trinity execution
-#
-# For more details, visit: http://trinityrnaseq.github.io
+# For more details, visit: http://trinityrnaseq.sf.net
#
###############################################################################
@@ -462,8 +465,8 @@ my $advanced_usage = <<_ADVANCEDUSAGE_;
#
# --INCHWORM_CUSTOM_PARAMS <string> :additional parameters to be passed on to Inchworm
# --FORCE_INCHWORM_KMER_METHOD :uses inchworm built-in kmer cataloger instead of jellyfish (not recommended)
+# --long_reads <string> :fasta file containing corrected pac bio reads
# --NO_PARALLEL_IWORM : turn off parallel iworm assembly
-# --iworm_opts <string> : options for inchworm
#
#
# Chyrsalis-related options:
@@ -486,7 +489,8 @@ my $advanced_usage = <<_ADVANCEDUSAGE_;
# Other:
# --monitoring :use collectl to monitor all steps of Trinity
#
-# --bypass_java_version_check : skip check for required java version 1.7
+# --compdir|component_directory : use a temporary or local directory for Components_bin
+#
#
@@ -495,6 +499,17 @@ _ADVANCEDUSAGE_
;
+my $ROOTDIR = "$FindBin::RealBin";
+my $UTILDIR = "$ROOTDIR/util";
+my $INCHWORM_DIR = "$ROOTDIR/Inchworm";
+my $CHRYSALIS_DIR = "$ROOTDIR/Chrysalis";
+my $BUTTERFLY_DIR = "$ROOTDIR/Butterfly";
+my $JELLYFISH_DIR = "$ROOTDIR/trinity-plugins/jellyfish";
+my $FASTOOL_DIR = "$ROOTDIR/trinity-plugins/fastool";
+my $COLLECTL_DIR = "$ROOTDIR/trinity-plugins/collectl/bin";
+my $COREUTILS_DIR = "$ROOTDIR/trinity-plugins/coreutils/bin";
+my $PARAFLY = "$ROOTDIR/trinity-plugins/parafly/bin/ParaFly";
+my $TRIMMOMATIC = "$ROOTDIR/trinity-plugins/Trimmomatic/trimmomatic.jar";
my $usage = $basic_usage . $usage_synopsis;
@@ -513,6 +528,7 @@ my $sort_exec = &COMMON::get_sort_exec($CPU);
my $NO_FASTOOL = 0;
my $NO_CLEANUP = 0;
my $FULL_CLEANUP = 0;
+my $FULL_CLEANUP_ERROR_TOLERANT = 0; ## NOTE, THIS IS AN AWFUL IDEA... //FIXME: add propper error-handling mechanisms
my $NO_BOWTIE = 0;
@@ -529,41 +545,27 @@ my $CUFFFLY_MODE = 0;
my $full_usage_info_flag;
my $NO_TRIPLET_LOCK;
+my $NO_EM_REDUCE;
## Genome-guided params:
+my $genome_fasta_file;
my $genome_guided_max_intron;
-my $genome_guided_bam;
+my $genome_guided_use_bam;
my $genome_guided_min_coverage = 1;
my $genome_guided_min_reads_per_partition = 10;
+my $GMAP_CPU;
+my $genome_guided_CPU;
+my $genome_guided_sort_buffer;
my $genome_guided_just_prep_flag = 0;
-## trinity complete flag
-my $TRINITY_COMPLETE_FLAG = 0;
-
my @ORIG_ARGS = @ARGV;
-my $CHRYSALIS_DEBUG_WELD_ALL = 0;
-my $iworm_opts = "";
-
-my $bypass_java_version_check = 0;
-
-my $SEE = 0;
-
-my $ANANAS_DIR = "";
-
-my $NO_VERSION_CHECK = 0;
-
-
&GetOptions(
'h|help' => \$help_flag,
'advanced_help' => \$advanced_help_flag,
'show_full_usage_info' => \$full_usage_info_flag,
-
- 'verbose' => \$SEE,
-
- 'no_version_check' => \$NO_VERSION_CHECK,
-
+
## general opts
"seqType=s" => \$seqType,
"left=s{,}" => \@left_files,
@@ -583,8 +585,7 @@ my $NO_VERSION_CHECK = 0;
"cite" => \$SHOW_CITATION_FLAG,
'CPU=i' => \$CPU,
- 'np=i' => \$np,
- 'mpiexec=s' => \$mpiexec,
+
'prep' => \$prep_only,
'KMER_SIZE=i' => \$KMER_SIZE,
@@ -601,6 +602,9 @@ my $NO_VERSION_CHECK = 0;
# Butterfly opts
+ 'no_run_butterfly' => \$NO_RUN_BUTTERFLY_FLAG,
+ 'no_triplet_lock' => \$NO_TRIPLET_LOCK,
+ 'extended_lock' => \$EXTENDED_TRIPLET_LOCK,
"group_pairs_distance=i" => \$group_pairs_distance,
'bfly_opts=s' => \$bfly_opts,
'bflyHeapSpaceMax=s' => \$bflyHeapSpaceMax,
@@ -611,7 +615,9 @@ my $NO_VERSION_CHECK = 0;
'bfly_jar=s' => \$BFLY_JAR,
'path_reinforcement_distance=i' => \$path_reinforcement_distance,
-
+ 'rerun_butterfly' => \$RERUN_BUTTERFLY_FLAG,
+
+ 'NO_EM_REDUCE' => \$NO_EM_REDUCE,
'no_path_merging' => \$NO_PATH_MERGING,
'min_per_id_same_path=i' => \$MIN_PER_ID_SAME_PATH,
'max_diffs_same_path=i' => \$MAX_DIFFS_SAME_PATH,
@@ -628,25 +634,27 @@ my $NO_VERSION_CHECK = 0;
'FORCE_INCHWORM_KMER_METHOD' => \$FORCE_INCHWORM_KMER_METHOD,
'INCHWORM_CUSTOM_PARAMS=s' => \$INCHWORM_CUSTOM_PARAMS,
'no_run_inchworm' => \$NO_RUN_INCHWORM_FLAG,
- 'iworm_opts=s' => \$iworm_opts,
- 'max_memory|M=s' => \$max_memory, # in GB
+ # Jellyfish
+ 'JM=s' => \$max_memory, # in GB
# Chrysalis -related opts
'min_glue=i' => \$min_glue,
'glue_factor=f' => \$glue_factor,
'min_iso_ratio=f' => \$min_iso_ratio,
'min_pcnt_read_iworm_kmers=i' => \$min_percent_read_iworm_kmers,
+ 'no_run_quantifygraph' => \$NO_RUN_QUANTIFYGRAPH_FLAG,
'max_reads_per_graph=i' => \$max_reads_per_graph,
'max_reads_per_loop=i' => \$max_reads_per_loop,
+ 'no_run_chrysalis' => \$NO_RUN_CHRYSALIS_FLAG,
'min_pct_read_mapping=i' => \$min_pct_read_mapping,
'weldmer_size=i' => \$weldmer_size,
+ "chrysalis_output=s" => \$chrysalis_output_dir,
"no_bowtie" => \$NO_BOWTIE,
"bowtie_comp" => \$BOWTIE_COMP,
- "no_run_chrysalis" => \$NO_RUN_CHRYSALIS_FLAG,
# Grid computing options
- 'grid_conf=s' => \$grid_conf_file,
+ 'grid_conf_file=s' => \$grid_conf_file,
"show_advanced_options" => \$show_advanced_options,
@@ -658,35 +666,28 @@ my $NO_VERSION_CHECK = 0;
'full_cleanup' => \$FULL_CLEANUP,
'version' => \$show_version_flag,
'monitoring' => \$run_with_collectl,
- 'no_distributed_trinity_exec' => \$NO_DISTRIBUTED_TRINITY_EXEC,
+ 'full_cleanup_ET' => \$FULL_CLEANUP_ERROR_TOLERANT,
# hidden (don't look here! ;)
'KMER_SIZE=i' => \$KMER_SIZE,
'jelly_s=i' => \$JELLY_S,
-
+ 'compdir|component_directory=s' => \$component_directory,
'NO_PARALLEL_IWORM' => \$NO_PARALLEL_IWORM,
- 'chrysalis_debug_weld_all' => \$CHRYSALIS_DEBUG_WELD_ALL,
-
-
+
+
+
# genome guided
- "genome_guided_bam=s" => \$genome_guided_bam,
+ "genome=s" => \$genome_fasta_file,
"genome_guided_max_intron=i" => \$genome_guided_max_intron,
-
+ "genome_guided_use_bam=s" => \$genome_guided_use_bam,
"genome_guided_min_coverage=i" => \$genome_guided_min_coverage,
"genome_guided_min_reads_per_partition=i" => \$genome_guided_min_reads_per_partition,
+ "genome_guided_CPU=i" => \$genome_guided_CPU,
+ "GMAP_CPU=i" => \$GMAP_CPU,
+ "genome_guided_sort_buffer=s" => \$genome_guided_sort_buffer,
"genome_guided_just_prep" => \$genome_guided_just_prep_flag,
-
- "trinity_complete" => \$TRINITY_COMPLETE_FLAG,
-
- "grid_node_CPU=i" => \$grid_node_CPU,
- "grid_node_max_memory=s" => \$grid_node_max_memory,
-
- "bypass_java_version_check" => \$bypass_java_version_check,
-
- "ananas_dir=s" => \$ANANAS_DIR,
-
- );
+ );
@@ -710,8 +711,7 @@ if ($help_flag) {
}
if ($show_version_flag) {
- &version_check();
-
+ print "Trinity version: $VERSION\n";
exit(1);
}
@@ -725,7 +725,9 @@ if ($KMER_SIZE > $MAX_KMER_SIZE) {
}
-
+if ($NO_TRIPLET_LOCK) {
+ $TRIPLET_LOCK = 0; # turn it off since on by default.
+}
if ($NO_PARALLEL_IWORM) {
# turn it off.
$PARALLEL_IWORM_FLAG = 0;
@@ -734,6 +736,13 @@ if ($NO_PARALLEL_IWORM) {
my $MIN_IWORM_LEN = $KMER_SIZE;
+unless ($GMAP_CPU) {
+ $GMAP_CPU = $CPU;
+}
+unless ($genome_guided_CPU) {
+ $genome_guided_CPU = $CPU;
+}
+
if (@ARGV) {
die "Error, do not understand options: @ARGV\n";
}
@@ -748,6 +757,25 @@ unless ($BFLY_JAR) {
}
+## Check options set:
+
+# Subroutine takes variable *reference* plus name of variable. Lower-cases
+# variable value and checks to see if it one of the allowed ones.
+# 'die' has new-line in order to keep line number from being shown to user.
+
+sub check_option {
+ my ($option, $name) = @_;
+ $$option = lc $$option;
+ if ($$option eq '') {
+ die "Error, option '--$name' is required.\n";
+ }
+ if (!defined $allowed_check{$name}{$$option}) {
+ die "Error, option '--$name' ($$option) not one of $allowed{$name}\n";
+ }
+}
+
+check_option( \$seqType, 'seqType' );
+
my $USE_FASTOOL = 1; # by default, using fastool for fastq to fasta conversion
if ($NO_FASTOOL) {
$USE_FASTOOL = 0;
@@ -757,33 +785,12 @@ if ($SS_lib_type) {
unless ($SS_lib_type =~ /^(R|F|RF|FR)$/) {
die "Error, unrecognized SS_lib_type value of $SS_lib_type. Should be: F, R, RF, or FR\n";
}
-
- if (@single_files) {
- if ($run_as_paired_flag) {
- die "Error, if you have paired-end reads and want to run as strand-specific, then you must specify the --left and --right parameters";
- }
- if (length($SS_lib_type) != 1) {
- die "Error, with --single reads, the --SS_lib_type can be 'F' or 'R' only.\n";
- }
- }
- if (@left_files && @right_files) {
- if (length($SS_lib_type) != 2) {
- die "Error, with paired end reads, the --SS_lib_type can be 'RF' or 'FR' only.\n";
- }
- }
-
}
-unless ($genome_guided_bam || (@left_files && @right_files) || @single_files ) {
- die "Error, need either options 'left' and 'right' or option 'single' or 'genome_guided_bam'\n";
-}
-unless ($genome_guided_bam) {
- unless ($seqType) {
- die "Error, need --seqType specified\n";
- }
+unless ( (@left_files && @right_files) || @single_files ) {
+ die "Error, need either options 'left' and 'right' or option 'single'\n";
}
-
if (@left_files) {
@left_files = split(",", join(",", @left_files));
}
@@ -799,39 +806,41 @@ if ($min_iso_ratio > 1) {
die "Error, --min_iso_ratio should be <= 1 \n";
}
-## keep the original 'xG' format string for the --JM option, then calculate the numerical value for jellyfish_ram
-my $jellyfish_ram = $max_memory; ## this one is used in the Chrysalis exec string
-if ($jellyfish_ram) {
- $jellyfish_ram =~ /^([\d\.]+)G$/ or die "Error, cannot parse jellyfish_ram value of $jellyfish_ram. Set it to 'xG' where x is a numerical value\n";
+## keep the original 'xG' format string for the --JM option, then calculate the numerical value for max_memory
+my $JM_string = $max_memory; ## this one is used in the Chrysalis exec string
+if ($max_memory) {
+ $max_memory =~ /^([\d\.]+)G$/ or die "Error, cannot parse max_memory value of $max_memory. Set it to 'xG' where x is a numerical value\n";
- $jellyfish_ram = $1;
- $jellyfish_ram *= 1024**3; # convert to from gig to bytes
+ $max_memory = $1;
+ $max_memory *= 1024**3; # convert to from gig to bytes
}
else {
- die "Error, must specify max memory for jellyfish to use, eg. --max_memory 10G \n";
+ die "Error, must specify max memory for jellyfish to use, eg. --JM 10G \n";
}
+unless ($genome_guided_sort_buffer) {
+ $genome_guided_sort_buffer = $JM_string;
+}
-## Check Java version:
-unless ($NO_RUN_INCHWORM_FLAG || $NO_RUN_CHRYSALIS_FLAG || $bypass_java_version_check) {
- my $java_version = `java -Xmx64m -version 2>&1 `;
- if ($java_version =~ /(java|openjdk) version \"1\.(\d)\./) {
- my $version_id = $2;
- if ($version_id != 7) {
- die "Error, Trinity requires access to Java version 1.7. Currently installed version is: $java_version";
- }
- }
- else {
- print STDERR "\n\n\n********************************************************************\n"
- . "** Warning, Trinity cannot determine which version of Java is being used. Version 1.7 is required. \n\nAttempting to continue in 30 seconds\n"
- . "********************************************************************\n\n\n";
- sleep(30);
- }
+## Try to remove stack limits
+if ($^O eq "linux") { # cannot set stacksize on newer macs for some reason...
+# &try_unlimit_stacksize();
}
+my $curr_limit_settings = `/bin/sh -c 'ulimit -a' `;
+unless ($curr_limit_settings && $curr_limit_settings =~ /\w/) {
+ $curr_limit_settings = `/bin/csh -c limit`; # backup, probably not needed.
+}
+
+print "Current settings:\n$curr_limit_settings\n\n";
-unless ($NO_VERSION_CHECK || $TRINITY_COMPLETE_FLAG) {
- &version_check();
+
+## Check Java version:
+unless ($NO_RUN_BUTTERFLY_FLAG || $NO_RUN_CHRYSALIS_FLAG) {
+ my $java_version = `java -Xmx64m -version 2>&1 `;
+ unless ($java_version =~ /(java|openjdk) version \"1\.[67]\./) {
+ die "Error, Trinity requires access to Java version 1.6 or 1.7. Currently installed version is: $java_version";
+ }
}
# Give the variable with memory size and a user-oriented name
@@ -853,28 +862,50 @@ if ($bflyHeapSpaceInitBytes > $bflyHeapSpaceMaxBytes) {
}
+if ($CPU > $CPU_MAX) {
+ print STDERR "Warning, --CPU $CPU might be excessive. Limiting it to $CPU_MAX for now.\n";
+ $CPU = $CPU_MAX;
+}
if ($inchworm_cpu > $CPU) {
$inchworm_cpu = $CPU;
}
-if ($bflyCalculateCPU && $jellyfish_ram) {
- $bflyCPU = int ($jellyfish_ram * 0.80 / $bflyHeapSpaceMaxBytes);
+if ($bflyCalculateCPU && $max_memory) {
+ $bflyCPU = int ($max_memory * 0.80 / $bflyHeapSpaceMaxBytes);
}
$bflyCPU = $CPU if !defined $bflyCPU;
+if ($bflyCPU > $CPU_MAX) {
+ print STDERR "Warning, --bflyCPU $bflyCPU might be excessive. Limiting it to $CPU_MAX for now.\n";
+ $bflyCPU = $CPU_MAX;
+}
+
if (defined($bflyGCThreads) && $bflyGCThreads > 32) {
die "Error, you probably want fewer than $bflyGCThreads java garbage collection threads. Try a number less than 32.";
}
-if ($genome_guided_bam) {
+if ($genome_fasta_file) {
## genome-guided mode.
unless ($genome_guided_max_intron) {
die "Error, must specifiy --genome_guided_max_intron <int> for genome-guided mode.\n";
}
+ unless ($genome_guided_use_bam) {
+ ## check for gsnap software
+ my @tools = qw(gmap_build gsnap);
+ foreach my $tool (@tools) {
+ my $path = `which $tool`;
+ if ($path =~ /\w/) {
+ print STDERR "Found $tool at $path\n";
+ }
+ else {
+ die "Error, cannot locate tool: $tool, required for genome-guided pipeline.";
+ }
+ }
+ }
}
@@ -888,7 +919,7 @@ if ($PAIRED_MODE && (!$NO_RUN_CHRYSALIS_FLAG) && (!$NO_BOWTIE)) {
my $bowtie_path = `which bowtie`;
my $bowtie_build_path = `which bowtie-build`;
if ($bowtie_path =~ /\w/ && $bowtie_build_path =~ /\w/) {
- print "Paired mode requires bowtie. Found bowtie at: $bowtie_path\n and bowtie-build at $bowtie_build_path\n\n" if $SEE;
+ print "Paired mode requires bowtie. Found bowtie at: $bowtie_path\n and bowtie-build at $bowtie_build_path\n\n";
}
else {
die "Error, cannot find path to bowtie ($bowtie_path) or bowtie-build ($bowtie_build_path), which is now needed as part of Chrysalis' read scaffolding step. If you should choose to not run bowtie, include the --no_bowtie in your Trinity command.\n\n";
@@ -896,7 +927,7 @@ if ($PAIRED_MODE && (!$NO_RUN_CHRYSALIS_FLAG) && (!$NO_BOWTIE)) {
my $samtools_path = `which samtools`;
if ($samtools_path =~ /\w/) {
- print "Found samtools at: $samtools_path\n" if $SEE;
+ print "Found samtools at: $samtools_path\n";
}
else {
die "Error, cannot find samtools. Please be sure samtools is installed and included in your PATH setting.\n";
@@ -925,32 +956,16 @@ elsif ($CUFFFLY_MODE) {
$butterfly_output_filename = "Trinity.Cufffly.fasta";
}
-
-
-my $PARALLEL_SAMTOOLS_SORT_TOKEN = "-\@ $CPU";
-
-
-unless (basename($output_directory) =~ /trinity/i) {
- die "Error, output directory must contain the word 'trinity' as a safety precaution, given that auto-deletion can take place.\n";
-}
-
-
-if ($grid_conf_file) {
- # Prep for HPC parafly use.
- $ENV{PATH} = dirname($PARAFLY) . ":$ENV{PATH}";
- &HPC::GridRunner::use_parafly();
-}
-
-
main: {
$ENV{OMP_NUM_THREADS} = $CPU;
+
- unless ($NO_RUN_INCHWORM_FLAG || $NO_RUN_CHRYSALIS_FLAG) {
- print STDERR "-since butterfly will eventually be run, lets test for proper execution of java\n" if $SEE;
+ unless ($NO_RUN_BUTTERFLY_FLAG || $NO_RUN_CHRYSALIS_FLAG) {
+ print STDERR "-since butterfly will eventually be run, lets test for proper execution of java\n";
&test_java_failure_capture();
}
- unless ($genome_guided_bam) {
+ unless ($genome_fasta_file) {
if (basename($chrysalis_output_dir) !~ /chrysalis/i) {
die "Error, chrysalis output directory name must include 'chrysalis' in the name."; # lets try to prevent bad things from happening... (security issue)
@@ -960,6 +975,20 @@ main: {
die "Error, working in full-cleanup mode. Specify a named directory for the output. The directory and contents are purged at end of a successful run.";
}
+ if ($FULL_CLEANUP_ERROR_TOLERANT) { # genome-guided mode
+
+ if (basename($output_directory) !~ /trinity/i) {
+ die "Error, in genome-guided mode, the output directory name must include 'trinity' in the name (precautionary measure)";
+ }
+ $FULL_CLEANUP = 1;
+
+ ## purge chrysalis directory from a previously failed run
+ if (-d $output_directory) {
+ print STDERR "WARNING: $output_directory exists. Since under full-cleanup mode, deleting this first before proceeding.\n:";
+ &process_cmd("rm -rf $output_directory");
+ }
+ }
+
if ($chrysalis_output_dir !~ /^\//) {
$chrysalis_output_dir = "$output_directory/$chrysalis_output_dir";
@@ -1000,7 +1029,8 @@ main: {
@single_files = &create_full_path(\@single_files, 1) if @single_files;
$output_directory = &create_full_path($output_directory, 0);
$long_reads = &create_full_path($long_reads, 1) if $long_reads;
- $genome_guided_bam = &create_full_path($genome_guided_bam, 1) if $genome_guided_bam;
+ $genome_fasta_file = &create_full_path($genome_fasta_file, 1) if $genome_fasta_file;
+ $genome_guided_use_bam = &create_full_path($genome_guided_use_bam, 1) if $genome_guided_use_bam;
$grid_conf_file = &create_full_path($grid_conf_file, 1) if $grid_conf_file;
@@ -1010,7 +1040,7 @@ main: {
$MKDIR_OUTDIR_FLAG = 1;
}
- if ((! $genome_guided_bam) && (! -d $chrysalis_output_dir)) {
+ if ((! $genome_fasta_file) && (! -d $chrysalis_output_dir)) {
&process_cmd("mkdir -p $chrysalis_output_dir"); # note, won't be auto-cleaned up if not in the trinity_out_dir/
}
@@ -1018,16 +1048,7 @@ main: {
collectl_start() unless ($FULL_CLEANUP);
&perfmon_start() unless ($FULL_CLEANUP);
-
- unless ($TRINITY_COMPLETE_FLAG) {
- print STDERR "\n\n";
- print STDERR "----------------------------------------------------------------------------------\n"
- . "-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------\n"
- . "----------------------------------------------------------------------------------\n\n";
-
- }
-
##########################
## Run Quality Trimming
##########################
@@ -1052,7 +1073,6 @@ main: {
my $left_file = shift @left_files;
my $right_file = shift @right_files;
- # note: trimmomatic can use gzipped files directly.
my ($left_file_trimmed, $right_file_trimmed) = &run_trimmomatic_PE($left_file, $right_file, $trimmomatic_quality_trim_params);
push (@trimmed_left_files, $left_file_trimmed);
push (@trimmed_right_files, $right_file_trimmed);
@@ -1087,81 +1107,21 @@ main: {
}
}
- if ($genome_guided_bam) {
- &run_genome_guided_Trinity();
-
- exit(0);
- }
-
-
- eval {
- &run_Trinity();
- };
-
- if ($@) {
- print STDERR "$@\n" if $SEE;
- if ($@ !~ /^NON_FATAL_EXCEPTION/) {
- die "Trinity run failed. Must investigate error above.\n";
- }
- }
-
-
- if ($FULL_CLEANUP) {
- print "Fully cleaning up.\n" if $SEE;
- $output_directory =~ s|/+$||g; # remove any trailing directory slash
-
- if (-s "Trinity.fasta.tmp") {
- rename("Trinity.fasta.tmp", "$output_directory.Trinity.fasta") or die "Error, cannot rename Trinity.fasta.tmp to $output_directory.Trinity.fasta";
-
- print "\n\n"
- . "###################################################################\n"
- . "Butterfly assemblies are written to $output_directory.Trinity.fasta\n"
- . "###################################################################\n\n\n" unless $TRINITY_COMPLETE_FLAG;
-
- }
- else {
- print "# No butterfly assemblies to report.\n" unless $TRINITY_COMPLETE_FLAG;
- }
-
- if ($MKDIR_OUTDIR_FLAG && basename($output_directory) =~ /trinity/i) { # ensure outdirectory as trinity in the name, just to be sure we dont delete something non-trinity related!!!
- system("rm -rf $output_directory &"); # ignore filesystem errors on failed cleanup
- }
- else {
- print STDERR "WARNING, cannot remove output directory $output_directory, since not created in this run. (safety precaution)\n";
- }
+ if ($genome_fasta_file) {
- }
- else {
-
-
- if (-s "Trinity.fasta.tmp") {
- rename("Trinity.fasta.tmp", $butterfly_output_filename) or die "Error, cannot rename Trinity.fasta.tmp to $butterfly_output_filename"; # now that process has finished.
- }
-
- if (-s $butterfly_output_filename) {
-
- print "\n\n";
- print "###################################################################\n";
- print "Butterfly assemblies are written to $output_directory/$butterfly_output_filename\n";
- print "###################################################################\n\n\n" unless $TRINITY_COMPLETE_FLAG;
+ if (@left_files && @right_files) {
+ &run_genome_guided_Trinity(\@left_files, \@right_files);
}
else {
- die "ERROR, no butterfly assemblies reported.";
+ &run_genome_guided_Trinity(\@single_files);
}
- }
-
- &perfmon_end() unless ($FULL_CLEANUP);
- exit(0);
+ exit(0);
+ }
-
-}
-####
-sub run_Trinity {
-
## create inchworm file name
my $inchworm_file = "inchworm.K$KMER_SIZE.L$MIN_IWORM_LEN";
unless ($SS_lib_type) {
@@ -1172,15 +1132,15 @@ sub run_Trinity {
my $trinity_target_fa = (@single_files) ? "single.fa" : "both.fa";
my $inchworm_target_fa = $trinity_target_fa; # change this later if we have long_reads
- my $bowtie_reads_fa = $trinity_target_fa; # dont include long reads in this... keep them separate.
+
## Don't prep the inputs if Inchworm already exists.... Resuming earlier operations.
my $inchworm_finished_checkpoint_file = "$inchworm_file.finished";
if (-s $inchworm_file && -e $inchworm_finished_checkpoint_file) {
print "\n\n#######################################################################\n"
. "Inchworm file: $inchworm_file detected.\n"
. "Skipping Inchworm Step, Using Previous Inchworm Assembly\n"
- . "#######################################################################\n\n" if ($SEE || ! $TRINITY_COMPLETE_FLAG);
+ . "#######################################################################\n\n";
#sleep(2);
}
else {
@@ -1215,7 +1175,7 @@ sub run_Trinity {
die "Error prepping sequences.";
}
- print("Done converting input files.") if $SEE;
+ print("Done converting input files.");
## Calculate input file sizes for performance monitoring
# this should be set as the created fasta otherwise results will differ for same data passed as .fq and .fa?
my $pm_temp = -s "left.fa";
@@ -1234,17 +1194,17 @@ sub run_Trinity {
unlink ("left.fa", "right.fa") unless $jaccard_clip; # no longer needed now that we have 'both.fa', which is needed by chryaslis
}
- foreach my $f ((@left_files, at right_files)){
- if (-s $f.'.readcount'){
- open (IN,$f.'.readcount');
- my $s = <IN>;
- close IN;
- $s=~/([0-9]+)$/;
- $count_of_reads += $1 if $1;
- }
- }
-
-
+ foreach my $f ((@left_files, at right_files)){
+ if (-s $f.'.readcount'){
+ open (IN,$f.'.readcount');
+ my $s = <IN>;
+ close IN;
+ $s=~/([0-9]+)$/;
+ $count_of_reads += $1 if $1;
+ }
+ }
+
+
}
elsif (@single_files) {
@@ -1254,13 +1214,13 @@ sub run_Trinity {
$pm_temp = $pm_temp / 1024 / 1024;
$pm_single_fa_size = sprintf('%.0f', $pm_temp);
foreach my $f (@single_files){
- if (-s $f.'.readcount'){
- open (IN,$f.'.readcount');
- my $s = <IN>;
- close IN;
- $s=~/([0-9]+)$/;
- $count_of_reads += $1 if $1;
- }
+ if (-s $f.'.readcount'){
+ open (IN,$f.'.readcount');
+ my $s = <IN>;
+ close IN;
+ $s=~/([0-9]+)$/;
+ $count_of_reads += $1 if $1;
+ }
}
}
@@ -1273,18 +1233,9 @@ sub run_Trinity {
$count_of_reads/=2;
}
if ($long_reads) {
-
- # adjust the inchworm target, tack on the longer reads.
-
$inchworm_target_fa .= ".wLongReads.fa";
$count_of_reads += `grep -c '^>' $long_reads | wc -l`; #AP we don't know if these will be one single line
-
- &process_cmd("cat $long_reads | sed 's/>/>LR\\\$\\\|/' > $inchworm_target_fa");
-
- ## merge the long reads with the short reads into a new target file.
- &process_cmd("cat $trinity_target_fa >> $inchworm_target_fa");
-
- #&process_cmd("cat $long_reads $trinity_target_fa > $inchworm_target_fa");
+ &process_cmd("cat $long_reads $trinity_target_fa > $inchworm_target_fa");
}
open (my $ofh, ">$inchworm_target_fa.read_count") or die $!;
@@ -1310,26 +1261,55 @@ sub run_Trinity {
unless (-s $inchworm_file) {
-
- die "NON_FATAL_EXCEPTION: WARNING, no Inchworm output is detected at: $inchworm_file";
+
+ ## No inchworm output under genome-guided flag, must be sparse data.
+
+ if ($FULL_CLEANUP_ERROR_TOLERANT && $FULL_CLEANUP && -e $inchworm_file && -e $inchworm_finished_checkpoint_file) {
+ ## GG-trinity mode, clean-up gracefully
+ if ($MKDIR_OUTDIR_FLAG) {
+ &process_cmd("rm -rf $component_directory") if $component_directory;
+ &process_cmd("rm -rf $output_directory");
+ }
+ else {
+ print STDERR "WARNING, cannot remove output directory $output_directory, since not created in this run. (safety precaution)\n";
+ }
+ exit(0);
+ }
+ else {
+ die "Error, no Inchworm output is detected at: $inchworm_file";
+ }
}
+
-
-
- if ($jaccard_clip && $TRINITY_COMPLETE_FLAG) {
-
- if ($jaccard_clip && -s 'left.fa' && -s 'right.fa') {
- $inchworm_file = &run_jaccard_clip_left_right($inchworm_file, \@left_files, \@right_files, $seqType, $SS_lib_type);
- #$inchworm_file = &run_jaccard_clip_left_right($inchworm_file, $left_file, $right_file, $seqType, $SS_lib_type);
+ if ($jaccard_clip) {
+
+ eval {
- }
- elsif ($jaccard_clip && -s 'single.fa') {
- $inchworm_file = &run_jaccard_clip_single_but_really_paired($inchworm_file, \@single_files, $seqType, $SS_lib_type);
- #$inchworm_file = &run_jaccard_clip_single_but_really_paired($inchworm_file, $single_file, $seqType, $SS_lib_type);
+ if ($jaccard_clip && -s 'left.fa' && -s 'right.fa') {
+ $inchworm_file = &run_jaccard_clip_left_right($inchworm_file, \@left_files, \@right_files, $seqType, $SS_lib_type);
+ #$inchworm_file = &run_jaccard_clip_left_right($inchworm_file, $left_file, $right_file, $seqType, $SS_lib_type);
+
+ }
+ elsif ($jaccard_clip && -s 'single.fa') {
+ $inchworm_file = &run_jaccard_clip_single_but_really_paired($inchworm_file, \@single_files, $seqType, $SS_lib_type);
+ #$inchworm_file = &run_jaccard_clip_single_but_really_paired($inchworm_file, $single_file, $seqType, $SS_lib_type);
+ }
+ };
+
+ if ($@) {
+ if ($FULL_CLEANUP_ERROR_TOLERANT) {
+ ## GG-trinity mode, clean up gracefully
+ system("rm -rf $output_directory &"); # ignore file system errors on failed cleanup
+ exit(0);
+ }
+ else {
+ die "Error, jaccard-clip failed: $@";
+ }
}
}
-
- if ($NO_RUN_CHRYSALIS_FLAG && ! $TRINITY_COMPLETE_FLAG) {
+
+
+ if ($NO_RUN_CHRYSALIS_FLAG) {
print "\n\n\n";
print "#########################################################################\n";
print "Inchworm is complete. --no_run_chrysalis was specified, so stopping here.\n";
@@ -1353,275 +1333,233 @@ sub run_Trinity {
## chrysalis will just run or resume depending on what's already been processed.
$pm_chrysalis_start = `date +%s`;
my $butterfly_cmds = &run_chrysalis($inchworm_file, $inchworm_target_fa,
- $min_contig_length, $group_pairs_distance, $SS_lib_type,
- $trinity_target_fa, $bowtie_reads_fa);
-
- if ($butterfly_cmds eq "RECURSIVE_TRINITY_COMPLETE") {
- ## stop here. all done! ## FIXME: this is very bad coding style!!! yes, I know.
- return;
- }
-
-
+ $min_contig_length, $group_pairs_distance, $SS_lib_type, $trinity_target_fa);
$pm_chrysalis_end = `date +%s`;
- print STDERR "Butterfly_cmds: $butterfly_cmds\n" if $SEE;
+ print "Butterfly_cmds: $butterfly_cmds\n";
if ($butterfly_cmds && -s $butterfly_cmds) {
+
+ if ($NO_RUN_BUTTERFLY_FLAG) {
- ## Run Butterfly
-
- print STDERR "Inchworm and Chrysalis complete. Butterfly commands to execute are provided here:\n"
- . $butterfly_cmds . "\n\n" if $SEE;
-
-
- print STDERR "---------------------------------------------------------------\n"
- . "-------------------- Butterfly --------------------------------\n"
- . "-- (Reconstruct transcripts from reads and de Bruijn graphs) --\n"
- . "---------------------------------------------------------------\n\n" if $SEE;
-
- $pm_butterfly_start = `date +%s`;
- if ($grid_conf_file) {
- my @bfly_cmds = `cat $butterfly_cmds`;
- chomp @bfly_cmds;
- my $grid_runner = new HPC::GridRunner($grid_conf_file, "chrysalis/butterfly_on_grid.cacheSuccess");
- my $ret = $grid_runner->run_on_grid(@bfly_cmds);
- if ($ret) {
- die "Error, not all butterfly commands could complete successfully... cannot continue.";
- }
+ print "\n\nYou've opted to run butterfly commands independently from this script, such as on a computing grid.\n\n";
+ print "Butterfly commands to execute are available here:\n"
+ . "\t$butterfly_cmds\n\n";
+ print "After executing Butterfly commands, concatenate all Butterfly outputs by running:\n"
+ . "\t\tfind $output_directory/ -name \"\*allProbPaths.fasta\" -exec cat {} + > $output_directory/Trinity.fasta\n\n\n";
+
+ exit(0);
+
}
else {
- my $cmd = "$PARAFLY -c $butterfly_cmds -shuffle -CPU $bflyCPU -failed_cmds failed_butterfly_commands.$$.txt "; # shuffle them since the first ones are usually the longest-running ones.
- &process_cmd($cmd);
- }
- $pm_butterfly_end = `date +%s`;
-
- ## capture results:
- # my $cmd = 'find ./chrysalis -name "*allProbPaths.fasta" -exec cat {} + > Trinity.fasta.tmp';
- # no longer scan the file system... we know which files should exist
- print STDERR "\n\n** Harvesting all assembled transcripts into a single multi-fasta file...\n" unless ($TRINITY_COMPLETE_FLAG);
- my $cmd = "$UTILDIR/support_scripts/print_butterfly_assemblies.pl $chrysalis_output_dir/component_base_listing.txt > Trinity.fasta.tmp";
- &process_cmd($cmd);
-
-
-
- }
-
-}
-
-
-####
-sub run_chrysalis {
- my ($inchworm_file, $reads_file,
- $min_contig_length, $group_pairs_distance, $SS_lib_type, $pairs_fa, $bowtie_reads_fa) = @_;
-
-
- my $butterfly_cmds = &create_full_path("$chrysalis_output_dir/butterfly_commands");
-
- my $quantify_graph_cmds = &create_full_path("$chrysalis_output_dir/quantifyGraph_commands");
-
- my $pair_links_file = "";
-
- ## Define iworm links via paired-end read mappings:
- if ($PAIRED_MODE && ! $NO_BOWTIE) {
-
- my $pipeliner = new Pipeliner(-verbose => ($TRINITY_COMPLETE_FLAG) ? 0 : 1);
-
- # generate the pair links.
- my $iworm_min100_fa_file = "$chrysalis_output_dir/" . basename("$inchworm_file.min100");
- my $cmd = "$MISCDIR/fasta_filter_by_min_length.pl $inchworm_file 100 > $iworm_min100_fa_file";
- $pipeliner->add_commands( new Command($cmd, "$iworm_min100_fa_file.ok"));
- $pipeliner->run();
-
- $pipeliner = new Pipeliner(-verbose => $SEE);
- $cmd = "bowtie-build -q $iworm_min100_fa_file $iworm_min100_fa_file";
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
- if (-s "$iworm_min100_fa_file") {
- $pipeliner->add_commands( new Command($cmd, "$iworm_min100_fa_file.bowtie_build.ok"));
-
- my $bowtie_sam_file = "$chrysalis_output_dir/iworm.bowtie.nameSorted.bam";
- $cmd = "bash -c \" set -o pipefail; bowtie -a -m 20 --best --strata --threads $CPU --chunkmbs 512 -q -S -f $iworm_min100_fa_file $bowtie_reads_fa | samtools view $PARALLEL_SAMTOOLS_SORT_TOKEN -F4 -Sb - | samtools sort $PARALLEL_SAMTOOLS_SORT_TOKEN -no - - > $bowtie_sam_file\" ";
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
-
- $pipeliner->add_commands( new Command($cmd, "$bowtie_sam_file.ok"));
+ ## Run Butterfly
- ## generate the scaffold info
- my $iworm_scaffolds_file = "$chrysalis_output_dir/iworm_scaffolds.txt";
- $cmd = "$UTILDIR/support_scripts/scaffold_iworm_contigs.pl $bowtie_sam_file $inchworm_file > $iworm_scaffolds_file"; # important, must use original inchworm file because positions are indexed for later use by GraphFromFasta
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
+ print "Inchworm and Chrysalis complete. Butterfly commands to execute are provided here:\n"
+ . $butterfly_cmds . "\n\n";
- $pipeliner->add_commands( new Command($cmd, "$iworm_scaffolds_file.ok"));
- $pair_links_file = $iworm_scaffolds_file;
+ print STDERR "---------------------------------------------------------------\n"
+ . "-------------------- Butterfly --------------------------------\n"
+ . "-- (Reconstruct transcripts from reads and de Bruijn graphs) --\n"
+ . "---------------------------------------------------------------\n\n";
- $pipeliner->run();
+ $pm_butterfly_start = `date +%s`;
+ if ($grid_conf_file) {
+ my @bfly_cmds = `cat $butterfly_cmds`;
+ chomp @bfly_cmds;
+ my $grid_runner = new HTC::GridRunner($grid_conf_file, "chrysalis/butterfly_on_grid.cacheSuccess");
+ my $ret = $grid_runner->run_on_grid(@bfly_cmds);
+ if ($ret) {
+ die "Error, not all butterfly commands could complete successfully... cannot continue.";
+ }
+ }
+ else {
+ my $cmd = "$PARAFLY -c $butterfly_cmds -shuffle -CPU $bflyCPU -failed_cmds failed_butterfly_commands.$$.txt -v "; # shuffle them since the first ones are usually the longest-running ones.
+ &process_cmd($cmd);
+ }
+ $pm_butterfly_end = `date +%s`;
+
+ ## capture results:
+ # my $cmd = 'find ./chrysalis -name "*allProbPaths.fasta" -exec cat {} + > Trinity.fasta.tmp';
+ # no longer scan the file system... we know which files should exist
+ my $cmd = "$UTILDIR/support_scripts/print_butterfly_assemblies.pl $chrysalis_output_dir/component_base_listing.txt > Trinity.fasta.tmp";
+ &process_cmd($cmd);
}
- }
-
-
-
- my $chrysalis_pipeliner = new Pipeliner(-verbose => ($TRINITY_COMPLETE_FLAG) ? 0 : 1);
-
- my $graphFromFasta_outfile = "$chrysalis_output_dir/GraphFromIwormFasta.out";
-
- { # GraphFromFasta
+ }
+
+ if ($FULL_CLEANUP) {
+ print "Fully cleaning up.\n";
+ $output_directory =~ s|/+$||g; # remove any trailing directory slash
- my $graphFromFasta_cmd = "-i $inchworm_file -r $reads_file -min_contig_length $min_contig_length -min_glue $min_glue -glue_factor $glue_factor -min_iso_ratio $min_iso_ratio -t $CPU -k " . ($KMER_SIZE-1) . " -kk " . 2*($KMER_SIZE-1) . " ";
- # use MPI if MPI Procs >1
- if ($np > 1) {
- $graphFromFasta_cmd = "$mpiexec -np $np $CHRYSALIS_DIR/GraphFromFasta_MPI $graphFromFasta_cmd"
+ if (-s "Trinity.fasta.tmp") {
+ rename("Trinity.fasta.tmp", "$output_directory.Trinity.fasta") or die "Error, cannot rename Trinity.fasta.tmp to $output_directory.Trinity.fasta";
+
+ print "\n\n";
+ print "###################################################################\n";
+ print "Butterfly assemblies are written to $output_directory.Trinity.fasta\n";
+ print "###################################################################\n\n\n";
+
}
else {
- $graphFromFasta_cmd = "$CHRYSALIS_DIR/GraphFromFasta $graphFromFasta_cmd"
- }
- if ($SS_lib_type) {
- $graphFromFasta_cmd .= " -strand ";
+ print "\n\n";
+ print "####################################\n";
+ print "## No butterfly assemblies to report.\n";
+ print "####################################\n\n\n";
}
- if ($pair_links_file) {
- $graphFromFasta_cmd .= " -scaffolding $pair_links_file ";
+
+ if ($MKDIR_OUTDIR_FLAG) {
+ system("rm -rf $output_directory &"); # ignore filesystem errors on failed cleanup
}
- if ($CHRYSALIS_DEBUG_WELD_ALL) {
- $graphFromFasta_cmd .= " -debug_weld_all ";
+ else {
+ print STDERR "WARNING, cannot remove output directory $output_directory, since not created in this run. (safety precaution)\n";
}
+
+ }
+ else {
- $graphFromFasta_cmd .= " > $graphFromFasta_outfile";
- if ($TRINITY_COMPLETE_FLAG) {
- $graphFromFasta_cmd .= " 2>/dev/null";
+ if (-s "Trinity.fasta.tmp") {
+ rename("Trinity.fasta.tmp", $butterfly_output_filename) or die "Error, cannot rename Trinity.fasta.tmp to $butterfly_output_filename"; # now that process has finished.
+ }
+
+ if (-s $butterfly_output_filename) {
+
+ print "\n\n";
+ print "###################################################################\n";
+ print "Butterfly assemblies are written to $output_directory/$butterfly_output_filename\n";
+ print "###################################################################\n\n\n";
+ }
+ else {
+ die "ERROR, no butterfly assemblies reported.";
}
-
- my $checkpoint = "$graphFromFasta_outfile.ok";
- $chrysalis_pipeliner->add_commands( new Command($graphFromFasta_cmd, $checkpoint) );
}
+ &perfmon_end() unless ($FULL_CLEANUP);
+ exit(0);
+}
- my $iworm_bundles_fasta_file = "$chrysalis_output_dir/bundled_iworm_contigs.fasta";
- {
- ## create iworm bundles
-
+
+####
+sub run_chrysalis {
+ my ($inchworm_file, $reads_file,
+ $min_contig_length, $group_pairs_distance, $SS_lib_type, $pairs_fa) = @_;
+
+
+ my $butterfly_cmds = &create_full_path("$chrysalis_output_dir/butterfly_commands");
+
+ my $quantify_graph_cmds = &create_full_path("$chrysalis_output_dir/quantifyGraph_commands");
- my $cmd = "$CHRYSALIS_DIR/CreateIwormFastaBundle -i $graphFromFasta_outfile -o $iworm_bundles_fasta_file -min $min_contig_length";
+ my $chrysalis_finished_checkpoint = "$chrysalis_output_dir/chrysalis.finished";
+
+ if (-e $chrysalis_finished_checkpoint) {
- unless ($SEE) {
- $cmd .= " 2>/dev/null ";
- }
+ print "###################################################################\n";
+ print "#### Chrysalis results already exist. Not rerunning Chrysalis. ####\n";
+ print "###################################################################\n\n\n";
- $chrysalis_pipeliner->add_commands( new Command($cmd, "$iworm_bundles_fasta_file.ok"));
+ #sleep(2);
}
-
-
- my $reads_to_components_output_file = "$chrysalis_output_dir/readsToComponents.out";
- {
- ## map reads to chrysalis components:
+ else {
+ ## run Chrysalis
+
+ my $cmd = "$CHRYSALIS_DIR/Chrysalis -i $reads_file -iworm $inchworm_file -o $chrysalis_output_dir -cpu $CPU "
+ . " -min_glue $min_glue -min_iso_ratio $min_iso_ratio -glue_factor $glue_factor -kmer_size " . ($KMER_SIZE-1) # chrysalis wants kmer overlap length
+ . " -weldmer_size $weldmer_size "
+ . " -min $min_contig_length -dist $group_pairs_distance -max_reads $max_reads_per_graph "
+ . " -sort_exec \"$sort_exec\" "
+ . " -sort_buffer_size $JM_string -max_mem_reads $max_reads_per_loop ";
+ if ($SS_lib_type) {
+ $cmd .= " -strand 1 ";
+ }
- my $cmd = ($BOWTIE_COMP) ? "$CHRYSALIS_DIR/ReadsToComponents.pl" : "$CHRYSALIS_DIR/ReadsToTranscripts";
- if ("$cmd" eq "$CHRYSALIS_DIR/ReadsToTranscripts" ) {
- if ($np > 1) {
- $cmd = "$mpiexec -np $np $CHRYSALIS_DIR/ReadsToTranscripts_MPI"
+ if ($PAIRED_MODE) {
+ $cmd .= " -paired ";
+ $cmd .= " -reads_for_pairs $pairs_fa ";
+
+ if ($NO_BOWTIE) {
+ $cmd .= " -no_pair_links ";
}
+
}
-
- $cmd .= " -i $reads_file -f $iworm_bundles_fasta_file -o $reads_to_components_output_file -t $CPU -max_mem_reads $max_reads_per_loop ";
- if ($SS_lib_type) {
- $cmd .= " -strand ";
+
+ if ($BOWTIE_COMP) {
+ $cmd .= " -bowtie_comp ";
}
+
if ($min_pct_read_mapping) {
$cmd .= " -min_pct_read_mapping $min_pct_read_mapping ";
}
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
-
- $chrysalis_pipeliner->add_commands( new Command($cmd, "$reads_to_components_output_file.ok"));
- }
-
- my $sorted_reads_to_components_file = "$reads_to_components_output_file.sort";
- {
- ## sort the read mappings:
-
- my $cmd = "$sort_exec -T . -S $max_memory -k 1,1n $reads_to_components_output_file > $sorted_reads_to_components_file";
+ $cmd .= " -butterfly $BFLY_JAR ";
- unless ($SEE) {
- $cmd .= " 2>/dev/null ";
+ if ($NO_CLEANUP) {
+ $cmd .= " -no_cleanup ";
}
- $chrysalis_pipeliner->add_commands( new Command($cmd, "$sorted_reads_to_components_file.ok"));
-
- }
-
- if (! $TRINITY_COMPLETE_FLAG) {
+ $cmd .= " 2>&1 ";
- $chrysalis_pipeliner->run();
+ eval {
+
+ &process_cmd($cmd);
+
+ };
- &run_recursive_trinity($sorted_reads_to_components_file);
- return ("RECURSIVE_TRINITY_COMPLETE"); # indicate to caller that we're in recursive trinity mode.
- }
-
-
-
-
- my $deBruijnGraph_outfile = "$iworm_bundles_fasta_file.deBruijn";
-
- {
- ## write the deBruijn graphs:
+ if ($@) {
+
+ if ($FULL_CLEANUP_ERROR_TOLERANT) {
+ ## Trinity GG mode - OK, not enough data that's worth pursuing.
+ return("");
+
+ }
- my $cmd = "$INCHWORM_DIR/FastaToDeBruijn --fasta $iworm_bundles_fasta_file -K " . ($KMER_SIZE-1) . " --graph_per_record --threads $CPU";
- if ($SS_lib_type) {
- $cmd .= " --SS ";
- }
-
- $cmd .= " > $deBruijnGraph_outfile";
-
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
+ my $errmsg = "$curr_limit_settings\n";
+ $errmsg .= "Error, the Chrysalis process failed:\n$@\n";
+ croak $errmsg;
}
- $chrysalis_pipeliner->add_commands(new Command($cmd, "$deBruijnGraph_outfile.ok") );
+
+ print "Chrysalis initial stage completed successfully.\n";
+ &process_cmd("touch $chrysalis_finished_checkpoint");
}
- $chrysalis_pipeliner->run();
+ ## partition the graphs and reads in prep for quantify graph and butterfly steps.
-
unless (-s "$chrysalis_output_dir/bundled_iworm_contigs.fasta.deBruijn") {
- die "NON_FATAL_EXCEPTION: WARNING, no deBruijn graphs generated based on inchworm contigs: $chrysalis_output_dir/bundled_iworm_contigs.fasta.deBruijn";
+
+ if ($FULL_CLEANUP_ERROR_TOLERANT) {
+ ## Trinity GG mode - OK, not enough data that's worth pursuing.
+ return("");
+ }
+
+ croak "Error, no deBruijn graphs generated based on inchworm contigs: $chrysalis_output_dir/bundled_iworm_contigs.fasta.deBruijn";
}
- #################################################################################
- ## partition the graphs and reads in prep for quantify graph and butterfly steps.
- #################################################################################
-
my $partitioning_checkpoint_file = "$chrysalis_output_dir/file_partitioning.ok";
- my $cmd = "$UTILDIR/support_scripts/partition_chrysalis_graphs_n_reads.pl --deBruijns $chrysalis_output_dir/bundled_iworm_contigs.fasta.deBruijn --componentReads $chrysalis_output_dir/readsToComponents.out.sort -N 1000 -L $min_contig_length ";
-
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
-
+ my $cmd = "$UTILDIR/support_scripts/partition_chrysalis_graphs_n_reads.pl --deBruijns $chrysalis_output_dir/bundled_iworm_contigs.fasta.deBruijn --componentReads $chrysalis_output_dir/readsToComponents.out.sort -N 1000 -L $min_contig_length --compdir $component_directory ";
+
&process_cmd($cmd) unless (-e $partitioning_checkpoint_file);
&process_cmd("touch $partitioning_checkpoint_file") unless (-e $partitioning_checkpoint_file);
-
+
## write the quantifygraph commands and butterfly commands
my $component_base_listing_file = "$chrysalis_output_dir/component_base_listing.txt";
- if (-e $component_base_listing_file && ! -s $component_base_listing_file) {
-
- die "NON_FATAL_EXCEPTION: WARNING, component base listing file: $component_base_listing_file exists and is empty - likely sparse data";
+ unless (-s $component_base_listing_file) {
+
+ if ($FULL_CLEANUP_ERROR_TOLERANT) {
+ ## Trinity GG mode
+ return("");
+ }
+ croak "Error, component base listing file: $component_base_listing_file does not exist";
}
@@ -1652,10 +1590,6 @@ sub run_chrysalis {
$quantify_graph_cmd .= " -no_cleanup ";
}
-
- unless ($SEE) {
- $quantify_graph_cmd .= " 2>/dev/null";
- }
print $qgraph_cmd_ofh $quantify_graph_cmd . "\n";
@@ -1678,6 +1612,17 @@ sub run_chrysalis {
$bfly_cmd .= " --path_reinforcement_distance=$path_reinforcement_distance ";
+ if ($TRIPLET_LOCK) {
+ $bfly_cmd .= " --triplet-lock ";
+ }
+ if ($EXTENDED_TRIPLET_LOCK) {
+ $bfly_cmd .= " --extended_triplet ";
+ }
+
+ unless ($NO_EM_REDUCE) {
+ $bfly_cmd .= " --EM_REDUCE ";
+ }
+
if ($NO_PATH_MERGING) {
$bfly_cmd .= " --no_path_merging ";
}
@@ -1710,126 +1655,70 @@ sub run_chrysalis {
}
- my $quantify_graph_cmds_finished = &create_full_path("$chrysalis_output_dir/quantifyGraph_commands.run.finished");
- if (! -e $quantify_graph_cmds_finished) {
- ## run it
-
- print STDERR "---------------------------------------------------\n"
- . "----------- Chrysalis: QuantifyGraph --------------\n"
- . "-- (Integrate mapped reads into de Bruijn graph) --\n"
- . "---------------------------------------------------\n\n" if $SEE;
-
-
- if ($grid_conf_file) {
- my @quantify_graph_cmds = `cat $quantify_graph_cmds`;
- chomp @quantify_graph_cmds;
-
- my $grid_runner = new HPC::GridRunner($grid_conf_file, "chrysalis/chrysalis_quantify_graph_on_grid.cacheSuccess");
- my $ret = $grid_runner->run_on_grid(@quantify_graph_cmds);
- if ($ret) {
- die "Error, not all Chrysalis quantify_graph commands completed successfully. Cannot continue.";
- }
- }
- else {
-
- my $cmd = "$PARAFLY -c $quantify_graph_cmds -CPU $CPU -failed_cmds failed_quantify_graph_commands.$$.txt -shuffle ";
- &process_cmd($cmd);
- }
+ # see if we need to run the quantifyGraph commands:
+ if ($NO_RUN_QUANTIFYGRAPH_FLAG) {
+
+ print "#############################################################################\n";
+ print "## Ceasing Trinity prior to execution of massively parallel operations.\n";
+ print "##\n";
+ print "## To complete Trinity, execute the following sets of commands:\n";
+ print "##\n";
+ print "## First, run the Chrysalis QuantifyGraph commands in parallel:\n";
+ print "## $quantify_graph_cmds\n";
+ print "##\n";
+ print "## Then, execute all the Butterfly commands:\n";
+ print "## $butterfly_cmds\n";
+ print "##\n";
+ print "## And, finally, concatenate all Butterfly assemblies into a single output file:\n";
+ print "##\n";
+ print "## find $output_directory/ -name \"\*allProbPaths.fasta\" -exec cat {} + > $output_directory/Trinity.fasta\n";
+ print "##\n";
+ print "##############################################################################\n";
+ print "\n\n";
- # write checkpoint
- &process_cmd("touch $quantify_graph_cmds_finished");
+ exit(0);
}
-
-
- return($butterfly_cmds);
-
-
-}
-
-
-####
-sub run_recursive_trinity {
- my ($reads_sorted_by_component_file) = @_;
+ else {
- my $target_files_per_dir = 100; # new Fb_\d/CBin_\d every (#components/100)
- my $file_bins_per_dir = 1000 * $target_files_per_dir; # new Fb_\d dir
-
- my $component_counter = 0;
-
- my $prev_component_id = -1;
- my $ofh = undef;
-
- my $read_filenames = "partitioned_reads.files.list";
- my $read_filenames_ok = "$read_filenames.ok";
- if (! -e $read_filenames_ok) {
-
- open (my $ofh_read_filenames, ">$read_filenames") or die $!;
- my $currdir = cwd();
-
- open (my $fh, $reads_sorted_by_component_file) or die $!;
- while (<$fh>) {
- chomp;
- my ($component_id, $read_name, $pct, $read_seq) = split(/\t/);
+ my $quantify_graph_cmds_finished = &create_full_path("$chrysalis_output_dir/quantifyGraph_commands.run.finished");
+ if (! -e $quantify_graph_cmds_finished) {
+ ## run it
- if ($component_id != $prev_component_id) {
+ print STDERR "---------------------------------------------------\n"
+ . "----------- Chrysalis: QuantifyGraph --------------\n"
+ . "-- (Integrate mapped reads into de Bruijn graph) --\n"
+ . "---------------------------------------------------\n\n";
+
+
+ if ($grid_conf_file) {
+ my @quantify_graph_cmds = `cat $quantify_graph_cmds`;
+ chomp @quantify_graph_cmds;
- $prev_component_id = $component_id;
- close $ofh if $ofh;
- my $base_dir = "read_partitions/Fb_" . (int($component_counter/$file_bins_per_dir)) . "/CBin_" . (int($component_counter/$target_files_per_dir));
- if (! -d $base_dir) {
- &process_cmd("mkdir -p $base_dir");
+ my $grid_runner = new HTC::GridRunner($grid_conf_file, "chrysalis/chrysalis_quantify_graph_on_grid.cacheSuccess");
+ my $ret = $grid_runner->run_on_grid(@quantify_graph_cmds);
+ if ($ret) {
+ die "Error, not all Chrysalis quantify_graph commands completed successfully. Cannot continue.";
}
- my $readsfile = "$currdir/$base_dir/c$component_id.trinity.reads.fa";
+ }
+ else {
- $component_counter++;
-
- open ($ofh, ">$readsfile") or die "Error, cannot write to file $readsfile";
- print $ofh_read_filenames "$readsfile\n";
+ my $cmd = "$PARAFLY -c $quantify_graph_cmds -CPU $CPU -failed_cmds failed_quantify_graph_commands.$$.txt -v -shuffle ";
+ &process_cmd($cmd);
}
- print $ofh "$read_name\n$read_seq\n";
-
+
+ # write checkpoint
+ &process_cmd("touch $quantify_graph_cmds_finished");
}
- close $ofh if $ofh;
- close $ofh_read_filenames;
+
- &process_cmd("touch $read_filenames_ok");
- }
-
+ return($butterfly_cmds);
- if ($ANANAS_DIR) {
- &run_ANANAS($read_filenames, "read_partitions");
- exit(0);
- }
-
-
- if (! -e "recursive_trinity.cmds.ok") {
- &write_trinity_partitioned_cmds($read_filenames, "recursive_trinity.cmds");
- &process_cmd("touch recursive_trinity.cmds.ok");
- print STDERR "Done prepping partitioned cmds." if $SEE;
}
- if ($NO_DISTRIBUTED_TRINITY_EXEC) {
- print STDERR "\n\n###################################################################\n"
- . "## Stopping here due to --no_distributed_trinity_exec in effect ##\n"
- . "###################################################################\n\n";
- exit(0);
- }
-
- &run_partitioned_cmds("recursive_trinity.cmds");
-
- print STDERR "\n\n** Harvesting all assembled transcripts into a single multi-fasta file...\n\n" unless ($TRINITY_COMPLETE_FLAG);
-
- my $cmd = "find read_partitions/ -name '*inity.fasta' | $UTILDIR/support_scripts/partitioned_trinity_aggregator.pl TR > Trinity.fasta.tmp";
- &process_cmd($cmd);
-
- return;
-
-}
-
-
-
+
+}
####
@@ -1855,11 +1744,11 @@ sub run_inchworm {
#####################################################
- ## Using Jellyfish kmer method (if in initial read partitioning phase (1) )
+ ## Using Jellyfish kmer method
#####################################################
- if (! ($FORCE_INCHWORM_KMER_METHOD || $TRINITY_COMPLETE_FLAG) ) {
-
+ if (! $FORCE_INCHWORM_KMER_METHOD) {
+
my $jelly_kmer_fa_file = "jellyfish.kmers.fa";
my $jelly_finished_checkpoint_file = "jellyfish.$min_kmer_cov.finished";
unless (-e $jelly_finished_checkpoint_file) {
@@ -1873,7 +1762,7 @@ sub run_inchworm {
my $read_file_size = -s $reads;
- my $jelly_hash_size = int( ($jellyfish_ram - $read_file_size)/7); # decided upon by Rick Westerman
+ my $jelly_hash_size = int( ($max_memory - $read_file_size)/7); # decided upon by Rick Westerman
if ($jelly_hash_size < 100e6) {
@@ -1894,10 +1783,6 @@ sub run_inchworm {
$cmd .= " $reads";
- unless ($SEE) {
- $cmd .= " 2> /dev/null ";
- }
-
&process_cmd($cmd);
@@ -1908,20 +1793,12 @@ sub run_inchworm {
my $jelly_db = "mer_counts.jf";
$cmd = "$JELLYFISH_DIR/bin/jellyfish dump -L $min_kmer_cov $jelly_db > $jelly_kmer_fa_file";
-
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
&process_cmd($cmd);
## write a histogram of the kmer counts.
$cmd = "$JELLYFISH_DIR/bin/jellyfish histo -t $CPU -o $jelly_kmer_fa_file.histo $jelly_db";
-
- unless ($SEE) {
- $cmd .= " 2>/dev/null";
- }
&process_cmd($cmd);
@@ -1931,7 +1808,7 @@ sub run_inchworm {
&process_cmd("touch $jelly_finished_checkpoint_file");
- if ($NO_RUN_INCHWORM_FLAG && ! $TRINITY_COMPLETE_FLAG) {
+ if ($NO_RUN_INCHWORM_FLAG) {
print STDERR "WARNING: --no_run_inchworm parameter in effect. Stopping here prior to running inchworm.\n";
exit(0);
}
@@ -1940,7 +1817,7 @@ sub run_inchworm {
}
- $inchworm_cmd = "$INCHWORM_DIR/inchworm --kmers $jelly_kmer_fa_file --run_inchworm -K $KMER_SIZE -L $MIN_IWORM_LEN --monitor 1 $iworm_opts ";
+ $inchworm_cmd = "$INCHWORM_DIR/bin/inchworm --kmers $jelly_kmer_fa_file --run_inchworm -K $KMER_SIZE -L $MIN_IWORM_LEN --monitor 1 ";
# hold on to the jellyfish file - we might use it for other applications.
#push (@tmp_files, $jelly_finished_checkpoint_file, $jelly_kmer_fa_file) unless $NO_CLEANUP;
@@ -1949,21 +1826,22 @@ sub run_inchworm {
else {
######################################################
- ## Using Inchworm kmer method (original, slow w/ large data)
+ ## Using Inchworm kmer method (original, slow method)
######################################################
- $inchworm_cmd = "$INCHWORM_DIR/inchworm --reads $reads --run_inchworm -K $KMER_SIZE -L $MIN_IWORM_LEN --monitor 1 ";
+ $inchworm_cmd = "$INCHWORM_DIR/bin/inchworm --reads $reads --run_inchworm -K $KMER_SIZE -L $MIN_IWORM_LEN --monitor 1 ";
if ($min_kmer_cov > 1) {
$inchworm_cmd .= " --minKmerCount $min_kmer_cov ";
}
}
+
## finish constructing the inchworm command to execute
unless ($strand_specific_flag) {
$inchworm_cmd .= " --DS ";
}
-
+
unless ($NO_CLEANUP) {
$inchworm_cmd .= " --keep_tmp_files ";
}
@@ -1986,12 +1864,8 @@ sub run_inchworm {
print STDERR "----------------------------------------------\n"
. "--------------- Inchworm ---------------------\n"
. "-- (Linear contig construction from k-mers) --\n"
- . "----------------------------------------------\n\n" if (! $TRINITY_COMPLETE_FLAG);
+ . "----------------------------------------------\n\n";
- unless ($SEE) {
- $inchworm_cmd .= " 2>/dev/null";
- }
-
eval {
@@ -2106,18 +1980,18 @@ sub create_full_path {
sub process_cmd {
my ($cmd) = @_;
- print STDERR &mytime."CMD: $cmd\n" unless ($TRINITY_COMPLETE_FLAG);
-
+ print &mytime."CMD: $cmd\n";
+
my $start_time = time();
- my $ret = system("bash", "-c", $cmd);
+ my $ret = system($cmd);
my $end_time = time();
if ($ret) {
die "Error, cmd: $cmd died with ret $ret";
}
- print STDERR "CMD finished (" . ($end_time - $start_time) . " seconds)\n" if $SEE;
-
+ print "CMD finished (" . ($end_time - $start_time) . " seconds)\n";
+
return;
}
@@ -2183,10 +2057,8 @@ sub run_jaccard_clip_single_but_really_paired {
####
sub test_java_failure_capture {
- if ($SEE) {
- print "#######################################\n";
- print "Running Java Tests\n";
- }
+ print "#######################################\n";
+ print "Running Java Tests\n";
my $java_prog = `which java`;
unless ($java_prog) {
@@ -2212,15 +2084,15 @@ sub test_java_failure_capture {
};
if ($@) {
- print "-we properly captured the java failure status, as needed. Looking good.\n" if $SEE;
+ print "-we properly captured the java failure status, as needed. Looking good.\n";
}
else {
print STDERR "-we are unable to properly capture java failure status. Please be sure that java (or any wrapper around java that's being used) can properly capture and propagate failure status before proceeding.\n";
exit(1);
}
- print "Java tests succeeded.\n" if $SEE;
- print "###################################\n\n" if $SEE;
+ print "Java tests succeeded.\n";
+ print "###################################\n\n";
return;
}
@@ -2232,7 +2104,7 @@ sub extract_reads_with_iworm_kmers {
my $extracted_reads_file = "$trinity_target_fa." . $min_percent_read_containing_kmers . "pcnt.iworm_extracted";
- my $cmd = "$INCHWORM_DIR/pull_reads_with_kmers "
+ my $cmd = "$INCHWORM_DIR/bin/pull_reads_with_kmers "
. "--target $inchworm_file "
. "--reads $trinity_target_fa "
. "--min_percent_read_containing_kmers $min_percent_read_containing_kmers ";
@@ -2351,7 +2223,7 @@ sub perfmon_start {
print FILE "===========\n";
print FILE "Trinity Version: $VERSION\n";
my $tempp="";
- $tempp=`ldd $INCHWORM_DIR/inchworm 2>/dev/null | grep "libgomp"`;
+ $tempp=`ldd $INCHWORM_DIR/bin/inchworm 2>/dev/null | grep "libgomp"`;
if ($tempp eq "") {
print FILE "Compiler: Intel\n";
} else {
@@ -2449,10 +2321,10 @@ sub collectl_stop {
kill("TERM", $collectl_pid);
waitpid($collectl_pid,0);
chdir($collectl_output_directory) or return;
- system("python $COLLECTL_DIR/make_data_files.py");
- system("python $COLLECTL_DIR/timetable.py");
+ system("$COLLECTL_DIR/make_data_files.sh");
+ system("$COLLECTL_DIR/timetable.sh");
$collectl_titlename = "${VERSION} ${CPU} @{left_files}@{single_files}";
- system("python $COLLECTL_DIR/plot.py \"$collectl_titlename\" ${CPU}");
+ system("$COLLECTL_DIR/plot.sh \"$collectl_titlename\" ${CPU}");
}
}
@@ -2484,18 +2356,10 @@ sub run_trimmomatic_PE {
&process_cmd($cmd);
- if ($NORMALIZE_READS_FLAG) {
- ## can't use the orphans:
- &process_cmd("cp $trimmed_left_file_base.P.qtrim $trimmed_left_fq");
- &process_cmd("cp $trimmed_right_file_base.P.qtrim $trimmed_right_fq");
- }
- else {
-
- ## append the orphans so we can still use them in assembly
- &process_cmd("cat $trimmed_left_file_base.P.qtrim $trimmed_left_file_base.U.qtrim > $trimmed_left_fq");
- &process_cmd("cat $trimmed_right_file_base.P.qtrim $trimmed_right_file_base.U.qtrim > $trimmed_right_fq");
- }
-
+ ## append the orphans so we can still use them in assembly
+ &process_cmd("cat $trimmed_left_file_base.P.qtrim $trimmed_left_file_base.U.qtrim > $trimmed_left_fq");
+ &process_cmd("cat $trimmed_right_file_base.P.qtrim $trimmed_right_file_base.U.qtrim > $trimmed_right_fq");
+
&process_cmd("touch $checkpoint");
# compress the trimmomatic direct outputs to conserve space:
@@ -2600,7 +2464,7 @@ sub normalize {
- my $cmd = "$UTILDIR/insilico_read_normalization.pl --seqType $seqType --JM $max_memory "
+ my $cmd = "$UTILDIR/insilico_read_normalization.pl --seqType $seqType --JM $JM_string "
. " --max_cov $max_read_coverage --CPU $CPU --output $normalize_outdir";
if ($SS_lib_type) {
@@ -2611,8 +2475,6 @@ sub normalize {
$cmd .= " --no_cleanup ";
}
- #@read_files = &add_fifo_for_gzip(@read_files);
-
my @ret_files;
if (scalar @read_files == 2) {
@@ -2632,9 +2494,9 @@ sub normalize {
my $checkpoint = "$normalize_outdir/normalization.ok";
if (&files_exist(@ret_files, $checkpoint)) {
- print STDERR "###############################################################################\n"
- . "#### Normalization process was previously completed. Skipping it and using existing normalized files: @ret_files\n"
- . "###############################################################################\n" if $SEE;
+ print STDERR "###############################################################################\n";
+ print STDERR "#### Normalization process was previously completed. Skipping it and using existing normalized files: @ret_files\n";
+ print STDERR "###############################################################################\n";
}
else {
@@ -2659,16 +2521,74 @@ sub files_exist {
return(0); # not exists
}
}
-
+
return(1); # all exist
}
####
sub run_genome_guided_Trinity {
- ## partition the reads according to coverage piles:
+ my ($left_files_aref, $right_files_aref) = @_;
+
+
+ my $bam_file;
+ if ($genome_guided_use_bam) {
+ $bam_file = $genome_guided_use_bam;
+ }
+ else {
+ ## run gsnap to align reads:
+
+ $bam_file = "gsnap.coordSorted.bam";
+
+ unless (-s "$bam_file" && -e "$bam_file.ok") {
+
+ my @files;
+ if ($left_files_aref && $right_files_aref) {
+ while (@$left_files_aref) {
+ my $left_file = shift @$left_files_aref;
+ my $right_file = shift @$right_files_aref;
+ push (@files, $left_file, $right_file);
+ }
+ }
+ else {
+ @files = @$left_files_aref; # really single files
+ }
+
+ @files = &add_zcat_gz(@files);
+
+
+ ## prep the genome
+ my $cmd = "ln -sf $genome_fasta_file gsnap_target.fa";
+ &process_cmd($cmd);
+
+ if (-s "$genome_fasta_file.gmap") {
+ &process_cmd("ln -sf $genome_fasta_file.gmap gsnap_target.gmap");
+ }
+ else {
+
+ my $cmd = "gmap_build -k 13 -D . -d gsnap_target.gmap gsnap_target.fa ";
+ &process_cmd($cmd) unless (-e "target.gmap");
+ }
+
+ if (-s "$genome_fasta_file.fai") {
+ &process_cmd("ln -sf $genome_fasta_file.fai gsnap_target.fa.fai");
+ }
+ else {
+ my $cmd = "samtools faidx gsnap_target.fa";
+ &process_cmd($cmd);
+ }
+
+ $cmd = "bash -c \"set -o pipefail; gsnap -d gsnap_target.gmap -D . -A sam --nofails -N 1 -t $GMAP_CPU -w $genome_guided_max_intron -n 20 @files | samtools view -bt gsnap_target.fa.fai - | samtools sort -o - - > $bam_file \"";
+ &process_cmd($cmd);
+
+ &process_cmd("touch $bam_file.ok"); # checkpoint
+ }
+
+ }
- my $cmd = "$UTILDIR/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM $genome_guided_bam -I $genome_guided_max_intron --sort_buffer $max_memory --CPU $CPU ";
+ ## partition the reads according to coverage piles:
+ my $cmd = "$UTILDIR/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM $bam_file -I $genome_guided_max_intron --sort_buffer $genome_guided_sort_buffer --CPU $CPU ";
+
if ($SS_lib_type) {
$cmd .= " --SS_lib_type $SS_lib_type ";
}
@@ -2682,85 +2602,11 @@ sub run_genome_guided_Trinity {
&process_cmd($cmd) unless (-s "read_files.list" && -e "read_files.list.ok");
&process_cmd("touch read_files.list.ok") unless (-e "read_files.list.ok"); # checkpoint
-
- if ($ANANAS_DIR) {
- &run_ANANAS("read_files.list", "Dir_\*");
- exit(0);
- }
-
-
-
- unless (-e "trinity_GG.cmds.ok") {
- &write_trinity_partitioned_cmds("read_files.list", "trinity_GG.cmds");
- &process_cmd("touch trinity_GG.cmds.ok");
- }
-
- if ($NO_DISTRIBUTED_TRINITY_EXEC) {
- print STDERR "\n\n###################################################################\n"
- . "## Stopping here due to --no_distributed_trinity_exec in effect ##\n"
- . "###################################################################\n\n";
- exit(0);
- }
-
- &run_partitioned_cmds("trinity_GG.cmds");
-
-
- ## pull together the final outputs:
- $cmd = "find Dir_* -name '*inity.fasta' | $UTILDIR/support_scripts/partitioned_trinity_aggregator.pl GG > Trinity-GG.fasta.tmp";
- &process_cmd($cmd);
-
- rename("Trinity-GG.fasta.tmp", "Trinity-GG.fasta"); # now that it's done.
-
- print STDERR "\n\nFinished. See Trinity-GG.fasta for reconstructed transcripts\n\n";
-
- return;
-}
-
-####
-sub run_partitioned_cmds {
- my ($cmds_file) = @_;
-
-
- print STDERR "\n\n";
- print STDERR "--------------------------------------------------------------------------------\n"
- . "------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------\n"
- . "--------------------------------------------------------------------------------\n\n";
-
-
- if ($ANANAS_DIR) {
- print STDERR " ************ Using Ananas Assembler ***************** \n\n";
- }
-
- ## Execute the commands:
- if ($grid_conf_file) {
- my @cmds = `cat $cmds_file`;
- chomp @cmds;
-
- my $grid_runner = new HPC::GridRunner($grid_conf_file, "$cmds_file.htc_cache_success");
- my $ret = $grid_runner->run_on_grid(@cmds);
- if ($ret) {
- die "Error, not all $cmds_file commands completed successfully. Cannot continue.";
- }
-
- }
- else {
- my $cmd = "$PARAFLY -c $cmds_file -CPU $CPU -v ";
- &process_cmd($cmd);
- }
-
- return;
-}
-
-
-####
-sub write_trinity_partitioned_cmds {
- my ($reads_list_file, $cmds_file) = @_;
-
##################################################
## write Trinity assembly commands for partitions:
##################################################
- my $cmd = "$UTILDIR/support_scripts/GG_write_trinity_cmds.pl --reads_list_file $reads_list_file --CPU $grid_node_CPU --max_memory $grid_node_max_memory ";
+ $cmd = "$UTILDIR/support_scripts/GG_write_trinity_cmds.pl --reads_list_file read_files.list --CPU $genome_guided_CPU ";
if ($run_as_paired_flag) {
$cmd .= " --run_as_paired ";
}
@@ -2768,7 +2614,8 @@ sub write_trinity_partitioned_cmds {
$cmd .= " --SS_lib_type F "; # all sequences already reoriented
}
- $cmd .= " --full_cleanup --seqType fa --trinity_complete";
+ $cmd .= " --full_cleanup_ET --seqType fa ";
+
my @potential_args = @ORIG_ARGS;
@@ -2776,15 +2623,15 @@ sub write_trinity_partitioned_cmds {
my $arg = shift @potential_args;
# single value options that aren't needed:
- if ($arg =~ /run_as_paired|normalize_by_read_set|trimmomatic|normalize_reads|prep|recurs|clean/) {
+ if ($arg =~ /run_as_paired|normalize_by_read_set|trimmomatic|normalize_reads|prep/) {
next;
}
-
+
# value specified options that aren't needed
- if ($arg =~ /seqType|left|right|single|genome|SS_lib_type|GMAP|quality_trimming|output|normalize_max_read_cov|grid_conf|max_mem|grid|long_reads/
+ if ($arg =~ /seqType|left|right|single|genome|SS_lib_type|GMAP|quality_trimming|output|normalize_max_read_cov|grid_conf/
||
# more precise identification of parameter
- $arg =~ /^(--CPU)$/
+ $arg =~ /^(CPU)$/
) {
# skipping these, already represented by opt configuration above.
@@ -2803,16 +2650,44 @@ sub write_trinity_partitioned_cmds {
}
}
- $cmd .= " > $cmds_file";
+ $cmd .= " > trinity_GG.cmds";
+
+ &process_cmd($cmd) unless (-e "trinity_GG.cmds.ok");
+ &process_cmd("touch trinity_GG.cmds.ok") unless (-e "trinity_GG.cmds.ok");
+
+ if ($genome_guided_just_prep_flag) {
+ print STDERR "###### Just prepping data for genome-guided assembly. Stopping here due to --genome_guided_just_prep invocation. #####\n\n";
+ exit(0);
+ }
+
+ ## execute the commands:
+ if ($grid_conf_file) {
+ my @trin_GG_cmds = `cat trinity_GG.cmds`;
+ chomp @trin_GG_cmds;
+
+ my $grid_runner = new HTC::GridRunner($grid_conf_file, "trinity_GG_cmds.htc_cache_success");
+ my $ret = $grid_runner->run_on_grid(@trin_GG_cmds);
+ if ($ret) {
+ die "Error, not all Trinity-GG commands completed successfully. Cannot continue.";
+ }
+
+ }
+ else {
+ my $cmd = "$PARAFLY -c trinity_GG.cmds -CPU $CPU -v ";
+ &process_cmd($cmd);
+ }
- &process_cmd($cmd) unless (-e "$cmds_file.ok");
- &process_cmd("touch $cmds_file.ok") unless (-e "$cmds_file.ok");
+ ## pull together the final outputs:
+ $cmd = "find Dir_* -name '*inity.fasta' | $UTILDIR/support_scripts/GG_trinity_accession_incrementer.pl > Trinity-GG.fasta.tmp";
+ &process_cmd($cmd);
+ rename("Trinity-GG.fasta.tmp", "Trinity-GG.fasta"); # now that it's done.
+ print STDERR "\n\nFinished. See Trinity-GG.fasta for reconstructed transcripts\n\n";
+
return;
}
-
sub add_zcat_gz {
my (@in_files) = @_;
@@ -2830,124 +2705,3 @@ sub add_zcat_gz {
return(@files);
}
-
-
-####
-sub add_fifo_for_gzip {
- my @files = @_;
-
- foreach my $file (@files) {
- if (ref $file eq "ARRAY") {
- my @f = &add_fifo_for_gzip(@{$file});
- $file = [@f];
- }
- elsif ($file =~ /\.gz$/) {
- $file = "<(zcat $file)";
- }
- }
-
- return(@files);
-
-}
-
-sub version_check {
-
- print "Trinity version: $VERSION\n";
-
- my $url = "http://rt-trinity.uits.indiana.edu/flask/version/" . $VERSION . "?timestamp=" . time;
- my $content = `curl --connect-timeout 10 -s "$url"`;
-
- ## get release info from here:
- ## https://api.github.com/repos/trinityrnaseq/trinityrnaseq/releases
-
- $url = "https://api.github.com/repos/trinityrnaseq/trinityrnaseq/releases";
- $content = `curl --connect-timeout 10 -s "$url"`;
-
- if ($?) {
-
- print STDERR "-ERROR: couldn't run the network check to confirm latest Trinity software version.\n\n";
- }
- else {
-
- if ($content =~ /\"tag_name\": \"([^\"]+)\"/) {
- my $latest_version_tag = $1;
- if ($VERSION eq '__TRINITY_VERSION_TAG__') {
- print STDERR "-using Trinity devel version. Note, latest production release is: $latest_version_tag\n\n";
- }
- elsif ($latest_version_tag ne $VERSION) {
- print "** NOTE: Latest version of Trinity is $latest_version_tag, and can be obtained at:\n"
- . "\thttps://github.com/trinityrnaseq/trinityrnaseq/releases\n\n";
- }
- else {
- print STDERR "-currently using the latest production release of Trinity.\n\n";
- }
- }
- else {
- print STDERR "-ERROR: couldn't parse latest version tag info from github: $content\n\n";
- }
- }
-
- return;
-}
-
-
-####
-sub run_ANANAS {
- my ($read_filenames, $base_out_dir) = @_;
-
- ## Create Ananas command set
- my $ananas_cmds_file = "ananas.cmds";
- my $ananas_cmds_checkpoint = "$ananas_cmds_file.ok";
-
- my $ananas_SS = "";
- my $ananas_dir = "na";
- if ($SS_lib_type) {
- $ananas_SS = " -strand 1 ";
- if ($PAIRED_MODE) {
- $ananas_dir = "ff";
- }
- }
- elsif ($PAIRED_MODE) {
- $ananas_dir = "fr";
- }
-
- unless (-e $ananas_cmds_checkpoint) {
- open (my $fh, $read_filenames) or die "Error, cannot open file $read_filenames";
- open (my $ofh, ">$ananas_cmds_file") or die "Error, cannot write to $ananas_cmds_file";
- while (<$fh>) {
- chomp;
- my $reads_file = $_;
-
- my $ananas_cmd = "$ANANAS_DIR/Ananas -i $reads_file -o $reads_file.out_dir -dir $ananas_dir $ananas_SS";
- print $ofh "$ananas_cmd\n";
- }
- close $fh;
- close $ofh;
-
- &process_cmd("touch $ananas_cmds_checkpoint");
- }
-
- if ($NO_DISTRIBUTED_TRINITY_EXEC) {
- print STDERR "\n\n###################################################################\n"
- . "## Stopping here due to --no_distributed_trinity_exec in effect ##\n"
- . "###################################################################\n\n";
- exit(0);
- }
-
-
- &run_partitioned_cmds($ananas_cmds_file);
-
-
- ## capture all outputs into a single output file.
-
- my $cmd = "find $base_out_dir -name \"*final.fa\" | $UTILDIR/support_scripts/partitioned_trinity_aggregator.pl ANANAS > Ananas.fasta.tmp";
- &process_cmd($cmd);
-
- rename("Ananas.fasta.tmp", "Ananas.fasta");
-
- print STDERR "Done. See Ananas.fasta \n\n";
-
-
-
- exit(0);
-}
diff --git a/galaxy-plugin/abundance_estimation_to_matrix_wrapper.py b/galaxy-plugin/abundance_estimation_to_matrix_wrapper.py
index 33df387..e906e3a 100644
--- a/galaxy-plugin/abundance_estimation_to_matrix_wrapper.py
+++ b/galaxy-plugin/abundance_estimation_to_matrix_wrapper.py
@@ -32,7 +32,7 @@ for i in range(1, len(sys.argv), 2):
# run the abundance estimation script
-cmd = os.path.dirname(sys.argv[0]) + "/trinityToolWrapper.py " + " util/abundance_estimates_to_matrix.pl --est_method RSEM --cross_sample_fpkm_norm none " + " ".join(label_list)
+cmd = os.path.dirname(sys.argv[0]) + "/trinityToolWrapper.py " + " util/abundance_estimates_to_matrix.pl --est_method RSEM --cross_sample_fpkm_norm TMM " + " ".join(label_list)
run_command(cmd)
diff --git a/galaxy-plugin/analyze_diff_exp.xml b/galaxy-plugin/analyze_diff_exp.xml
new file mode 100644
index 0000000..a28907f
--- /dev/null
+++ b/galaxy-plugin/analyze_diff_exp.xml
@@ -0,0 +1,41 @@
+<tool id="Analyze_Diff_Exp" name="Analyze_Differential_Expression" version="0.0.1">
+
+ <description>Analyze differential expression</description>
+ <requirements>
+ <requirement type="package">trinity</requirement>
+ </requirements>
+ <command interpreter="python">
+
+ analyze_diff_exp_wrapper.py $EdgeRTarGz $TMM_Matrix_FPKM $Pvalue $Cvalue
+
+ </command>
+ <inputs>
+ <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="file"/>
+ <param name="TMM_Matrix_FPKM" label="TMM Normalized FPKM matrix" type="data" format="file" />
+ <param name="Pvalue" label="P-value" value="0.05" type="float" />
+ <param name="Cvalue" label="C-value" value="0" type="float" />
+
+ </inputs>
+ <outputs>
+ <data format="data" name="diffExpr_matrix" label="${tool.name} on ${on_string}: Diffexp" from_work_dir="diffExpr.matrix"/>
+ <data format="data" name="diffExpr_correlation_matrix" label="${tool.name} on ${on_string}: Diffexp" from_work_dir="diffExpr.matrix.log2.sample_cor.dat"/>
+ <data format="data" name="diffExpr_correlation_matrix_pdf" label="${tool.name} on ${on_string}: Diffexp" from_work_dir="diffExpr.matrix.log2.sample_cor_matrix.pdf"/>
+ <data format="data" name="Heatmap" label="${tool.name} on ${on_string}: Diffexp" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
+ </outputs>
+ <tests>
+
+
+ <test>
+ <param name="target" value="trinity/Trinity.fasta" />
+ <param name="aligner" value="bowtie" />
+ <param name="paired_or_single" value="single" />
+ <param name="library_type" value="None" />
+ <param name="input" value="trinity/reads.left.fq" />
+ </test>
+
+
+ </tests>
+ <help>
+ .. _Trinity: http://trinityrnaseq.sourceforge.net
+ </help>
+</tool>
diff --git a/galaxy-plugin/analyze_diff_exp_wrapper.py b/galaxy-plugin/analyze_diff_exp_wrapper.py
new file mode 100644
index 0000000..d4d7fae
--- /dev/null
+++ b/galaxy-plugin/analyze_diff_exp_wrapper.py
@@ -0,0 +1,63 @@
+import sys, os, subprocess
+
+TRINITY_BASE_DIR = ""
+if os.environ.has_key('TRINITY_HOME'):
+ TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
+else:
+ sys.stderr.write("You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this");
+ sys.exit()
+
+usage= "usage: " + sys.argv[0] + " " + "edgeR.tar.gz " + "TMM_normalized_FPKM_matrix " + "P-value " + "C-value"
+print sys.argv
+print usage
+print " "
+
+if len(sys.argv)<5:
+ print "Require atleast two parameters"
+else:
+ print "All good- command going ahead"
+print " "
+
+Normalized_Matrix=sys.argv[2]
+Pvalue=sys.argv[3]
+Cvalue=sys.argv[4]
+
+def run_command(cmd):
+ print "The command used: " + cmd
+ pipe= subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE)
+ pipe.wait()
+ ret= pipe.returncode
+ if ret:
+ print "command died: " + str(ret)
+ print pipe.stderr.readlines()
+ sys.exit(1)
+ else:
+ return
+print " "
+
+Final_tar_gz= "edgeR.tar.gz"
+run_command("cp "+ sys.argv[1] + " " + "Final_tar_gz")
+run_command("tar -xvf " + "Final_tar_gz")
+run_command("mv " + "edgeR_results" + "/* ." )
+
+# run the analyze command
+cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/analyze_diff_expr.pl "+ "--matrix " + Normalized_Matrix + " -P " + Pvalue + " -C " + Cvalue
+run_command(cmd)
+
+origMatrixName= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix"
+# diffExpr.P0.001_C2.0.matrix
+run_command("mv " + origMatrixName + " diffExpr.matrix")
+
+SampleCorName= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.sample_cor.dat"
+# diffExpr.P0.001_C2.0.matrix.log2.sample_cor.dat
+run_command("mv " + SampleCorName + " diffExpr.matrix.log2.sample_cor.dat")
+
+CorMatrix= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.sample_cor_matrix.pdf"
+# diffExpr.P0.001_C2.0.matrix.log2.sample_cor_matrix.pdf
+run_command("mv " + CorMatrix + " diffExpr.matrix.log2.sample_cor_matrix.pdf")
+
+Heatmap= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.centered.genes_vs_samples_heatmap.pdf"
+#diffExpr.P0.001_C2.0.matrix.log2.centered.genes_vs_samples_heatmap.pdf
+run_command("mv " + Heatmap + " diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf")
+
+sys.exit(0)
diff --git a/galaxy-plugin/trinityToolWrapper.py b/galaxy-plugin/trinityToolWrapper.py
index 5d80fbf..957ae12 100755
--- a/galaxy-plugin/trinityToolWrapper.py
+++ b/galaxy-plugin/trinityToolWrapper.py
@@ -17,9 +17,8 @@ TRINITY_BASE_DIR = ""
if os.environ.has_key('TRINITY_HOME'):
TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
else:
- sys.write("You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this");
sys.stderr.write("You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this");
- sys.exit(1)
+ sys.exit()
diff --git a/galaxy-plugin/trinityrnaseq.xml b/galaxy-plugin/trinityrnaseq.xml
index b57a9ab..621ff5e 100644
--- a/galaxy-plugin/trinityrnaseq.xml
+++ b/galaxy-plugin/trinityrnaseq.xml
@@ -6,12 +6,12 @@
<requirement type="package">trinity</requirement>
</requirements>
<command interpreter="python">
- trinityToolWrapper.py Trinity --JM $JM --CPU $CPU
+ trinityToolWrapper.py Trinity --max_memory $JM --CPU $CPU
## Inputs.
#if str($inputs.paired_or_single) == "paired":
--left $inputs.left_input --right $inputs.right_input
- #if $inputs.left_input.ext == 'fa':
+ #if $inputs.left_input.ext == 'fa':
--seqType fa
#else:
--seqType fq
diff --git a/notes b/notes
index 61cbe10..06a36c6 100644
--- a/notes
+++ b/notes
@@ -2,6 +2,28 @@
git clone https://github.com/trinityrnaseq/trinityrnaseq.git
+
+
+#############
+
+notes for developer:
+
autoreconf --install
+# merging devel to master, set new release
+
+git checkout master
+git pull --rebase origin devel
+# edit release tag
+git commmit -m 'release v...' -a
+git push
+
+git checkout branch
+# continue working...
+
+#############################
+
+Release info:
+
+curl https://api.github.com/repos/trinityrnaseq/trinityrnaseq/releases
diff --git a/sample_data/Makefile b/sample_data/Makefile
index 7126011..15931db 100644
--- a/sample_data/Makefile
+++ b/sample_data/Makefile
@@ -2,10 +2,10 @@
DIRS = test_GenomeGuidedTrinity \
test_InSilicoReadNormalization \
test_Trinity_Assembly \
-test_Trinity_Coding_Extraction \
-test_edgeR_diff_expr \
-test_full_edgeR_pipeline \
-test_align_and_estimate_abundance
+test_DE_analysis \
+test_align_and_estimate_abundance \
+test_full_edgeR_pipeline
+
test:
diff --git a/sample_data/test_full_edgeR_pipeline/rnaseq_reads/Sp_ds.10k.left.fq.gz b/sample_data/test_DATA/Sp_ds.10k.left.fq.gz
similarity index 100%
rename from sample_data/test_full_edgeR_pipeline/rnaseq_reads/Sp_ds.10k.left.fq.gz
rename to sample_data/test_DATA/Sp_ds.10k.left.fq.gz
diff --git a/sample_data/test_full_edgeR_pipeline/rnaseq_reads/Sp_ds.10k.right.fq.gz b/sample_data/test_DATA/Sp_ds.10k.right.fq.gz
similarity index 100%
rename from sample_data/test_full_edgeR_pipeline/rnaseq_reads/Sp_ds.10k.right.fq.gz
rename to sample_data/test_DATA/Sp_ds.10k.right.fq.gz
diff --git a/sample_data/test_full_edgeR_pipeline/rnaseq_reads/Sp_hs.10k.left.fq.gz b/sample_data/test_DATA/Sp_hs.10k.left.fq.gz
similarity index 100%
rename from sample_data/test_full_edgeR_pipeline/rnaseq_reads/Sp_hs.10k.left.fq.gz
rename to sample_data/test_DATA/Sp_hs.10k.left.fq.gz
diff --git a/sample_data/test_full_edgeR_pipeline/rnaseq_reads/Sp_hs.10k.right.fq.gz b/sample_data/test_DATA/Sp_hs.10k.right.fq.gz
similarity index 100%
rename from sample_data/test_full_edgeR_pipeline/rnaseq_reads/Sp_hs.10k.right.fq.gz
rename to sample_data/test_DATA/Sp_hs.10k.right.fq.gz
diff --git a/sample_data/test_full_edgeR_pipeline/rnaseq_reads/Sp_log.10k.left.fq.gz b/sample_data/test_DATA/Sp_log.10k.left.fq.gz
similarity index 100%
rename from sample_data/test_full_edgeR_pipeline/rnaseq_reads/Sp_log.10k.left.fq.gz
rename to sample_data/test_DATA/Sp_log.10k.left.fq.gz
diff --git a/sample_data/test_full_edgeR_pipeline/rnaseq_reads/Sp_log.10k.right.fq.gz b/sample_data/test_DATA/Sp_log.10k.right.fq.gz
similarity index 100%
rename from sample_data/test_full_edgeR_pipeline/rnaseq_reads/Sp_log.10k.right.fq.gz
rename to sample_data/test_DATA/Sp_log.10k.right.fq.gz
diff --git a/sample_data/test_full_edgeR_pipeline/rnaseq_reads/Sp_plat.10k.left.fq.gz b/sample_data/test_DATA/Sp_plat.10k.left.fq.gz
similarity index 100%
rename from sample_data/test_full_edgeR_pipeline/rnaseq_reads/Sp_plat.10k.left.fq.gz
rename to sample_data/test_DATA/Sp_plat.10k.left.fq.gz
diff --git a/sample_data/test_full_edgeR_pipeline/rnaseq_reads/Sp_plat.10k.right.fq.gz b/sample_data/test_DATA/Sp_plat.10k.right.fq.gz
similarity index 100%
rename from sample_data/test_full_edgeR_pipeline/rnaseq_reads/Sp_plat.10k.right.fq.gz
rename to sample_data/test_DATA/Sp_plat.10k.right.fq.gz
diff --git a/sample_data/test_DATA/Trinity.fasta b/sample_data/test_DATA/Trinity.fasta
new file mode 100644
index 0000000..86d3e4e
--- /dev/null
+++ b/sample_data/test_DATA/Trinity.fasta
@@ -0,0 +1,4443 @@
+>TRINITY_DN10_c0_g1_i1 len=334 path=[312:0-333] [-1, 312, -2]
+TTCACGACGGTCTTGCCCGTGGTATTCGCGAGGCTTCCAAGGCTCTTGACCGCCGTCAAG
+CTCACCTTTGCGTTCTTTGCGAGTCCTGTGACCAAGAAGCTTATGTTAAATTGGTTGAGG
+CTCTTTGCGCTGAATCTGAGACTCCTTTGATCAAGGTTGCCGACCCCAAGGTTTTGGGTG
+AATGGGCTGGCCTTTGTGTCCTTGACCGTGACGGTAATGCCCGTAAGGTTGTTGGATGCT
+CTTGTGTTGCTGTTACCGACTATGGTGAGGATTCCGCTGCTCTTCAAAAGCTTTTGGAAA
+GCTTCTCTGCCTAAACTATCTAGTGGTAAACGAA
+>TRINITY_DN11_c0_g1_i1 len=319 path=[297:0-318] [-1, 297, -2]
+ACAGTGCCTGTAAGTTGCAACAATGCAGCGATCGAGTACGACTGAACTGCTGTACTAAGG
+AAATTGCTAACATAAGTTGTAGCAACCTTCTTGGTTTTACTTCCAGCGTCATATTCGACG
+TGAGGTGCAGTGCTCATTGCCCTTTTCCAAATATCGCCCATTAGGGGTCCATAAACGAGG
+AAAGAAGCAGCATGGTCGAAGGCAATCCCCAAGAGAATTGCACTAGGGCGTACATACGGC
+ATGTGAGTGTAGGATGGCATTTCTTGTATTAATATTTAGTTTGAGTTAGAACAAGATTAA
+TATGAATGTGAATATTTTG
+>TRINITY_DN12_c0_g1_i1 len=244 path=[222:0-243] [-1, 222, -2]
+ACATCGGTTATGATATTGCTAAGGATCGTTTTGTTGATTTAAATGAAATTGGTGTTTTGG
+ATCCCCTAAAGGTCGTACGTACCGGTTTAGTTGATGCTAGTGGAGTCGCCTCATTAATGG
+GTACCACCGAATGTGCCATCGTCGATGCTCCTGAAGAGTCCAAGGCCCCTGCTGGTCCTC
+CCGGAATGGGTGGCATGGGTGGAATGCCCGGTATGATGTAAGGTATCAAAAAAATGCCGA
+CGTG
+>TRINITY_DN17_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2]
+CGCCGTTGAGAGCGATGTAAATACCAACAACGAGGCTGTTGAGTCTTCTACCAAGGAGGA
+GTCTTCCAACACTCCTTCCACCGAAACTCAACCCGAGAAGAAGGCAGAGGAGCCTGAAGC
+CGCTGCCGAACCCTCCGAGTCTACCTCTACCCCTACTAATGCTAGTTCGGTTGCCACTCC
+CTCTGGCACTGCTCCCACCAGTGCTTCCTTGTACGTTGGTGAGCTCGAT
+>TRINITY_DN18_c0_g1_i1 len=633 path=[611:0-632] [-1, 611, -2]
+TTATCATATAATATAGGTTTTGAAAGATGTCCTCTTCTGCTGTCTCTCCTAAGCAATGGG
+TCGCCGGCCTCAACAGCGAGCTTGATATCCCCGCTGTCAACCGTCGTACCTCCATCATTT
+GCACCATTGGTCCCAAGTCCAACAACGTTGAGACCTTGTGCAAGCTCCGTGATGCTGGTA
+TGAACATTGTTCGTATGAACTTCTCTCACGGTTCCTACGAATACCACCAATCCGTCATTG
+ACAATGCCCGTAAGGCCTCTGCCACCAACCCTCTCTTCCCCTTGGCCATTGCCTTGGATA
+CTAAGGGACCTGAGATTCGTACTGGTCTCACCGTTGGCGGTACTGACTACCCCATCTCCT
+CTGGTCACGAGATGATCTTCACCACCGACGATGCTTATGCCGAGAAGTGTAACGACAAGG
+TCATGTACATTGACTACAAGAACATCACCAAGGTCATTCAACCTGGCCGTATCATCTACG
+TTGATGATGGTATCCTTTCCTTCACTGTCATCGAGAAGGTTGATGACAAGAATTTGAAGG
+TCCGTGTCAACAACAACGGTAAGATCTCTTCCAAGAAGGGTGTCAACTTGCCTAAGACTG
+ATGTCGATTTGCCCGCTTTGTCCGAGAAGGACA
+>TRINITY_DN18_c1_g1_i1 len=289 path=[267:0-288] [-1, 267, -2]
+TGTCCGAGAAGGACAAGGCCGATCTCCGCTTCGGTGTCAAGAACGGTGTCGACATGATCT
+TTGCTTCCTTCATCCGTCGTGCTGAGGACGTTATCCACATCCGTGAAGTTTTGGGTGAGG
+AGGGTAAGAACATCAAGATCATCTGCAAGATCGAGAACCAACAAGGTGTTAACAACTTTG
+ACTCTATCCTTGACGTTACCGACGGTATCATGGTTGCCCGTGGTGACTTGGGTATTGAAA
+TCCCTGCCTCTCAAGTTTTCGTCGCCCAAAAGATGATGATTGCCAAGTG
+>TRINITY_DN19_c0_g1_i1 len=283 path=[261:0-282] [-1, 261, -2]
+AGCTCAAAGCAAGCGTGGTATTTTGACCTTGAAGTACCCCATTGAGCACGGTATTGTCAA
+CAACTGGGATGATATGGAAAAGATTTGGCATCACACTTTCTACAACGAGCTTCGTGTTGC
+TCCTGAGGAGCACCCTTGCTTGTTGACTGAGGCTCCTTTGAACCCCAAATCCAACCGTGA
+GAAGATGACTCAAATTATTTTCGAAACCTTTAATGCACCTGCCTTTTATGTTGCTATTCA
+AGCTGTTTTGTCTTTGTATGCCTCTGGTCGTACCACTGGTATC
+>TRINITY_DN21_c0_g1_i1 len=242 path=[220:0-241] [-1, 220, -2]
+GACGACTCCGTTGGGAGCGGTAGTGCGAACGCTCAATAAGGTAGCTCCGACAGGGAAATC
+GCGTTGCAATAAGTCGTTGCATAATTTGTTAATAGCGGCATAAGCAGGTGGAGCCATTGT
+TGCTAATCAATCGAGTATAGTATAATGAGATCACGAGGAAAAAGAACAAGCAGATAAATG
+TAAAATAATTAGCTAGCTAATTTCAAAAAGCTGGTAAACTAAGTACGGGTATTGGGTATT
+TT
+>TRINITY_DN22_c0_g1_i1 len=537 path=[540:0-194 541:195-218 542:219-536] [-1, 540, 541, 542, -2]
+CAAAAACTAACCACGAAAAATGGCTACTAACGTTGGCCCTCAAATCCGTTCCGGTGAGCT
+TGTTTTCGGCGTTGCTCACATCTTCGCCTCCTTTAATGATACATTCGTTCACATCACTGA
+TTTGACCGGCAAGGAAACCATTGTTCGTGTCACCGGTGGTATGAAGGTCAAGACTGATCG
+TGATGAGTCTTCTCCTTACGCTGCTATGTTAGCCGCCCAAGACGCTGCTGCTAAGTGCAA
+GGAAGTTGGTATCACTGCTCTTCACATCAAGATCCGTGCTACTGGTGGTACTGCTACCAA
+GACCCCTGGTCCTGGTGCTCAAGCTGCCCTTCGTGCCTTGGCCCGTGCTGGTATGCGTAT
+TGGCCGTATTGAGGATGTTACTCCCATCCCCACTGATTCTACTCGTAGAAAGGGTGGTCG
+TCGTGGTCGCAGACTTTAAGTGTGCTGTCGTATCTGCCAGTGTCTCGAATTTTATTTCGG
+TACTTTTCTGTCACATGGGAGGAATTTCACTGGAATTGTTATTCGTTTAGGATATCT
+>TRINITY_DN43_c0_g1_i1 len=249 path=[227:0-248] [-1, 227, -2]
+CTTCTTGCCTCTGTTCTTACGTTGCTTGCGTTGCTGACGAGCAACCTTTTGGATAGGCTC
+AGCTTGACCAACACGAACAAGACGGTAGTGAGGCTCAAACTTCTTCATGGACTCAGTAGA
+GTCATAGATCAAAGCGAAGCCGGTAGATCTGCCACCACCAAAATGAGTGCGAAGACCAAA
+GGCTTGAACGCATTCGGAATCAGTCTTGTACATTTGAGCCAACTTCTCACGAATTTCATT
+CTTGGAAAG
+>TRINITY_DN45_c0_g1_i1 len=224 path=[202:0-223] [-1, 202, -2]
+CGGTCTTGACGAGTTTTGCCCATAAAGATTGAACCAAAAATACGGTTGATCCCCAAAGGT
+GAAAGCCAACCGCGAACAAAAAGAAGAAAGCGGGATAGGAACTGACCGGAATCCTTCAAG
+GTCTGAACAGACCCAGCATCAACGAACACTATTCCTTTCACCTCAGATAGATGGCGAGCG
+GCAAATACATTGGAGTAAACACCGCCGATTCCATGAGCGACAAG
+>TRINITY_DN46_c0_g1_i1 len=638 path=[616:0-637] [-1, 616, -2]
+CCTACACAATTTTAGGAACTTGGAATAATTAGCAGAAATGGCAGAAAGCGCACCCAGAGG
+ATTTGGAAGAGGTGGACGTGGTGGTCGTGGTCGCGGACGTGGCCGTCGTGGAGCCAAGCG
+TGATGAGGAGAAGGAATGGGTTCCCGTCACCAAGTTGGGCCGTCTGGTGAAGGCTGGTAA
+GATCAAGTCTATTGAAGAGATCTACTTGTACTCTCTCCCCATCAAGGAGTACCAAATTGT
+CGACTACTTCTTGCCTCGTTTGAACGACGAAGTTATGAAGGTCGTTCCCGTCCAAAAGCA
+AACTCGTGCCGGTCAACGTACCCGTTTCAAGGCTTTCGTTGTTATTGGTGACAGCGATGG
+TCACGTTGGTTTAGGTATCAAGTGCGCTAAGGAAGTTGCTACTGCTATTCGTGGTGCTAT
+CATCATGGGCAAGCTTTCCATCATGCCTATTCGTCGTGGTTACTGGGGTACTGCTTTGGG
+TGATCCTCACACTGTCCCCGTCAAGGTTTCTGGCAAGTGCGGTTCCGTTACTGTTCGTCT
+CGTCCCTGCTCCCCGTGGTGCTGGTCTTGTTGCTGCTCCCGTTACCAAGCGTTTCCTTCA
+ACTCGCTGGTATCGAAGATTGCTACACCCAATCTCGTG
+>TRINITY_DN51_c0_g1_i1 len=408 path=[386:0-407] [-1, 386, -2]
+CTGGTGATATAATCCAAGGTGAACATGTGCACAACGAATTTATTCCGAGCGTTCGAACAT
+TTCGTCTTTGAATCAGTGTAATAAAATCTTAAATTAAAAACAGCAGCAACTTAAAATGCG
+TTCCATATATACAAAGATTCGTCCCAACCAACACTTGCAATCCAAGATCCATCGCCGAAA
+TCACTCCAATCAACATCACGGACAAATTCAGAATGCAAATCAACTTTTCTTATGCAAGAG
+TGCTGTTCCGGGTCAAAAATTCGAGAAGTCATATCGTAACTTGCTGTAGCCAAAAGATCA
+TGGGCGGAATTGGACGATTTTATACTTCGAACAGCAAGTTGGTGACCAGACAATACGGAC
+AGAGGCGTCTTTAAATTCGCGATATCGTAACAGTAAACCAGATTGTTA
+>TRINITY_DN51_c1_g1_i1 len=461 path=[439:0-460] [-1, 439, -2]
+TACCAGATTGTTATTGTCGGCCGTGTAAACCATACGATGATTAGACTTGCTCCAATTCAT
+GCAAGTAATTTGATTCGGTATTTCAATGGACATAAATTTATCGGAAGACCGGAAATCCCA
+AAATTTGCATAATCCATCACTTGATGTATACCCGAGTAAATTTGGAGAGCTATAATGTGT
+AGCAACTGTAAGAATCCTTGAATTCGAACCATTGTTGAGCGTCTGCACACTGTTAGGCAA
+ATTGCCTAACCATAATTTGATAGTCCCATCCCAGGAGCCCGTAACTACAATTCTTCGATC
+AACCGTATTTGTGTCTATTGCGACAATCTCCGCTTTATGCTCTTTCCATTTATGGATGGG
+CTTAGAGGGCATAGTCAAATCAAATAGTCTCAAAGAACCATCACCACAGCAAGCGTAGAC
+TTGATTTTCACAATTCTGAGACCAGCGCACACCAAACAAAG
+>TRINITY_DN52_c0_g1_i1 len=658 path=[636:0-657] [-1, 636, -2]
+GAAGAAGACCCAAGAGCAGTCTAGTGAACAGCGTGTTGCTGCCGCTGCCGAGAAGAAAGC
+TGCTCAACAAAAGAAGCGTGAGCTCATTGCAAAGCGCGCCGAATCTTACGATGCTGAGTA
+CCGCAAGGCCGAACGTGAGCAAATCGAACTCGGTCGCAAGGCTCGTGCTGAGGGCAACTA
+CTACGTCCCTGACGAAACCAAGTTGGTCTTTGTCATCCGTATTCGTGGTATCAACAACAT
+TCCTCCCAAGGCCCGTAAGATCATGCAATTACTCCGTCTTATTCAAATCAACAACGGTGT
+CTTTGTTAAATTTAACAAGGCTACCAAAGAAATGCTTCAAGTCGTTGAACCTTATGTTAC
+TTATGGTATTCCTAACCTCAAGACTGTTCGTGAGCTCCTTTACAAGCGTGGTTTTGGTAA
+GGTCAACAAACAACGCATTGCTCTTTCTGACAATGCTATCATCGAAGCTGCTTTGGGCAA
+GTACTCTATCTTGTCTATCGAGGATTTGATTCACGAAATTTACACCGTCGGTCCCAACTT
+CAAGCAAGCTGCCAACTTCATCTGGCCCTTCCAACTTTCTTCTCCCTTGGGTGGCTGGAG
+AGATCGCAAGTTCAAGCATTTCATCGAAGGTGGTGATGCTGGCAAGCGTGATGAGCAA
+>TRINITY_DN58_c0_g1_i1 len=692 path=[670:0-691] [-1, 670, -2]
+CAAAAATGGCACCCAAGTCTAAAAAGGTCGCACCCTCACCTTTTGCTCAGCCTAAGGCTG
+CAAAAACTACTAAGAACCCTTTGTTCGTGAGCCGTCCCCGTTCCTTTGGTATTGGACAAG
+ACATCCAACCTAAGCGTGACTTGAGCCGTTTTGTTAAGTGGCCTGAGTATATCCGCCTTC
+AACGCCGTCGCAAGATTTTGAACTTGCGTTTGAAGGTTCCTCCTGCCATTGCTCAGTTCC
+AGAAGACTTTGGACAAAAACACTGCTACTCAGGTCTTCAAGTTGCTTAACAAGTACCGTC
+CTGAGACTGCTGCTGAAAAGAAGCAACGTTTGGTTGCTGAAGCCGAGGCTGTTGCCAACG
+GCAAGTCTGCTCAAGACGTCTCTAAGAAGCCTTACAATGTTAAATATGGTTTGAACCATG
+TTGTAGCTCTCATTGAGGCCAAGAAGGCTAAGTTGGTTCTCATTGCCAGCGATGTCGACC
+CCATTGAACTCGTCGTTTTCTTGCCTGCTTTGTGCAAGAAGATGGGTGTTCCTTATGCCA
+TTGTCAAGAACAAGGCCCGCCTTGGTACTGTCATTCACCAAAAGACTGCTGCTGTTTTAG
+CTGTCACTGAGGTCCGTGAGGAAGACAAGAACGAACTCGCTTCTATTGTCTCCGCCGTTG
+ATGCTAACTTCTCTGCTAAGTACGACGAAAGC
+>TRINITY_DN6_c0_g1_i1 len=203 path=[181:0-202] [-1, 181, -2]
+TCGGTGTCGTCGAACTTGAAGACAGAGGCGAGTGGGCCGAATGTTTCCTCGCTAGCAACC
+AACATGTCTTGAGTTACACCGGAGAGCACGGTTGGTTCAAAAAAATAACCTTTGCTTGAG
+GAAATCTCCTTTCCACCAACAGTGATTTTGGCACCCTTTGAAACAGCATCTTCAATGTGC
+TTGCTGACCTTTTTGCATCCATC
+>TRINITY_DN61_c0_g1_i1 len=510 path=[488:0-509] [-1, 488, -2]
+AATCAACTGGGCAGCAATTAAGCTTGGGTTTCATCATCAATTTCTTCAAGGGCTCTTTGG
+GCGCGGGTTTTGGCTTGCTTGGATACATTAGGATTATGCATAGTAGCTTTATAACCTCCT
+CGGACATTTTCAATGTTCTTGCCCTCAAGTTGATCTTCTTCGACCAAATCACCTGTTTTC
+ATAGGATCATCAACAAAACCCGACTCATCTCCCAACACATTTAGACCCTCCTCGTTGTCA
+AAGTCTGCATCCTCATCATAATCACCGAGATCCTCATAATCAAGATCACGGCCTCCAGCT
+TGAGCGGAATAATCACCAGTCTCTTGGCCGGAAGAATGACTTTCTATATAGTCTTCGGCT
+CTTTCTTTGGCTTGTTGTGATACATTGGGATTGTGTAGGGTGGCTTTCTTGCCAGCGAGA
+ACACGATTAGGATCAGGCATTGTTTATAAATAAAATTGGAGTTCTTTCTGATTTAATAAA
+ACGGCTTACAAAAAGTACTACGGTGCGAAA
+>TRINITY_DN65_c0_g1_i1 len=269 path=[267:0-57 268:58-268] [-1, 267, 268, -2]
+CTAATTGAACACGCTTAACTTTGCAAAGCTTGTATTTAGCCTCTTCAGCAGTAATACGGT
+GGACAGTGAAACGGCCCTTAATGTCATAGACAAGGCGGAAGTGCTCACCAGTCTTTTCAA
+CGGAGATCACATCCATAAAGCCGGTAGGGAAAGTAGAGTCGGTACGAACCTTTCCATCTA
+CCTTAATGAGACGTTGCATAAGGATAGCCTTAACCTCACGTCCGTTCAAAGCATATTTAA
+GACGGTTACGCAAGAAAACAATCAAAGGA
+>TRINITY_DN67_c0_g1_i1 len=253 path=[231:0-252] [-1, 231, -2]
+ACTTGAGGGCGTAACAAAATTCTTTCCTTGTAGTAATCATAGTTTGAGTAGAATTTTTCA
+AATCCCTGAGGAGAAAAACGGGTTGAGGTAGCAGTAGCAAAACGTAACTTTTCAGAGTCA
+AAGAGAGGCAAGAAAGTATCTTGTAAGACTTCTGTCCACACTTCGAGATCTTTAAAGGGA
+GAATGGGCAAGACCACCGATAATAGCGTTGGCAATGTTTCCAATACCGGATTGCAAAGGA
+TGAAGATTTTTGG
+>TRINITY_DN70_c0_g1_i1 len=429 path=[407:0-428] [-1, 407, -2]
+GCAATGGCACAGGTCGGACGCCCCAACATACTGAATGCTACTGATGAGGACATCAAGCAG
+CTCCTCGCTGCCAACTGCCACATTGGCTCCAAGAACTTGGAGGTCCGCATGGATAACTAC
+GTCTGGAAACGTCGTAGTGATGGCGTCCACATTTTAAACCTTGGTAAGACCTGGGAAAAG
+TTGGTTTTGGCTGCTCGTGTCATCGCAACTATTGAAAACCCTGCCGATGTTTGCGTTGTT
+TCAACTCGTACTTATGGACATCGTGCTGTTTTGAAATTTGCTGCTCACACTGGTGCTACT
+GCCATCGCTGGCCGCTTTACTCCTGGTAACTTCACCAACTACATTACTCGTACTTACCGT
+GAGCCTCGTCTCATCGTCGTCACTGATCCCCGTGCCGATGCTCAAGCTATCAAGGAGGCT
+TCTTTCGTC
+>TRINITY_DN71_c0_g1_i1 len=269 path=[247:0-268] [-1, 247, -2]
+CTTTTCAATCGAGGTAGGACGAGGTTCAATACGGTCAAGAACGGAAGGGTTTAGAATGTA
+AATACCACCATTAATTCTGTTGGATACAAACTCAACAGGCTTTTCAACAAAGCGCTCAAT
+CAAGGATTCTGAGTTGGGATAATGAACGACAACACCATACTTAGAAGGCTCCTCAACCTT
+GGTAACAACGATAGTACCCTCGGCACCATGAGCCTTATGGAAAGCTGCCAAATCCGCGAA
+AGGATACTCACAAATAACATCACTATTCA
+>TRINITY_DN75_c0_g1_i1 len=238 path=[292:0-42 299:43-116 291:117-237] [-1, 292, 299, 291, -2]
+CAAAATCCAAGACAAAGAAGGAATTCCTCCTGATCAACAACGTCTTATTTTCGCTGGTAA
+GCAGTTAGAAGATGGACGTACTTTGTCTGATTACAACATCCAAAAGGAGTCCACTCTTCA
+CCTCGTTTTGCGTCTTCGTGGTGGTGGTAAGAAGCGTAAAAAGAAGACTTACACTACTCC
+CAAGAAGATCAAGCACAAGCACAAGAAGGTTGAGCTCGCCGTCCTCAAATACTACAAG
+>TRINITY_DN75_c0_g2_i1 len=238 path=[294:0-42 298:43-116 297:117-237] [-1, 294, 298, 297, -2]
+CAAAATCCAAGACAAAGAAGGAATTCCTCCTGATCAACAACGTTTGATCTTTGCTGGCAA
+GCAACTCGAGGACGGACGTACTTTGTCTGATTATAACATCCAAAAGGAGTCCACTCTTCA
+CCTCGTTTTGCGTCTTCGTGGTGGTGGTAAGAAGCGTAAAAAGAAGACTTACACTACTCC
+CAAGAAGATCAAGCACAAGCACAAGAAGGTTGAGCTCGCCGTCCTCAAATACTACAAG
+>TRINITY_DN78_c0_g1_i1 len=242 path=[220:0-241] [-1, 220, -2]
+GCTTTTTGGAAGCACAGCATGCAGTTTTGGGAGTCTTTGAAAATACAGCGCTGATTGTAA
+ATACAATGCCAGCAATAGCGGTACAGGTGCAAAGAGTACGATTGTTAAGGGTTCCAGATT
+GACGGCTTTTCAAGAGATATGCAGAGATGGCGCCAAGACTGAGGAGGTTGATTGATATGG
+CAGCAGAAGCTGGAACTTTATGAGCATTGACAAAATTGCAAGCTTTGGAGTAAATAGATT
+TC
+>TRINITY_DN8_c0_g1_i1 len=214 path=[192:0-213] [-1, 192, -2]
+GATGTCCGAGCCACGAGCGTCCTCCTGAAGATAGCGACTGAACAAGCTGAAAAAGTTGTC
+CATCTCCTTTTGAAAGGCCTTCTTAGCCAAGGGATCCTTTACGGTGCTAGCCAAGTGATT
+CAGCTCATTCTTCATAGTACTGGCAGCAATACTGGTAGCGGTGTTGTCAAAAGCAAAAGC
+CGATTGCGACTTGCTGTGCTGACGACCGAGGGGA
+>TRINITY_DN83_c0_g1_i1 len=357 path=[335:0-356] [-1, 335, -2]
+AATGAAATCAGCGAAATCAGCAATGCCAACAGCCGTCAAAACGTCCGTAAGTTGATTAAG
+GACGGTTTGGTTATTCGCAAGCCTAACTTGATGCATTCTCGCTTCCGCATTCGTAAGACC
+CATGCCGCCAAGCGTCTTGGTCGTCACACCGGTTACGGTAAGCGTAAGGGTACTGCCGAA
+GCTCGTATGCCCTCTGCTGTTGTTTGGATGCGCCGTCAACGTGTTTTGCGTCGTCTTCTT
+CGCAAGTATCGTGAGTCTGGCAAGATTGATAAGCATCTTTATCACACTCTTTATTTGGAA
+GCTAAGGGTAACACCTTTAAACACAAGCGTGCTTTAATTGAGCATATTCAACGTGCC
+>TRINITY_DN85_c0_g1_i1 len=247 path=[225:0-246] [-1, 225, -2]
+CGCATTTTGTTAAGTCGACTGTATACTTTTGAAGCTTTGGCTTTACTTCTGGTTTCTCTG
+GGTTCCAGCGATAAATCTCGAAAGTTTTTAAATTTTCACCCTGTGACTGAGGATTAGCAG
+AAGTGGCAGATATGTTGGCCTCTGTAGCCATCATACGGGCATTTCTGTTAACAAAATGCT
+TCAAAAACGGGCTCAAAACTTGAATTCGACGGCTGAACATCTCGATATGTTTTGATTTTT
+AATATTG
+>TRINITY_DN9_c0_g1_i1 len=215 path=[230:0-164 231:165-214] [-1, 230, 231, -2]
+CGGTTTCCCCATCACTGTTGAAGGTGTTAATGGCACTGGCCGATTCATTCTCTTCAACCT
+CTCCTCCGTTGCCAACGATTCTACTGTCTACTCCAACCGTCCCAACCGCATTGCCGAAAT
+TGGACGTTTCAACTGCTCTAGCTCTGGTTGCGATTATGCTACCAATGTTACATGCCCCGA
+CTCTTATACTGCGGTCTCTTATGAAATGATGGCTC
+>TRINITY_DN9_c0_g2_i1 len=202 path=[232:0-164 233:165-201] [-1, 232, 233, -2]
+CGGTTTCCCCATCACTGTTGAAGGTGTTAATGGCACTGGCCGATTCATTCTCTTCAACCT
+CTCCTCCGTTGCCAACGATTCTACTGTCTACTCCAACCGTCCCAACCGCATTGCCGAAAT
+TGGACGTTTCAACTGCTCTAGCTCTGGTTGCGATTATGCTACCAACGTTACATGCCCCAA
+CTCATACACCGCGGTTTCTTAT
+>TRINITY_DN96_c0_g1_i1 len=1156 path=[1156:0-792 1157:793-1155] [-1, 1156, 1157, -2]
+CAATTTTGTACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATCGTTTATTTGATAGT
+ACCTCAACTACTTGGATAACCGTGGTAATTCTAGAGCTAATACATGCTAAAAATCCCGAC
+TTTTTTGGAAGGGATGTATTTATTAGATAAAAAACCAATGCCTTCGGGCTTTTTTTGGTG
+AGTCATAATAACTTTTCGAATCGCATGGCCTTGCGCCGGCGATGGTTCATTCAAATTTCT
+GCCCTATCAACTTTCGATGGTAGGATAGAGGCCTACCATGGTTTTAACGGGTAACGGGGA
+ATTAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAG
+CAGGCGCGCAAATTACCCAATCCCGACACGGGGAGGTAGTGACAAGAAATAACAATGCAG
+GGCCCTTTCGGGTCTTGTAATTGGAATGAGTACAATGTAAATACCTTAACGAGGAACAAT
+TGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAA
+GTTGTTGCAGTTAAAAAGCTCGTAGTTGAACTTTGAGCCTGGTCGACTGGTCCGCCGCAA
+GGCGTGTTTACTGGTCATGACCGGGGTCGTTAACCTTCTGGCAAACTACTCATGTTCTTT
+ATTGAGCGTGGTAGGGAACCAGGACTTTTACCTTGAAAAAATTAGAGTGTTCAAAGCAGG
+CAAGTTTTGCTCGAATACATTAGCATGGAATAATAAAATAGGACGTGTGGTTCTATTTTG
+TTGGTTTCTAGGACCGCCGTAATGATTAATAGGGATAGTCGGGGGCATTCGTATTCAATT
+GTCAGAGGTGAAATTCTTGGATTTATTGAAGACGAACTACTGCGAAAGCATTTGCCAAGG
+ATGTTTTCATTAATCAAGAACGAAAGTTAGGGGATCGAAGACGATCAGATACCGTCGTAG
+TCTTAACCATAAACTATGCCGACTAGGGATCGGGCAATGTTTCATTTATCGACTTGCTCG
+GCACCTTACGAGAAATCAAAGTCTTTGGGTTCCGGGGGGAGTATGGTCGCAAGGCTGAAA
+CTTAAAGGAATTGACGGAAGGGCACCACAATGGAGTGGAGCCTGCGGCTTAATTTGACCC
+AACACGGGGAAACTCA
+>TRINITY_DN96_c0_g2_i1 len=408 path=[1158:0-44 1159:45-407] [-1, 1158, 1159, -2]
+AATAATAAAATAGGACGTGTGTTTCTATTTTGTTGGTTTCTAGGACCGCCGTAATGATTA
+ATAGGGATAGTCGGGGGCATTCGTATTCAATTGTCAGAGGTGAAATTCTTGGATTTATTG
+AAGACGAACTACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTT
+AGGGGATCGAAGACGATCAGATACCGTCGTAGTCTTAACCATAAACTATGCCGACTAGGG
+ATCGGGCAATGTTTCATTTATCGACTTGCTCGGCACCTTACGAGAAATCAAAGTCTTTGG
+GTTCCGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAATTGACGGAAGGGCACCAC
+AATGGAGTGGAGCCTGCGGCTTAATTTGACCCAACACGGGGAAACTCA
+>TRINITY_DN100_c0_g1_i1 len=443 path=[446:0-204 447:205-228 448:229-442] [-1, 446, 447, 448, -2]
+CACGGCTAGAATCCTTGGTACGGACAGACATCAAAACTTGACCGATGTTTACACGGGCGA
+CCAAACCATTGGGCTTACCAAAGGCGTGACGCATACCGGTTTGCAATCTATCGGCACCGG
+CACATGAAAGCATTTTGTTGATACGAACAACATGGAAGGGGTGTGCACGGACACGAAGGT
+GGAAACTATCCTTACCACCAATCTTAACCAAGTACTTGTTGGCACAGATACGAGCAGCTT
+CAAGAGCCTCTGAGGTGATTTGCTCGTATTCGTTAGAGACCAAGTGGATGCAAAGAGGGA
+ACTCGTCAACACCAGCACGCTTACGACCCAAGTCGAAAATACGAATCTTGGAATCGGGAA
+CGGCACGGTTGTAACGAGACTTGGGGTAAGGCTTATTCTTACAATAACGATAGCAGCGAG
+CAGGTCTACGTGCCATTGTGAAA
+>TRINITY_DN101_c0_g1_i1 len=251 path=[229:0-250] [-1, 229, -2]
+GTTTTTTATTTTTATTATTTTAATTTTCGCTTTCTCTCTCTCTCTTTTTTTTTTTTTTCA
+ATCAATTCAATGAAGTCATTCGTTTGGACCTTGTTGGGTGCCCTCTCCTTGGGTTCCCTC
+ACCACCGCTTATGGTGCCAACGCTTCTAACTCAAGTGTTCCCACTCCTGATAACACCTTG
+GTTGTTAGCTACACCAACACTTCTTGCTACACCAGTGGCCCTCTTTCCCCTGACACCCGT
+TTCAACAGGAC
+>TRINITY_DN103_c0_g1_i1 len=1219 path=[1223:0-387 1224:388-1218] [-1, 1223, 1224, -2]
+CCTGGTGAGTTTCCCCGTGTTGGGTCAAATTAAGCCGCAGGCTCCACTCCATTGTGGTGC
+CCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCAAAGA
+CTTTGATTTCTCGTAAGGTGCCGAGCAAGTCGATAAATGAAACATTGCCCGATCCCTAGT
+CGGCATAGTTTATGGTTAAGACTACGACGGTATCTGATCGTCTTCGATCCCCTAACTTTC
+GTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTAGTTCGTCTTCAATAAA
+TCCAAGAATTTCACCTCTGACAATTGAATACGAATGCCCCCGACTATCCCTATTAATCAT
+TACGGCGGTCCTAGAAACCAACAAAATAGAACCACACGTCCTATTTTATTATTCCATGCT
+AATGTATTCGAGCAAAACTTGCCTGCTTTGAACACTCTAATTTTTTCAAGGTAAAAGTCC
+TGGTTCCCTACCACGCTCAATAAAGAACATGAGTAGTTTGCCAGAAGGTTAACGACCCCG
+GTCATGACCAGTAAACACGCCTTGCGGCGGACCAGTCGACCAGGCTCAAAGTTCAACTAC
+GAGCTTTTTAACTGCAACAACTTTAATATACGCTATTGGAGCTGGAATTACCGCGGCTGC
+TGGCACCAGACTTGCCCTCCAATTGTTCCTCGTTAAGGTATTTACATTGTACTCATTCCA
+ATTACAAGACCCGAAAGGGCCCTGCATTGTTATTTCTTGTCACTACCTCCCCGTGTCGGG
+ATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCC
+TCTCCGGAATCGAACCCTAATTCCCCGTTACCCGTTAAAACCATGGTAGGCCTCTATCCT
+ACCATCGAAAGTTGATAGGGCAGAAATTTGAATGAACCATCGCCGGCGCAAGGCCATGCG
+ATTCGAAAAGTTATTATGACTCACCAAAAAAAGCCCGAAGGCATTGGTTTTTTATCTAAT
+AAATACATCCCTTCCAAAAAAGTCGGGATTTTTAGCATGTATTAGCTCTAGAATTACCAC
+GGTTATCCAAGTAGTTGAGGTACTATCAAATAAACGATAACTGATTTAATGAGCCATTCG
+CAGTTTCACAGTACAAAATTGCTTATACTTAGACATGCATGGCTTAATCTTTGAGACAAG
+CATATGACTACTGGCAGGA
+>TRINITY_DN103_c0_g2_i1 len=414 path=[1225:0-387 1226:388-413] [-1, 1225, 1226, -2]
+CCTGGTGAGTTTCCCCGTGTTGGGTCAAATTAAGCCGCAGGCTCCACTCCATTGTGGTGC
+CCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCAAAGA
+CTTTGATTTCTCGTAAGGTGCCGAGCAAGTCGATAAATGAAACATTGCCCGATCCCTAGT
+CGGCATAGTTTATGGTTAAGACTACGACGGTATCTGATCGTCTTCGATCCCCTAACTTTC
+GTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTAGTTCGTCTTCAATAAA
+TCCAAGAATTTCACCTCTGACAATTGAATACGAATGCCCCCGACTATCCCTATTAATCAT
+TACGGCGGTCCTAGAAACCAACAAAATAAAACCACACGTCCTCTTTTTTTTTTT
+>TRINITY_DN104_c0_g1_i1 len=408 path=[386:0-407] [-1, 386, -2]
+CTTGGCAACTGAAATTAAGACACCACCAACACCTTGATCGCCGATACCCAAAATACCTTC
+AGAATCGGTAATGATAATGTATTCGACACTATCGGATTTTCCAAACTCGGAAAGCTGTTG
+CTTGATATAAGACAAATCGTTATGATCAATATCCAAATAACAACCCTCAGGATAACGATA
+TATATCGGAAAACTGCTTGATGGCATCGCCTTCGGTAGGTGTATAGATGATAGGAATCAT
+TTCGATCAAATGTTGGCTGATGAGTGCGTAAAACAGAGTTTGGTTGGTGACGCTTAATTG
+AGAAAGATACAAATTCTTCTGTAAGGGCTCATCACCGATTGCTTTGTACTGGTCATAACA
+GCGATCCACTTGTTGTTGCAAAGTTTCAACAATGGGGGGAAGACGTGA
+>TRINITY_DN106_c0_g1_i1 len=1111 path=[1089:0-1110] [-1, 1089, -2]
+AATAACTTCCTCACCGTCAACGTTTTCAAGATGAGCGGCACTTTCGCCTTGAACACCACG
+GGATTTTTCACGAACCTCTTCTTGTTGCTTGGTGAAGTTACCAAGGTTCTTAGGTCTAGG
+CATCCAGGGCTTAGCACCAGAGATATATAGTTCGTTAATCTCTTCCAAGGTAAGACCTTT
+GGTTTCATGAGCAAACAAGAAAATAATACAAGCAGCACACAAGTTACAAGCAGCGAAAAT
+GTAACCATACTTGAATCCAATGGAGTTGGTAATGAAGGGAGTGAAAAAGGAAATAAGGAA
+ACCCCACAACCAGTTACCAGTGGTAGCGACGGCAGCACACTTGGAACGATAACGAATGGG
+ATACGATTCACCAACGATAACGTATGCGGCAGGACCCCAAGTTTGAGCAAAACTGAAAAT
+GAAAAGACATGAGAACACAATCATAACGGCACCGGCACGATGGTTTGAGGTACCATTCTT
+ACGAGTAAGAGCACGATTACCAACAGCTGCGTAAATGAAGAAAGTAATGGATTGCCAAAG
+AGCACCAATAATCAATGGCATACGACGACCAAAGAACTCTAGGACGAAAAGACCACCAAA
+CGTACATCCAAAGTTAACGGCATCAAGAATCAAAGCAGAAAGATAAGGAGAGTTCATACC
+AGTACCCTCAAACACCTCGAAACCATAGTAGAAGTAGTAGTTATCACCGGTAAGTTGTTG
+AAGAGACATGACACCAAGACCAAGGAAGGTACGATAACGAATGTCGGGACCAAAAATTTC
+GGGCCAAGTAGCGGGACCACCAGCCAATTCAGCTTCACAATCAGACTTAATAACATGGTA
+TTCCGTTTGGATAACTTCGTGTTCGATAGGAAGATCGTTGTTCTTGGCCATAATTTGAAG
+AGCCTCTTCATCTCTACCAACAGAGATCAAATAACGAGGGGATTCAGGAAGGAAAGAAAT
+ACCGATGAAGGTGATGATACCCCAAAGCAAGTTAATACCCATGGATACACGCCATTGAGC
+AGTCTTGTGCAACTTGTGAGTACCCATGTTGATACAAGCGGCAATGAAAATACTACTAGT
+GACAGCCAATTGATCGGTGGCGACAATGGTA
+>TRINITY_DN106_c1_g1_i1 len=339 path=[317:0-338] [-1, 317, -2]
+TTCTGGGTATTCATTCATTTATCTTCCAAATGCAGCGAGTGAGACAAGAATAAATTAGTT
+CCAATCTTTAAAAAATGCCACCGCTACTCCTAACAAACATCAGAAATTTTCAGGGATATA
+ATAAAAAACAACAACAGGAATCAACGAACCACGACAAACATTAAGCTTAAAATAAGCGCA
+TTTTAAGCTTTTTATAAATATTGTTGTTATCAATCAGCAATCTATGCGAATTGTTCTTCC
+TGATCGTGGTAGCTAGATTCGGGCTTGGCACGGCCATCCGAAGATGTTGTGGAACTAATG
+TCATTGCTAGAGTCCTCAATACCTTCCTCACCGTCAACG
+>TRINITY_DN107_c0_g1_i1 len=208 path=[186:0-207] [-1, 186, -2]
+CAAACTTCTTCTTGCTCCATGAGGGAACTCGTTCAAAAGCTCATTCCTGAGGTCATTGGC
+CGTGAAATTGAAAGAGCTACTGGCAGTATTTTCCCTCTCCAAAATGTTCTTGTCCGTAAG
+GTCAAGATCCTCAAGGCCCCTAAGCATGATGCTCAAAAGCTCCTCGAGTTACATGGTGAG
+AGTCAAGATGTTGGCACAAAGGTTGTCA
+>TRINITY_DN110_c0_g1_i1 len=345 path=[323:0-344] [-1, 323, -2]
+CTTCGTCGTAGTAAAGGACCTTTAATAGTGTTTACTTACTTGGCATTCAACAACTTAGGA
+AGCACTCTTTGACCTAAATTTATTAATTCTATTTAATAAGCCATGTCTCCGGTTTTTTTA
+CCCAGCGGTGAAACTTACGATCAAGAGCATCTTGATGACAACCGTGTCTTAGGTTACAAC
+CCTTTGGTTCCTGCCGCTTTGGTTCAACAAGAGATTCCTGTTTCTGAAACTTCTCGCAAA
+GTCATCACTGACTCCAGAAAGGAGATTCAAGCTATTCTCAACAAACAAGATGACAGAATT
+ATCGTTGTTGTCGGTCCTTGCTCCATTCATGACCCTAAATTGGCC
+>TRINITY_DN114_c0_g1_i1 len=232 path=[210:0-231] [-1, 210, -2]
+CATAGCACGGAAATGAGCAAAAGTCTCAATAGGTTGATGGGTAGGACCGTCCTCACCCAA
+ACCAATAGAATCATGGGTAGCAACATAAATGACACGGCTGTTGTTCAAGGCAGCCATACG
+AACGGCACCGGCAGCATAAGAAACAAAGTTCAAGAAAGTACCACCGTAAGGGATGATAGG
+ACCATAGACGGCCAAACCGTTCATGATACCAGCCATACCATGCTCACGAATA
+>TRINITY_DN115_c0_g1_i1 len=232 path=[210:0-231] [-1, 210, -2]
+CCGGGCTTGTAAACAGGAAGATGCTTCTCCCAACCCTCGGGGAATTTACGGCTCAAGATA
+CGCTCAAGCTGATTGGAAAGATCAGGGTAAGATTGCTTGTAAGAAGCATACATTTTTTTG
+TACTCTTCTTCAGCAGAGGAAGCGATGGCGACACGCTCCTTGTAGTAGGCATAAACCTCG
+GGAGGAACTTGGAAAGTCTTGGTGGGGTCGAAACCAAAGAGTTTCTTGACAT
+>TRINITY_DN118_c0_g1_i1 len=242 path=[220:0-241] [-1, 220, -2]
+ATGCGACTCCAAGGAGGAAGCCCAATTTTATTTGGGTAAGCGTGTTTGCTATGTTTATAA
+GAGCTCCAAGGCCGTCCGTGGATCCAAGATTCGTGTTATCTGGGGTACCATTGCTCGTCC
+TCATGGAAACTCCGGTGCTGTTCGTGCTCGCTTCGTTCACAACTTGCCTGCTAAAACTTT
+TGGCTCTTCTCTCCGAGTCATGCTTTACCCCTCCAACATTTAAATAAAATAGTGGTATTT
+CG
+>TRINITY_DN120_c0_g1_i1 len=296 path=[274:0-295] [-1, 274, -2]
+GCTGCTCAGCTCCGTACTTTGGACTTTGCTGAACGCCATGGTTATATTCGTGGTGTCGTC
+CAAAAGATCATTCATGATCCTGGTCGTGGCGCTCCTTTGGCTAAGGTTGCCTTTCGTAAC
+CCTTATCATTACAGAACCGATGTTGAGACCTTTGTTGCAACTGAGGGTATGTACACGGGC
+CAATTTGTCTACTGCGGTAAGAACGCTGCTTTGACTGTTGGTAATGTGCTGCCTGTTGGT
+GAAATGCCTGAGGGTACCATCATTTCAAACGTTGAGGAAAAGGCTGGTGACCGTGG
+>TRINITY_DN121_c0_g1_i1 len=245 path=[223:0-244] [-1, 223, -2]
+CACGCACTGCACTCCTCGTCAAAATGAAGTACCTTGCAGCTTATTTACTCTTGACCGTTG
+GTGGAAAGGACTCCCCTTCCGCTTCTGATATCGAGTCTGTTTTGTCTACTGTCGGTATTG
+AAGCTGAATCTGAGCGCATTGAAACTTTGATCAACGAGCTTAACGGTAAGGATATCGACG
+AGCTCATCGCTGCTGGTAACGAGAAGCTTGCTACTGTCCCCACTGGTGGTGCTGCTTCTG
+CTGCT
+>TRINITY_DN122_c0_g1_i1 len=210 path=[188:0-209] [-1, 188, -2]
+GTTCTAGCGGTGGCCGTGGTGGAGCCAAAGGAGGTGCTAAAGTTATTATTGAGCCTCATC
+GTCATGCAGGTGTCTTCATTGCTCGCGGAAAAGAAGATTTGCTTGTCACCCGCAATCTGG
+TGCCTGGTGAATCAGTATACAATGAAAAACGTATTAGCGTTGATTCCCCAGATGGTACCA
+AAGTTGAATACCGTGTATGGAATCCTTTCC
+>TRINITY_DN124_c0_g1_i1 len=375 path=[353:0-374] [-1, 353, -2]
+GTGGTAATACGTTCTTGCATAGCACCCATATCAGTGGCTAACGTGGGTTGGTAACCGACG
+GCAGAGGGAATACGACCAAGCAAAGCTGATACTTCAGAACCTGCTTGAGTAAAACGGAAA
+ATGTTATCAATGAAAAGCAAAACGTCTTGTCCTTCAATATCGCGGAAATATTCAGCAACA
+GTCAAACCAGTGAGAGCAACACGTGCACGAGCACCTGGAGGCTCATTCATTTGACCAAAG
+ACAAGAGCAGCCTTAGACTCGCCTTCTAATTTAATGACACCGGTTTCTTGCATTTCCCGG
+TATAAATCGTTACCCTCACGGGTACGTTCACCGACACCAGTAAAGACAGAGTAACCACCA
+TGAGCTTTGGCAATG
+>TRINITY_DN124_c1_g1_i1 len=351 path=[329:0-350] [-1, 329, -2]
+AATCAATTCCTGGATAAAAACTGTTTTACCAACACCTGCACCACCGAATAGACCAATCTT
+ACCACCACGAGCATATGGGGCAAGCAAATCTACAACTTTAATACCGGTCTCCAAGATTTC
+TGGGGTTGTTGATTGTTCTTCGAAAGAAGGAGCATCAGCGTGGATTGGGGAGTATTTAAC
+GGCTTTAATGGGACCGCGTTCATCTACGGGTTCACCAATAACGTTCATAATACGGCCTAA
+TGTACCCGGGCCAACAGGAATGCTGATGGGTGACCCAGTATCGATAACGGCTGTTCCACG
+AACAAGACCCTCAGTACCATCCATAGCAATAGTACGAACAGTATTTTCACC
+>TRINITY_DN125_c0_g1_i1 len=504 path=[482:0-503] [-1, 482, -2]
+ACATAACGAAAATATCGACAAAAATAATCGGCCGGACTCGAGAAGAAACATGTTAAAGAA
+AACGGGAAGTTATAAGCGAATGAAGTAACATCATAGGTATCTACTGGAAATATTTCTGTA
+ACTTCAATATGTAAAAGGCTAGCTCTGCATTCGTCTATAATGAAAAAAAGAAAACAGAGC
+AAGAAAACGATAGTAATCAGAAAGTATATAAAACACTCCAATAATAAATACCCAAAGTTC
+CTCATGAGATGTTAAGAGCGGAAAAAGGTGGTTAAATAGGTAAAAAAAGATTGAAATTTA
+TATATATCAGAAGAATCGATGTTATTCAAAAGTATGTAAAAAACGTTACAAAAAGTAAGA
+GGAGCTTAGAAGCACTTACGGTAAACGATACCAGGTCCGCTCTCATCATACTCTTGCTTG
+GAGATCCACATCTGTTGGAAAGTAGAAAGAGAAGCAAGAATGGATCCACCAATCCAGACA
+GAGTATTTACGCTCAGGAGGAGCA
+>TRINITY_DN126_c0_g1_i1 len=374 path=[352:0-373] [-1, 352, -2]
+CGTCAGATGAATGTAATCCACCGTGCCAGCCGTCCTTCTCGTCCTGACAAGGCTCGTCGT
+TTGGGTTACAAGGCTAAGCAAGGTTATGTTATCTACCGCATCCGTGTCCGCCGTGGTGGT
+CGTAAGCGCCCTGTCCCCAAGGGTCAAACATATGGTAAACCCGTCCACCAGGGTGTTAAC
+CATCTCAAGTACCAACGCTCTGCTCGCTGTACCGCTGAGGAGCGTGTTGGCCGCTACTGC
+TCTAACTTGCGTGTATTGAACTCTTACTGGGTTAACCAAGATGCTACTTACAAGTTCTTT
+GAGGTTATCCTTGTTGATCCCTCTCACAAGGCTATCCGTCGCGATCCTCGTATCAACTGG
+ATTGTCAACCCCGG
+>TRINITY_DN128_c0_g1_i1 len=449 path=[427:0-448] [-1, 427, -2]
+TGGAAAAATGTTAGATAAGTTTCAATGAGGCTCAATTTTGAGGTTTAAAATTATTTGAGA
+AATGAAAAAATTGAATAAGGATTAATGAGGAAATTATGCCTTAAGCTCACCAACACCACC
+CCAGCTACAAGAATCGGCACCATGATCCTGAGTGTAAGCGTTAAGAGCAATGCTAAGTTG
+TTGGACACCAGTGCAACCAGTGTAGTTACCATAGGTACCCTCATAAGGATCGCTGCTAAT
+AGAAGAACAGGCCTTGTTATCGTAGTAGCAAAGTTCGCTCAAGACCTGAGAGATCTTGCT
+ACCGGAAGGAGTTCCATTTGCTGAACACTTGAGATTCTTAACGGCATTGGAGCAAATCGT
+AGTGTTGGGAGTTACTGGGAAAGCATTAGCACTGACAGCCCAGCTGGTCTTGTTTCTGGA
+TGGACATTCAGGAATAGTACCGTTGGGAT
+>TRINITY_DN128_c1_g1_i1 len=890 path=[868:0-889] [-1, 868, -2]
+TGGGATTGTAGGAGTGCTTATAGGTAATGTTGGGGCTAATGGAAGCCCATTGCTTCTTCA
+AGTTGTTATAGTCAGTAGTCAAGACACGCTCACCAGTGGAAGAAACGTTAACAAGACCAT
+AGTCGTTAACCTCTTGAGAATATTCGTAGACAATACCACCGCTCCAAACATTGGTCATGT
+TATCAGAATAGATGGCTTGGACTTCAGTGAAAACACGAGGAGTGACCTTGTTGCAACCAA
+ACTCGGAAAGGAAGATAGGAATAGTAAAGTTCTCAAGCTCTTGAGTACGGGCAGCATAAC
+CAGAAGTGTAGAAGTCAGAATGACCGCACCACTCGTACATGTTGTAACCCAAGAAATCGG
+TCTCAGAGTTGGTGTCATTGTTCAGCTTGGTAGCATTGCAAGACAAATAAGCGGCGAGTT
+CAGTACGAACGACGGGAATATCGGCACCAGCATAACCGACAGGGATCGTACGATACTTCT
+TAGATTTAATGTAGTTCTTGGAATCACGAACGGCAGCACGAACGTAAGCGACAGCGGGAG
+CATTCGAGGCATTGTTGACAACTTCGTTACCGGCAAAGAAGGCACCAGTGTTGTTGTACT
+TTTGGAAAGTATCAATAACAGATTGATAGGATGAGAATTGATCGGTGTTCCATGTAGGGG
+TATCACGATCGATACCGGTCTTGGGGTTGGCAAGATCCAAAAAGACGTAGATGCTTTCGT
+TACGGAAAGCCTCCATACATTTGTCATGGTTCAAGCTAGCGTTGACGGCATAGACACGAA
+TAACGTTAGCGCCCAAGTTGGAAATGATCTTAGCATCTTCGGTACAGTTCTTGTAATTGA
+CCTCGGCTAAGGGATCAACGATGGTGCTGGTTTCTTCAGCATCAACGGCG
+>TRINITY_DN129_c0_g1_i1 len=596 path=[574:0-595] [-1, 574, -2]
+GGTAAGACCACGTTCGTCAAGCGTCATTTGACTGGTGAATTTGAAAAGAAGTATATTGCA
+ACTTTGGGTGTTGAGGTCCATCCTTTGCATTTTCATACTAATTTTGGTGAAATTTGCTTT
+AATGTTTGGGATACCGCTGGTCAAGAAAAGTTAGGTGGCCTTCGTGATGGTTACTATATT
+CAAGGTCAATGTGGTATTATCATGTTTGATGTTACTTCCCGTATTACCTATAAGAATGTT
+CCCCATTGGTGGCGTGATCTTGTCCGTGTTTGTGAAAACATTCCCATTGTTCTTTGCGGT
+AACAAAGTTGATGTTAAAGAGCGTAAAGTCAAGGCTAAGGCTATCACTTTCCATCGCAAG
+AAAAACCTTCAATACTACGACATCTCCGCCAAGTCCAATTATAACTTCGAAAAACCTTTC
+TTATGGCTTGCCCGTAAGCTGGTTGGCAACCCCAACCTGGAGTTTGTTGCTTCGCCTGCC
+CTTGCTCCTCCTGAGGTTCAAGTCGATCAGCAATTGTTAGCTCAATACCAACAGGAAATG
+AACGAGGCTGCTGCTATGCCTTTACCTGATGAGGATGACGCTGATTTGTAAACCAA
+>TRINITY_DN131_c0_g1_i1 len=1518 path=[1496:0-1517] [-1, 1496, -2]
+GTGAGAGCCATCATTTCATAAGAGACCGCAGTATAAGAGTCGGGGCATGTAACATTGGTA
+GCATAATCGCAACCAGAGCTAGAGCAGTTGAAACGTCCAATTTCGGCAATGCGGTTGGGA
+CGGTTGGAGTAGACAGTAGAATCGTTGGCAACGGAGGAGAGGTTGAAGAGAATGAATCGG
+CCAGTGCCATTAACACCTTCAACAGTGATGGGGAAACCGCTAGTATCGAGATGGAAGTTA
+AGTTCGCAACTACCGGAAACTTGAGGAACATCAAATGTGAAAATCGTGTTGGTATGATTG
+TTTTGCTTCTGAAAGACGACGGGTGAGTAAACATTACCGGAGTTAGCTTCAGGCTTAGTC
+GAATCAATTAAACGAATGCCATGGGGGAACAAAGGATATACAGCAGCAGAAGGTGATGGA
+GTTGCAGCTTCACTTTGGCTAGCGGCAGTGGTGATAACAGGGACAACAATACACTTGGTG
+GTATAAGCAACGACGCTAGAAGCAGAAGGACTGGGTCCAACATATGTGGTAGTTTTAGTA
+GTAGTGGCAGTGTTTTTACGTTGGGTAGAAGTAACGGTAGAGGGCTGAGTGGATGTAACA
+GTGGAAGCTCCGGTGGAAGTGATAGTGGAGCCTCCGTTCGTGGCTGTTACTGTGTAGGTT
+TCAGTAGCCGTAACGGTGACAGCTGTGGTGGTCGTAACAGTGGTGGCTTCGGTAGATGTA
+ACGGTAGAGGCCTTAGTGGAAGTGATAGTAGGAGGTGGAGTAGAGGTAGAATTATGATAG
+GAAGAGGTAGTACTATTATAAGTGGAAGATGAAGAGATGGGTTGAGGCAAAACAGCCAAA
+ACAGCAATACCTACACAACTAGGGTTACCGTTTCCAACTCCAAAGAATACCTGATAAACC
+TGGTTATTGACGAGAGAAGGACAAGCAACGGCGGATTCAGTTCCATTATATTTTAAGCTA
+TATCCGGAACTAATAGCCTCACCGACACTGAATCCAGAAGAAGTAGAATTAGTATCAGAT
+TTGAAAACTATTTCACCATTGGCGCTCACGGAAGCATAGCGATTACCAACAGATAGTTGT
+CCATTAGACATAGTAAAGGTGGCAGCGTCATCAGTGCCATCAGCGGGGTCCAAGTAAACA
+GAACCAGAATCTCCAACATAAAATCCGTGCAAATGGACGTATTCATTGCCGGAGTGAAGA
+GCCAAAAGACCAAATTGTCTGCCGTTCAAAGGGTCATCGCGTCTACGCAATGGGGAAGCT
+GTCACACTGGAGGCAACGAGCAAAGAGAGTAATGTGGAAGCAATGGGAATCGAAGAAAAC
+TTCATGGTGCGTGTAATAAAAATCCAAGATTTTCAATGAATAGATGCCAATTAATTAACT
+GTTTTTTATAAACCAAAAAGTCCTCGCAAAGATATGGAGGTTTTGTTAATATAATAATAA
+TAATTATAATGAGAGATTAAAGGGAATTGATGAAGACTTATTTACTTTGTTTAGTAAGGC
+TTCGAAGATTATTACAAA
+>TRINITY_DN132_c0_g1_i1 len=419 path=[1313:0-34 1314:35-418] [-1, 1313, 1314, -2]
+GCCGCCAGGGTGGGCTCTGCCACCGCCGAGGAGGGTATCCCCGACGGATGGATGGGTTTG
+GACTGTGGACCCAAGTCCTCTGCTAAGTTTGCCGAGGTTATCACCACCTCCAAGACCATT
+GTCTGGAATGGTCCCGCTGGTGTCTTTGAGTTTGACAACTTTGCCAAGGGTACCAAGTCT
+ATGCTTGATGCTTGTGTCAAGACCTGTGAAGCTGGTAACGTTGTTATTGTTGGTGGTGGT
+GACACTGCTACTGTTGCCAAGAAGTACGGTAAGGAGGATGCTCTTTCCCACGTCTCTACC
+GGTGGTGGTGCTTCTCTTGAACTCTTGGAGGGTAAGGCTCTTCCCGGTGTCGTTGCTCTT
+TCTTCCAAGTAAGATGCCACTTCCTTCTCAATGCCTTTCTCATCTGACTCTATTCTATA
+>TRINITY_DN132_c0_g2_i1 len=1323 path=[1315:0-938 1316:939-1322] [-1, 1315, 1316, -2]
+TCTCAATCCAGAATCAATCAATCACATAACCATGTCTTTGTCTACTAAGCTCGCTATCAC
+CGACGTCGACTTGAAGGGCAAGAACGTCTTGATCCGTGTCGACTTCAACGTCCCTTTGGA
+CGGTGACCGTATCACCAACAATGCCCGTATCGTTGGTGCTCTCCCCACCATCAAGTACGC
+TCTTGAGCAACAACCCAAGGCTGTCATCTTGATGTCTCACTTGGGCCGTCCCAACGGTGC
+TCGTGTTGCCAAGTACTCCTTGAAGCCTGTTGCTGCTGAGCTCAGCAAGCTTTTGGGCAA
+GCCCGTCAAGTTCCTTGACGACTGTGTTGGCCCTGAGGTCGAAAAGGCCTGCAAGGAAGC
+CAAGGGTGGTGAGGTCATCCTTTTGGAGAACTTGCGTTTCCACATCGAGGAGGAGGGTTC
+CGCCAAGGTTGACGGTAAGAAGGTTAAGGCTGACGCTTCTGCCGTCGAGGCTTTCCGTAA
+GTCTTTGACTTCTCTCGGTGACATCTTTGTCAACGATGCTTTCGGTACCGCTCACCGTGC
+TCACTCCTCTATGGTCGGTGTCGATCTCCCCCGTGTCTCCGGTTTCCTTATGAAGAAGGA
+GCTCGACTACTTCTCCAAGGCTTTGGAGAACCCCGCTCGTCCCTTCCTTGCCATCTTGGG
+TGGTGCCAAGGTTGCTGACAAGATCCAACTTATTGACAACCTTCTTGACAAGGTCAACCG
+CCTTATCATCTGCGGTGGTATGGCTTTCACCTTCTTGAAGGTCCTTAACGGTATGAAGAT
+TGGTGACTCTCTTTTCGATGAGGCTGGTTCCAAGAACGTCGAATCCATGATGGCCAAGGC
+CAAGAAGAACAACGTCGAGGTCTTCCTCCCCGTTGACTTCGTCACTGCCGACAAGTTCGA
+CAAGGACGCCAAGGTTGGCTCTGCCACCGCCGAGGAGGGTATCCCCGACGGATGGATGGG
+TTTGGACTGTGGACCCAAGTCCTCTGCTAAGTTTGCCGAGGTTATCACCACCTCCAAGAC
+CATTGTCTGGAATGGTCCCGCTGGTGTCTTTGAGTTTGACAACTTTGCCAAGGGTACCAA
+GTCTATGCTTGATGCTTGTGTCAAGACCTGTGAAGCTGGTAACGTTGTTATTGTTGGTGG
+TGGTGACACTGCTACTGTTGCCAAGAAGTACGGTAAGGAGGATGCTCTTTCCCACGTCTC
+TACCGGTGGTGGTGCTTCTCTTGAACTCTTGGAGGGTAAGGCTCTTCCCGGTGTCGTTGC
+TCTTTCTTCCAAGTAAGATGCCACTTCCTTCTCAATGCCTTTCTCATCTGACTCTATTCT
+ATA
+>TRINITY_DN134_c0_g1_i1 len=1178 path=[1156:0-1177] [-1, 1156, -2]
+CTTTTAGCAAAACAAATTTATTAACCTGGTACAACAGTAGCTCGTAAATTCATAATCGTT
+AAAAATAAAACGTCAAATAACAGCATAAATAAGACCAAAAAGGGTATGCAATGATTACAT
+CTTTTAATACCTTTCAGAGTGATGGCCAGTCTTCAAATCTTCACCCTTCTGGACGAGTTC
+AGGGTCTCTGGTCAATTTACCAGCCATTTTCTCCATATTACCCTTCATTTTGTCACCCAT
+ACTGACATGCTCATCCTCGGCCAACTGTGCATTTCTTTGTGCAGTTGTACGAGCATTACG
+GGTACCAGTTGCGGCACGGCGATTAGCTTCAGCAGTGGTATCAGTAGCATAGGTACCTTT
+GCCATATCCCTCACCGCTGTAACCAGCAGAGGAAACAGCGCCTCTGGTCTTGTTAGCAGT
+ATTGTCGTTGCCATAGGAGCCTCCACGATGCTCAGTACCATGAGAACCACCATGGGTATG
+GGAGCCAGAGCTTGAATAATCATAGGCACCACCACCGACTGTGTCAGAAGGAGTTGCTTT
+TTGGCGACTGCCATAGGTATCAGTGGGGTAACTTTGACTGTAATCTTCACCGTAGTCACC
+ACCTTGGGTGGTTTTACGACTTTGGTTGTATTGGCTTTGGCCGTAAGATGCAGTATCATC
+TGTACGACTAGGGTCGGTGGTGTAACTACCTCCGCTGGTAGAGTAATCCTCGTTGCGTCC
+GCCGGAAGAATAACTGTCATTGCCTCCTGTAGAGTACTTGTTAGAAGAGTAAGAAGAATC
+ATCGTGTCTTCTCGAGTAAGAGGTATCACCTCCACGGACATCTGATTGTTCCTTCTTACG
+TGACTCGACACTATTGAATCCCTTCTTAGTGTCGCTAGTCATTCCAGCATAAGGATCCCC
+GGATCCAATGTCTGTTCCCATGTCGTTAGCAGCACGACTAGAATTGCTGGGAATTTCAGA
+TGTGTAAGAGGTGTCAAAGTTGCGATTTTGAGGGGCACCACTAGAAGAGAAGGGCTCATC
+ACTGTTGTGGACAGCACCAGCGCTTGAGCTGTATTGCTTAGCAGAGTTCATAGAATCGTT
+TGCACGTTGTTGGTAAGACATTTTATGAAAATATTTGTAGTATTGTAAGTAGAATAATAT
+TTACTTTTCAAGATTCGAATTTATTTTGCGAATATCGA
+>TRINITY_DN136_c0_g1_i1 len=240 path=[218:0-239] [-1, 218, -2]
+TGGTGATAAATACTCATTCTATCACACTTAAACACTAGGTGAGATTAAAGTTATTAATTG
+CTTTTGTCCCTATACATTTGCGAAGTTTTGATAATACGACCAACCTTGAATTTTTTGTAC
+ATCCTCTGAAATTATAAATAATGGAACGCGAAGGTAAAGAAGACGTTCGTAAAGCCGACC
+ACAAGATTGTTTATGGTATTGAACGTGTGCGACATGGAATTAACAACTTTTTTGATGACG
+>TRINITY_DN138_c0_g1_i1 len=287 path=[265:0-286] [-1, 265, -2]
+CCGGTGCTAAGAACCTTTACATTGTCTCCGTTTTTGGTACTGGTGCTCGTCTTAACCGTC
+TCCCTGCTGCCAGTTGTGGTGATATGGTTCTTGCTACCGTCAAGAAGGGTAAGCCTGACT
+TGCGTAAGAAGATCATGCCTGCTATTGTTGTTCGTCAACGTAAGGCCTGGCGCCGTAAGG
+ACGGTGTTTATCTTTACTTCGAAGATAACGCTGGTGTTATTGTCAACCCCAAGGGTGAAA
+TGAAGGGTTCTGCTATCACTGGTCCCGTTGCTAAAGAATGTGCTGAC
+>TRINITY_DN139_c0_g1_i1 len=273 path=[251:0-272] [-1, 251, -2]
+AGCTACGAGTACGACTTGACTAGCATTGTTAGCTTGTTCGGAAAGAACTGGACTGTTGAT
+GAACTCGGATGGGGAACCTATATTGCTCATAGCCTCAACGAGATCAGCAGCAACACCACC
+GGTGCTGCTAATGCCACCCTTTTCATTGACACTCAAACCAAGAGCGACTGCTACAAGTTG
+GCTAGCACCATCGAGAGCTGGAAGTATGCTCCCCTTTCCGCTTTCCCCAACTATGGTCCC
+TTCTATATTTATGGACAATGTGTCGCTACTTTC
+>TRINITY_DN143_c0_g1_i1 len=204 path=[182:0-203] [-1, 182, -2]
+CCGTTACCATGATTACTACCAATGTTCTTGGTATGATGGCTATGACTCGTGCGGTTCTTC
+CTATATTCTACAGCAAAAACAAGGGTGATATTTTGAACGTTGGCAGTATTGCCGGCAGAG
+AATCATACGTAGGCGGCTCCGTTTACTGCTCTACCAAGTCTGCCCTTGCTCAATTCACTT
+CCGCTTTGCGTAAGGAGACTATTG
+>TRINITY_DN144_c0_g1_i1 len=286 path=[264:0-285] [-1, 264, -2]
+CTTGCACCAACGCCAAGTCTGCTAAGGATTGGTTTTTGGCCTCTGCCAAGGATCCTTCTC
+ATGTTGCTAAGCATTTCGTTGCTTTGTCTACCAACGAAAAGGAGGTTACCGCTTTTGGCA
+TCAGTGCTCAAAACATGTTTGAGTTTAGCGACTGGGTAGGTGGTCGTTACTCCGTTTGGA
+GCGCCATTGGTTTGAGCGTTGCTCTTTATATTGGTTATGAAAACTTTGAGGCTTTCCTCA
+GCGGTGCCCACGCCATGGATGAGTATTTCTGCAGTACTCCTTTAGA
+>TRINITY_DN144_c1_g1_i1 len=459 path=[437:0-458] [-1, 437, -2]
+TTCGGGAGTACCCTCAGCCTTAACTTCAGCAGGAGTCTTACCAAGCATCAAAGCCTCGGT
+TTGAGCGGCAAAGTTTGAGAACAACATACGATGATGCTTGTTGTTATCAATAGGGTTGTG
+AGATTCAATGGGAATCAAGAAATCGGCGGGAATCAATTTGGTACCTTGATGGATTAATTG
+GAAGAATGAGTGTTGAGAGTTGGTACCAGGCTCACCCCAAAGGATTTTGCCAGTTGTGTA
+GTTAACCATATCGCCAGAACGAGTGATGGCCTTACCGTTAGACTCCATACTCAATTGTTG
+TAAGTAGGCAGGGAAACGGTGTAAATATTGATCATAGGGAGCAACCAAATGAGTCTGAGC
+TCCAAAGAAGTCAGAGTACCAAATGGAAATCAAAGCGGCCAAAGCAGGAATGTTCTTCTC
+TAAAGGAGTACTGCAGAAATACTCATCCATGGCGTGGGC
+>TRINITY_DN146_c0_g1_i1 len=289 path=[267:0-288] [-1, 267, -2]
+TCGGGCTTTTTTGTTTCATTTTAGATTTTTATATCAGTATTCCCCTCAATACCCCTTTTC
+TATTGTCGGTAATACCTACCCCATCTCGTTTATTCTTTTGAATACATTTACACTTGTTTT
+TCTTTAGTTTTTTCGTTATCTATCTTTCTCATTACTTTCGTTAACTATGGCTGATAACGC
+TGGTGAATACCATGACGCTGAAAAGCATGCTCCCGAGCAACAAGCTCCCCCTCCTCAACA
+ACCCGCTCATGCAGCTGCTCCCGCTCAAGACGATGAGCCTGATGATGAC
+>TRINITY_DN148_c0_g1_i1 len=230 path=[208:0-229] [-1, 208, -2]
+TACCATTGTTGTCAATAACCTTAAAGGGCCAGTGCTTAATATCCTTTTGAGTCTCAGGGT
+CTTCGTAACGACGACCAATAAGACGCTTGGCGTCAAAAACGGTGTTACGAGGGTTCATAG
+CAGCCTGGTTCTTGGCGGCATCACCGACTAAACGCTCAGTTTCGGTGAAAGCGACAAATG
+AGGGAGTGGTACGTGCACCTTGGTCATTGGGGATAATCTCAACATTGGCG
+>TRINITY_DN151_c0_g1_i1 len=383 path=[361:0-382] [-1, 361, -2]
+AGCAGCGTGGATACCCTCATAGGTGGAGGCAATCTTGATGAGAACACGCTCACGACCAAT
+GCCCTCGGCTTCGTACAACTTGATGAGGTGACGAGCCTTCTCGATAGTAGTTTGGGTGTC
+AAAAGAGTAACGAGCATCAACTTCGGTGGAGACACGGCCAGGGACGATAGCGAGGATCTT
+GGTACCGAATTCGATCAAAAGACGATCAAAAGCAATCTCAATTTGAGAGTTGATGGAACC
+ACCCTTTGCCTTGGCATAGTCAACAGCAGCGTCGACGAGAGCAGCATATTGGGGCTTCTT
+AGAAGCGGCCAAGATGAGAGAAGGGTTTGTGGTGGCATCTTGGGGTTTGTATTTGGCGAT
+CGATTCAAAATCTCCAGTATCGG
+>TRINITY_DN151_c1_g1_i1 len=252 path=[230:0-251] [-1, 230, -2]
+TGACAATGGTCTTGTAACCGAATTTTTTGTAGTAGTTGAAGATGTTAGAGACACTGACGA
+CACCGGGGTCTTCTTGAGCGGTATAGTCACGGTTATTCTTAGCCTTGTAGAAATCGAGAA
+TACGACCGACGAAAGGAGAAATCAAGGTAACGTTAGCCTCGGCGCAAGCAACAGCTTGGA
+CAAAAGAGAACAAGAGAGTCAAGTTGCAGTGGATGCCCTCTTCCTCGAGTTGCTTAGCAG
+CTTGGATACCCT
+>TRINITY_DN152_c0_g1_i1 len=284 path=[262:0-283] [-1, 262, -2]
+TTTCATGTACAACGCAACATATGCACACAGACATTGAAAAGGTTTAGTGACTTTACATCA
+ATCTCGAAATTTCGAACCAAGCAAATAATAATAATAAAGAGAAGAGAATAAGTGAAAGAG
+TGGCAGATTTCTCTGTGCAAGAACTCGAAAAAGTCACGGGGAAAAAAGATGAACGGGTAA
+TCTTGTAGACTAATTAGGATTAATAAGAAAACCGTGTCACCAAACCCAACGTTTTAAAAA
+AATTCCCCCCTAATGCTACGTTTTCAAGTAAAAGAAAAAGAAAC
+>TRINITY_DN153_c0_g1_i1 len=233 path=[211:0-232] [-1, 211, -2]
+CTCGTGGACGCGGTGCAGCTTCCGGTACTAAGTACAGGATGACCTTGGGTCTTCCTGTTC
+AAGCCATCATGAATTGTGCTGACAACTCTGGTGCTAAGAACCTTTATATCGTGTCTGTCT
+TCGGCACTGGTGCACGTCTTAATCGTCTACCAGCTGCAAGCTGTGGTGATATGGTCCTTG
+CTACTGTGAAGAAGGGTAAACCCGACTTGCGTAAGAAGATCATGCCTGCTATT
+>TRINITY_DN155_c0_g1_i1 len=274 path=[252:0-273] [-1, 252, -2]
+TGAGGCCGTTGCCAACCATGGTAGTGTTGCCGCTGATGTCGAGCCTTACTTGGTCGAGTT
+GTTGCCCGCCGTCATCGCCAAGGTTGCTGACAAGCAAAACGCTGTCAGAGATGCTGCCAT
+TGCTGCTTCTAAGGCTATTGTCCGTTGCACTACCCCTTATGCCGTCAAGGCCATCGTCCC
+CTCTGTTCTCGAGTCCATCCACACCACTGGTAAGTGGAATGAGAAGATGAACTCTTTGCA
+ACTTTTGGATGTTCTCGTTGAGGTTGCTCCTTCC
+>TRINITY_DN160_c0_g1_i1 len=267 path=[245:0-266] [-1, 245, -2]
+AACAATCGTTACTGACAAACGATAATGGGTTTATGATATTCTTCCTTCGTTTGTCGACTC
+TTTTTTACTACTCTTTTCCCCAGGTCCTTGTTTGGTCATAATTTATTTTCTTTATTAAAG
+AATAATTGTATGTGTCATCTGGTTCCTTTCTCTCTTTTCTTTTGTCATAGAAGGAAGAAG
+GAAGGTGGTGTATGATTGAATTGCTTCGACGAAATTGGCGTTTAAAAAAAAAGACAGGCT
+AAAGGCATTGCAAATTCCACACCTCTC
+>TRINITY_DN160_c1_g1_i1 len=593 path=[571:0-592] [-1, 571, -2]
+TAAAATAATTGCGACATCTCCGCCTTATAATAACTATGTAAAAATTGAACAGTTTCTTAG
+CTATGAGCAAACTAGGGTTTCCGTCTAACATGCTCTCCTTCGCGCACGCCAGCTTATTAA
+ATTAAGTTTTCTTTCAGCTCATACCTGTCACTGACGAAAAAAATAAACCAATCAAACTCT
+CGGTCGATTGAATTCTCAAAGCAACATATATCCACGATTGTAATAAAATAAAATAAAAGG
+AAAAAGGGGAGAAAAAAAGACAGTTTAAAAAATTTTTTTTCCATGGATAACAAAAACACA
+ACCAACAAATATTGAAAACTTTTGACGTTTTTTTAACCCCTTTCATTCAATCAAACAAAT
+CTTTCTCTATTCCGTCCACAAAGGGAATATAGATAGATAGATAGATAGATACCACCACAC
+CTTCAACAAACTTTTATCCGTCCGCATCATTTTTTCATAACTCTTTATAAAAAACGAGAG
+GTGTGGAATTTGCAATGCCTTTAGCCTGTCTTTTTTTTTAAACGCCAATTTCGTCGAAGC
+AATTCAATCATACACCACCTTCCTTCTTCCTTCTATGACAAAAGAAAAGAGAG
+>TRINITY_DN162_c0_g1_i1 len=306 path=[284:0-305] [-1, 284, -2]
+TATATATTTTTAACTTAATTTCCCATTTCATTTATATACAACATGGTGAAACAAGTCTCC
+GACTCTTCTGAATTTAAATCTATTGTTTGCCAAGACAAGCTTGTCGTTGTCGACTTCTTT
+GCTACTTGGTGTGGACCTTGCAAGGCCATTGCTCCTAAGTTTGAGCAATTTTCCAACACT
+TACTCTGATGCCACTTTCATCAAGGTTGATGTCGATCAATTAAGTGAAATTGCAGCTGAA
+GCTGGCGTTCACGCTATGCCCTCTTTCTTCCTTTACAAGAATGGTGAGAAGATTGAAGAA
+ATCGTA
+>TRINITY_DN163_c0_g1_i1 len=542 path=[520:0-541] [-1, 520, -2]
+TCAAATACGAAATCATAGGGTCCTAGATCAGCCAAGCGCTCAACGAGGTTGTCCTTTTTA
+TAGTCGAGTGTATGAGTGGCACCCAAAGATTTACAGAGATCCAAGTTCTCGGTTGAGGAA
+ATCGTAGTGACTTCACATTCCAAAGCTTTAGCTAACGCAACTGCAAACGTACCAACACCT
+CCACTAGCTCCCTCGATAACCAATTTGGTACCTGGCTTTACCTTCATTTGTCGGACCAAT
+ACCTCCCAGGCGGTTAATCCAGCAATACCGAACCCGGCACCCTCATTGAACGAAACACCA
+TCGGGAAGGTGCCAAACATCCTTATCGCCCGTAACGATGTGTGTAGCACATGAACCACCT
+TGGCGACCTGCACGAGGAAAGGACTGACAACCCCAAACACGCTGAGTGGCGGAGAATTCC
+TTGACCTCTGATCCCACAGCTAGTACACGACCAGCAAAATCATAACCCGGAATGTTTGGA
+AGCTTGAAGAGTGCCTTGGCAATCATTTGGTAAGTGTTCATCAGCTTGTAATCAAGCGGA
+TT
+>TRINITY_DN166_c0_g1_i1 len=771 path=[749:0-770] [-1, 749, -2]
+TGACAAGGCTGAGCTCGTCAAGTCCTTTGGTGCTGAGGTCTTCCTTGACTTCAAGAAGGA
+AGCCGACATGATTGAGGCTGTCAAGGCTGCCACCAACGGTGGTGCCCACGGTACCTTGGT
+CTTATCCACCTCCCCCAAGTCTTACGAGCAAGCTGCTGGCTTTGCCCGTCCCGGTTCCAC
+CATGGTCACTGTTTCCATGCCTGCCGGTGCCAAGCTCGGTGCTGATATCTTCTGGTTGAC
+CGTTAAGATGCTTAAGATCTGCGGTTCTCACGTCGGTAACCGTATTGACTCTATCGAGGC
+TCTTGAATACGTTTCCCGTGGTCTCGTCAAGCCTTACTACAAGGTCCAACCCTTCTCTAC
+TCTTCCCGACGTCTACCGTCTCATGCATGAGAACAAGATTGCCGGCCGTATCGTCTTGGA
+CCTTTCCAAGTAAGGGAATGAGAATGTGATCCACTTTTAATTCCTAATGAATACATGCCT
+ATAGTTCTTTTCTTTTGTTCTTTATGTCGTTTTTCGATGGTACGGCCGTTGTCAATCTCA
+GTTTGTGTGCTTGGTTGCAGCTTGGTTTCAAATCTGTTCATCTCATGAATCTTTTACCAT
+TTCACCACACGTTTATACCATTCTCTCATAGAATCTTCATCAAACCATCTCGGGGTTAGA
+GTGGAAAGAAAGTCTTGTTCTTTTATTTCCTTTTTTCCATCTTCAAGGCTTTTCTTTTCT
+TCCTCCTCCTCGTTCATCTTGAGGTTTGACGTGTCTGTTTAGAATTTTGAG
+>TRINITY_DN169_c0_g1_i1 len=239 path=[217:0-238] [-1, 217, -2]
+CGAACGAGCAATTCGATTAGGACTAGCATATCCTTGGTTTTCTTGCGTGTTCAATTACTA
+AAAACCCTGTTTTCTGTTTGTTAATATATATTTTTTTACTCTCCCTCTCTTAGGTATACA
+GGATGGCCCAGACGTTTCAGGAGAAACAACAGAGTCGAAGGATTAAAATGAGCACTGGAA
+ACTTTTTTTCTAGAATGTGGAATGCCGTCGTGTTCGGCTCCGGTGCGGCCATTGGCGCC
+>TRINITY_DN172_c0_g1_i1 len=454 path=[432:0-453] [-1, 432, -2]
+GCTAGATTGACCGACATTCTTTATGCCCTGTTTAGCAGATTGGGCGGTTTCCTTAGCGCC
+GATTTTCATGTTTTGCATTGATTCGTTAATAGTTCCAACCATGATGATGAAGAATAGAAG
+AATGTAAGAGAATCAAAAGTGTTGTTGATAAATAAGAAGGGGATTTTTAAACGTAAAAGC
+GTTAAAAACGTGATAAAGAGTTAAATAAATAAATAAATAACAAGTTCGTTAAAACAATTG
+AAACGTAGAGACAAGAGAGATCACTTGGGGGAAAGAGAAATCGAAAACTTGTCGAGAGTC
+GTAAAAAAGAAAAGAGTCGTTAAAAAACAAACGTAACAAACAAATAATTAATATTGATAA
+TAAATCGGGTTATATATCAATATATATTATATATATATATATATAGATAGATAGAATGTG
+TGTAATTGATATATAATATAAATAATAAGAGAAA
+>TRINITY_DN172_c1_g1_i1 len=534 path=[512:0-533] [-1, 512, -2]
+AATAAGAGAAATTAGATATAGAGAGTATCAATCACAGAGACCTTGAACACAAAAAAAAGG
+AGATGAAAATGTGTTTTTTTTAGGGGTACAAACAGTAAATCAAGGAAGGAAACGAGGAAG
+AATTGAATAAATACAAAAATTCACTCAGTCAGTCAGTAGAAGTACTAGTAACAATAGTAG
+TATGTTAAGACTAGTAAAAAAATAAAATAAAAAGACAAAGACAAAAAAAGGCGAGGGGGT
+GCAAACTTTTTGACTATGACTTTTATGTATAGGAGAGAATTATAACAAGACTATGTAGTA
+GAGGGTAGAAGAATAGTCGTGTTATGAGGGCTGAATGAAAAAAGAAAAATTAAAATAGTA
+TAGTATAGTATAGTATAAGAGTATGAGAAATCGTTTAGTACAAATTGAGGTAGAAATGTA
+CTATAGACAAGAGAGTAATCAAATCAAATCAAATGAATCGAGTAAATAAGAGTCGTTTGA
+ATAAGATGGGATAAAAGCAAACAAGAAGCGAATCTTTTTTTTAATCTTTTTTCT
+>TRINITY_DN174_c0_g1_i1 len=238 path=[216:0-237] [-1, 216, -2]
+GAAAAGTTATCCGAAGGTCGTGTTATTTCCGTCGGAAAGGGCGGTTATAACAAGGAAGGT
+AAACTGGCTCAACCCAGCGTAGCCGTTGGTGATCGTGTCTTGCTGCCTGCTTATGGTGGA
+AGCAACATCAAGGTGGGCGAAGAGGAGTATTCGTTGTACCGTGATCACGAGTTGTTGGCT
+ATCATCAAGGAATAAATTAATTAATGGGTAATTTTTTCTTCGTCAGCCACTGCCTATT
+>TRINITY_DN174_c1_g1_i1 len=201 path=[179:0-200] [-1, 179, -2]
+TGCCTATTAAGCATACTAAAAAAAAAGCTGTTGGACGCAAAAACATCTTTTGTTATTGTT
+CTTGCAGCAAATTACGATAAACTGGTACAAGATGGCTTTTTTAACAGCTCTAATTTTAAG
+GACGATTGCACTCAGATTTAAATGTGATGTAAATGCGGACATTTTTAAAGAAAATGACAG
+TGATTATGCGTTTGATGATCG
+>TRINITY_DN175_c0_g1_i1 len=219 path=[197:0-218] [-1, 197, -2]
+GAATGTTTTAGTTTTTTATTTCCCTTATATGTGAGTACTATAGTGCAGCACGGCTTATGT
+ATGTAGAAGGAATTGTATATAAAAGGGAAGGGAGATGGATGATTTTATGAGAAAAGGAAG
+AAACAGGGAGTAGTTTGCTTATTTGTCAATTGTTTTTGTGTTTTTTTTTATCTTTTAAAC
+GACCCGCTTTGAAGTTACAGCAACAATTTTAGAGCTATT
+>TRINITY_DN176_c0_g1_i1 len=406 path=[384:0-405] [-1, 384, -2]
+CTTTGCGTAAGAACGGACACGTCGTCATCAAGGGCCGTCCTTGCAAGATCGTCGACATGT
+CCACCTCTAAGACTGGTAAGCACGGACATGCCAAGGTCCACATTGTTGCCCTTGATATCT
+TCAATGGTCGCAAGTACGAAGATATGTCTCCCTCTACTCATAACATGGACGTTCCTGTTG
+TCAAGCGTGACGAATACCAACTAGTCAACATTGATGATGGCTACTTGAACCTCATGACTA
+CCGATGGTACTACCAAGGACGATGTTCGTCTTCCCGAAGGCGAACTCGGCAACGAAATTG
+AAGAGGGCTTTGAAGAGGGTAAGGATTTAATCATTACCGTTGTCTCTGCCATGGGTGAAG
+AGATTGCTCTCGCTTGCCGTGATGCTCCCAGCGCCTAAATATAAAC
+>TRINITY_DN177_c0_g1_i1 len=342 path=[320:0-341] [-1, 320, -2]
+AGCAGAAGAAGAATACTTGGTGACGGATTTGGTACCTTCGGTAACGGCGTGCTTGGCTAA
+CTCACCGGGAAGAATCAAACGAACAGCAGTCTGGATTTCACGGGAAGAAATAGTGGACTT
+CTTGTTGTAAGCAGCAAGCTTGGAAGCCTCAGTGGCAATACGCTCAAAAATATCGTTGAC
+GAAAGAGTTCAAGATACGCATGGCTTGGTTGGAAATACCAGTATCAGGGTGAACTTGCTT
+CAACACCTTGTAAATATAGGATGAATAAGTTTCCTTTCTGTTTTTACCACGCTTCTTATC
+AGCAGACTTCATGGTATCCCTAGGAGCCTTACCGGCGGGAGC
+>TRINITY_DN182_c0_g1_i1 len=257 path=[235:0-256] [-1, 235, -2]
+TTTGTCTAGAACAAAATTTTATTCAATAATCAAGACATGCAAGATATGAACAAGACCTTT
+TAGTTCTTTCTTCTGAAAGAGCATCCCTCCATAAGACGAGCCTTACCACCAGTAGGTTGG
+CAAAGGACAGAGGCACAAGAACCGCAAATAACAACGGTTTGAGCATGAGAGAAAACTGTG
+GTGATGTTGAAGCATCCAGGGCACTTGACATCCATGAAGAAACTGCGAGGGCCTTGAACA
+AGCTGCTTCAGCTTGTG
+>TRINITY_DN186_c0_g1_i1 len=285 path=[287:0-76 288:77-284] [-1, 287, 288, -2]
+TACAAGGATGTCGGTTTGGGATTCAAGACCCCTGCCGAAGCTATCTACGGTGAGTATGTT
+GACAAGAAGTGCCCTTTCGTTGGTCAAGTCTCTATCCGTGGCCGTATCTTGACCGGTACC
+GTTGTTTCCACCAAGATGCACCGTACCATCATTATCCGTCGTGAGTACTTGCATTTCATT
+CCCAAGTACAATCGTTATGAGAAGCGCCACAAGAACTTGGCTGCCCACGTCTCTCCTGCT
+TTCCGTATTAACGAGGGTGATGTTGTCACTGTCGGTCAATGCCGT
+>TRINITY_DN189_c0_g1_i1 len=379 path=[357:0-378] [-1, 357, -2]
+TTATATTCAGCAGTTTTAATTTTTTTAATTTTTGAAACTTATTTTTTCGTAACATACAAC
+AACTGAACAATTTTGGCTTAAATACGGGTTCTATTTATTTTTTTTTGTTTTTTTTTTTTT
+TTCTAGTTAATTTTTTAATTACTCTTACTCATTTACGACAACGACCCCTTTTCTCAATTT
+TTTAATACAAACTTTTCAAAATGTCTACAAAACTCGTTGATCACGTCGAAATTACCGTTC
+CTACAGGAAAAACTTACATTCAACCTGTCGGTCTCTTTATCAATAACCAACATGTCGATT
+CCGTTCACGGTGGTCGTGTGAAGGTTTACTCTCCTTCTACTGAGAAACTTATTTGTGAGG
+TAGCTGACGCCGACGAAGA
+>TRINITY_DN191_c0_g1_i1 len=1134 path=[1112:0-1133] [-1, 1112, -2]
+CTTGTACAGAGGGGACTCCACAAAGGTGCATTCCTCAACGCCAGACTCACCAGCCAAAGC
+ACGGAGTACGGAGGAGGCCATACGAGCACCGGCATAGGCCATAGACAAGGTCGCACTTCC
+AGCACCAGCCTTCGCCTTTACAACCTCATCACCACCAAATTGGATACGGTGAATAAGTGC
+GTCACGCTTTTCACCAGTCAATTCAACACCGCCTTGGGACAACAAAGGTACGATGGTCGC
+ACCGGAATGACCGCCAACAACAGGAATATGAAGAAGTTCTGCCTTGCCATTAGTGACTTG
+AGAGGTGAAACGGCTGGCACGAACAGAGTCAAGTGTGGTGACACCAAACAAATGTTTGGG
+TTGATGAACGCCAACACGTTCTAAAGCCTTTTTAAAGATGGGCACAGTAGAGTTTACGGG
+GTTAGTGACAACGAGATATTTGGCTTCGGGACAAGTTTCACCTGCTGCAAAAGCAAGGTC
+CCGCACAATCGATGCGTTAGTAGCAAAGAGATCATCACGAGTCATTCCGGGCTTACGGGG
+AACACCAGCAGGAATAATGACCACATCAGCACCGTTCAAGGCTTTTTCAAGTCCCTTGTC
+ATCAGGAGCATAGCCAACAACATTGGAAGTGGTATTGATATGTCCAATATCGGCAGCAAC
+GCCAGGAGCTCCCCTAATATCGAACAAGGCCAATTCACTAACCTTATCGTTCAGTTTTAA
+AAGCATTGACAAAGGCTGGCCAATACCTCCTCCAGCACCCAAAACGGCTACTTTGAATGC
+GCGACTGGAGGTCGTAGAAAAAGAACGGGGAGCGATACTCTTAAGGGGAGTAAAGTTTTT
+GAAAGCTACTTTGGCAAACATCTTTGAAAGGTACAAATTCGCAAAGCAAAGTAGAGAACA
+CGGGTATTTAAAAAAAATAGAGAGAGTGTGTGTGAGACAGAGAGGGGGGTAAAAGAAATT
+TCAATAGAAAATGTCCAGTTGAAAGGTTGATTCTTCTTTTCTTCAGAAGATACTAGACAC
+TTAAACTTAACAAGTTCGAGGTACGCTTTTGGAAGTCGTTTTAGATACTTTTAGGCAAGG
+TCCCGAGCTTTGTTGATTATACGTTGACTATTTGGAAGATATGTTGAAGTTGAG
+>TRINITY_DN193_c0_g1_i1 len=443 path=[421:0-442] [-1, 421, -2]
+ATTTAAAAAGAGTCGTAAAATTTATATGTTGCTTCGTCATTGATCAATTAAAATAGTGAA
+GGTCTGATGTCTGCTATAGAGTGACCAAACCTCCAAAATTTTTCTGGCAATTTTTAAGCT
+GTAATAAGTGTTTAAACCTAATCCACTTCTTCAACCTCAGGTCCATTGTCAGCACCGCCC
+GGAGCACCACCAGGGGCACCGCCAGGCATACCACCAGGTGCACCACCAGGTGCGCCTCCT
+GCTTGATAAATCTTGGCCATGATGGGATTCGCGACACCTTCAAGTTCTTTTTGCTTGTCC
+TCATACTCATCTTTGGCAGCAGTGGTGTTGTGATCCAACCATTCAATGGTTTCTTTGACA
+GCCTTATCAATGGCTTCCTTATCTGAAGCATCGACCTTATCCTTGAGATTAGGATCGTCC
+AAGGAATTACGAAGAGAATATGC
+>TRINITY_DN194_c0_g1_i1 len=201 path=[179:0-200] [-1, 179, -2]
+CAAGAACGTTGGTAAAACCCTTGTCAACCGTACAGCCGGTTTAAAGAATGCCAATGATTC
+TTTGAAGGGTCGTATCTTGGAAGTCTCTCTTGCTGATCTTCAAAAGGATGAGGAACACTC
+ATTCCGTAAGGTCAAGCTTCGTGTTGAGGACATCCAAGGTAAGAGCTGCCTCACCAGCTT
+TAACGGTTTCGATATGACCTC
+>TRINITY_DN195_c1_g1_i1 len=230 path=[208:0-229] [-1, 208, -2]
+CAACGAGATCCACAATCACAGAAACTTGAGAGTTTTGATCGACTTGTTCAAAAGTAACGA
+CACCACTGACCTTAGAGTCACCACGAAGAACTGCTACAGCTCTAACCATTTTGTATGACG
+ATAATTTACTTTAAAAAAATACAACAAGAGAAGGGGTGTTTTGAGTAATTAAGTGTTTTG
+AAGGAAAATCAATAAGATTTTAACCACACTTCAAAGTTGGAGATTTCGAA
+>TRINITY_DN196_c0_g1_i1 len=373 path=[351:0-372] [-1, 351, -2]
+GGCAATCTTTTGAATGGTCTCGTGTTCAATAAGCTTGGGAATCTTACTTTCGTAAATGGT
+GTTTTGATTGCCAAAAGGTGAGTAGGCGGTGACGTGGATACCAAGCTTCTTATGCTTTTC
+GACAAATTCAGTTTGAGGTAAGAAGGGATGAAGCTCCATTTGATGAACGGCTGGCTTAAC
+CTTGGCAACCTTTAAGATACGCTCCAAGTTTGTATCGTTGAAGTTGGAAAGACCAATGTG
+ACGTACCTTGCCAGTTTCCAAAAGCTTCTCCATTGCCTTCCAGGTTTCCTCAATGGGGTT
+TTTCTCGTAAATGAGATTTCCATCCTTGTCTTTGGGGAATTTATCCTCACCAGTCTTAAA
+GCTGACAGGCCAA
+>TRINITY_DN196_c1_g1_i1 len=218 path=[196:0-217] [-1, 196, -2]
+AAAGATTGCCAAGTCTAAAGGTGAAGGTGTAACTGGAGCCACTATTGCTGTTTCTTGGGC
+AATTACCCGTGGTACTTCTGTAATTCCCAAATCCGTTAATGAACAACGTATCAAGTCTAA
+CTTCAAATACATTCCTCTCACCAAGGAGGATATGGACGAAATTAATAGTATCGGTATTCG
+TGCCCGTTTTAACCAAGCTACTTTTAGCAATGAACCTG
+>TRINITY_DN197_c0_g1_i1 len=219 path=[197:0-218] [-1, 197, -2]
+TCATAGGCACCAGTAATGCGATCACATTCCTCTTGGGACATAATAGGACCGTAAGGGCTC
+TCGCAAGCCATTTTTCCGTAAAAGTAGTATTGGACCAAAGGATCAGTCAAACCATTTCCA
+ATCAAGACACTCTTCAAATTGATGTATTGCTTCTCCATTTCATAGCCGCTGGCAACAAAG
+AAGTTAGCACCTTGGTTATGCTCCATAATTTCCTTGGCA
+>TRINITY_DN199_c0_g1_i1 len=253 path=[231:0-252] [-1, 231, -2]
+GAAAAGGTGATCGCTGATAAGAAAATTAAGGCTCAGGTATACCAGATTGACCTTATGAAC
+AACGGTGATGAGATTCAATCTTACTTATTGAAGAAGACCGGTCAACGTACCGTACCCAAT
+ATCTTTATTCACCAAAAGCATGTTGGTGGTAACTCGGATTTCCAAGCATTATTCAAGAAG
+GGCGAGCTCGACTCTCTTTTTAATACTGCCTAATGAAATTCTATGAGCAATAAATTTTTT
+TCTTTAAATTAAA
+>TRINITY_DN201_c0_g1_i1 len=386 path=[364:0-385] [-1, 364, -2]
+CGTACGTTAGAAAAAATCAAACAACAGCAACATGGGCCGCGATATTTACAAGGACGAGAC
+ATTGACGATCCCTGAGGGCGTTTCAGTTGACATCAAGGCTCGTTTGGTGACTGTAAAAGG
+CCCTCGTGGTGTTTTGAAGCAAAACTTGCGCCGTGTGGATATTGAGTTGAAGAAGCAAGG
+CAACACTATCAAGTTTATTGTCTGGCATGGCTCTCGTAAGCATAATGCTTGCATTCGTAC
+CGCCTATTCCATCATCAATAACATGATCATTGGCGTTACCCAAGGTTTCCGCTACAAGAT
+GCGTCTTGTCTATGCTCACTTTCCCATCAACATCAATTTGACTGAGAACGGAACCGTTGT
+TGAGATCCGTAACTTTTTGGGCGAAC
+>TRINITY_DN202_c0_g1_i1 len=720 path=[698:0-719] [-1, 698, -2]
+CAGAAAGGAAACTTATTCATCCTATATTTACAAGGTGTTGAAGCAAGTTCACCCTGATAC
+TGGTATTTCCAACCAAGCCATGCGTATCTTGAACTCTTTCGTCAACGATATTTTTGAGCG
+TATTGCCACTGAGGCTTCCAAGCTTGCTGCTTACAACAAGAAGTCCACTATTTCTTCCCG
+TGAAATCCAGACTGCTGTTCGTTTGATTCTTCCCGGTGAGTTAGCCAAGCACGCCGTTAC
+CGAAGGTACCAAATCCGTCACCAAGTATTCTTCTTCTGCTCAGTAAGCGAATCGCACGAT
+TGTGCAATCGTCTTTTAGTCAGCTGATGAGTTTCCACAGCCTTCCATTTCGACAATGACA
+ACCTCACGAAACAAAAGGGGGTAGGTTATTTGCTCTTTTGGAAATATATATTTTCCTCCT
+CCCTTTTTTAACGTTTTCGTTCCCTCCTCTTTTCCATTTCCGCCTTTTGTATCGCATTCC
+TATTTTATTCCCCGTACAATGACGACAACAACAACACAGGTGCAGCACATCACGCGATAG
+TTTTTTTTACATTACACATGGTTCTTCATTTCTATGACCGGTTCGTGGAGTTGAAAGGTG
+TTTTGTTTTGCACAAGTCGTACTGGATCAAATTGGGTTTTGTGTTCGATTCGACGGGGAC
+GAGATGCTTTTTCTTCCCTTGGTTAATCTTCTTCCCTTGTGCATTTTATAGCTATCACCA
+>TRINITY_DN204_c0_g1_i1 len=227 path=[205:0-226] [-1, 205, -2]
+TCCATGTAGACAAAATGTTAAGTCCAGGAGCGAAGATGTCAACACAGCTACCATAGTTAG
+AGAAGTAGGCCATTTGGTCGTTTATAGTGGAAGCGCCAACGGTGATGGCTTTCTTAGAAG
+CAGCAGGAGATGAATGGCAAGCGTCATCATACTCATTTCCAGCAGCAACGGCATAAATAA
+CACCGTTGGTAACGGCAGAATCAACAGCCATATCCAAAACAAAGCTG
+>TRINITY_DN205_c0_g1_i1 len=210 path=[188:0-209] [-1, 188, -2]
+TATATATTGACGAATTGTTGTATTAGCAGGATTGGTTGCCTTCCAAGCGAAAGCAATTCT
+TGCAGCACGAAACGCCATGTTAACAATATGAAGATAAAAAAAATAAAGCAAAAAATATAA
+AATTTGTGTAAGTTTTAGTTACCAACGCTAGTGGGTATGAACTAAAACGTTATACTTTAT
+CTGTTTATGGTGCCTTAGCAATTTTCCAAT
+>TRINITY_DN206_c0_g1_i1 len=255 path=[233:0-254] [-1, 233, -2]
+TGGCCTTTACTGAAGACGAACGTTTGGTTGGTGAGGCCGCTAAGAACCAAGCTCCTTCCA
+ATCCTGAAAACACCATTTTTGACATCAAGCGTCTTATTGGACGTAAGTTTGACGAAAAGA
+CAATGGCCAAGGATATTAAATCTTTTCCTTTCCATATTGTAAATGACAAGAACCGTCCTT
+TGGTTGAGGTTAATGTAGGTGGTAAGAAGAAAAAGTTTACCCCTGAAGAAATTTCAGCCA
+TGATTCTTAGTAAAA
+>TRINITY_DN207_c0_g1_i1 len=303 path=[281:0-302] [-1, 281, -2]
+CAGGCTATGAGAAAGTGCATTGGACAAATAAAAATAAGAAGCAAGTAAGACAGCATATGA
+CTTGATCCCCAACAGGCTAAAGAAGAAGTAAAAGAGAGGGGAGAAAAAGGAGGGAGGAAA
+TCAGCTAGGACAAAAGTTTTTGAGCGAAATAAATTTTATCCGATGATAATTTTGCTTCCT
+TCAAACGTATAAGCAGGAATCGCCAAGTTAAGAGGTGCAGGACCACGGCGAATACGACCA
+GAGATATCATAATGAGAACCGTGACAAGGGCAGAACCATCCGCCATAGTCACCAGCTTCG
+CCA
+>TRINITY_DN208_c0_g1_i1 len=203 path=[181:0-202] [-1, 181, -2]
+CACAAAAATTATATTGATAGATAATTCAAATTTCACGAACAATTGCACAACATTTATAGC
+AGACAGGGGTAAAAAAGGAATTAAGTGGTAAATAATAAAGTGATATACAAACAAGGAGAA
+AAAAATCAATGTAATAGGAGTTTAACCACCGAAACCATAAATGGTACGGCCTTGACGCTT
+CAAAGAATAGACAACGTCCAAAG
+>TRINITY_DN209_c0_g1_i1 len=330 path=[308:0-329] [-1, 308, -2]
+GGCAGAGAAGGCTCAAAACCCCATGAAGGAGCTTCGTATCTCCAAGCTTGTCTTGAACAT
+TTCTTTGGGAGAATCTGGTGATCGTCTCACCCGTGCTGCCAAGGTTTTGGAGCAACTTTC
+GGGTCAAACCCCCGTTTTTTCTAAGGCTCGTTATACCATTCGTCGTTTTGGTATCCGCCG
+TAATGAGAAGATTGCTTGCCATGTTACTGTTCGTGGTCCCAAGGCCGAGGAGATTTTAGA
+GCGTGGCCTTAAGGTCAAGGAATACGAGTTGAAAAAGCGTAACTTTTCTGCCACCGGTAA
+CTTTGGTTTTGGTATCCAGGAGCACATTGA
+>TRINITY_DN210_c0_g1_i1 len=386 path=[364:0-385] [-1, 364, -2]
+ACCCAAGATGCCTCCTAAATTCGATCCCAATGAAGTAAAGACCATCTTTATGAGAGCCGT
+CGGTGGTGAAGTCGCCGGTGGCTCCACCCTTGCTCCCAAGATTGGTCCCTTGGGTTTGTC
+CCCCAAGAAGGTTGGTGAAGATATTGCCAAGGCTACCAAAGATTGGAAGGGTCTCCGTGT
+GACCGTCAAGTTGACTATTCAAAACCGTCAAGCCGCTGTCTCGGTTGTTCCCTCTGCCTC
+TGCTTTGGTCATTAAGGCTTTGAAGGAGCCTGCTCGTGACAGAAAGAAGGACAAGAACGT
+CGCTCACTCTGGCAATGTCTCTCTTGACGAAATCATTGAGGTCGCCCGTACTATGCGCTT
+CAAGTCTCTTGCTAAGGAGCTTTCTG
+>TRINITY_DN211_c0_g1_i1 len=312 path=[290:0-311] [-1, 290, -2]
+TTCGGCTAGGAGAGAAAACTCATGATAAGGAAAGAAACATAAATTCAGTGTTCATAGCAA
+GAAGTAAACAAAATGGGCATGTTACTTCAGTTTAGAAATAATGGCATCGGTATATTGAAC
+ATTGTTTGACTTGCCGCCCAAATCCTTGGTGCGAGCATCGGGATTGTTTGCAAGGGTATC
+AAAGATAGCTGATTCGATGCGTTTGGCATAATCATTTAAATTCATGTGCTTCAACATCAT
+TACAGAAGATAACAGTAAAGCAGTAGGGTTGGCTAAACCTTTTCCAGCAATATCAGGGGC
+AGTACCATGAAC
+>TRINITY_DN215_c0_g1_i1 len=308 path=[286:0-307] [-1, 286, -2]
+GAGGATTCTTTGAAAGAGGTTCTAAAGCGTGCACTTGTCCATGATGGACTTGCTCGCGGT
+ATCCGTGAAGCTTCCAAAGCCCTTGACCGTCGCCAAGCCCACCTTTGTGTTCTATGCGAG
+AGCTGTGATCAAGAAGCTTATGTTAAGCTTGTTGAAGCCCTTTGTGCTGAATCCCAAACC
+CCTTTGGTTAAAGTAGCTGATCCTAAGATCTTAGGTGAATGGGCTGGTTTGTGCGTTCTT
+GACCGTGATGGAAATGCCCGTAAGGTTGTTGGCTGCTCTTGTGTTGCTGTAACTGACTAT
+GGTGAGGA
+>TRINITY_DN216_c0_g1_i1 len=274 path=[252:0-273] [-1, 252, -2]
+GGGCATCCAAGCAAAGTTAGCGGCCAACTGTGCAATGTATAAAATGGATCCATTTCGAGA
+GGCATTCGTAATCATCAAAGGGTCAGCCTTGTACGCCAAATGGGATGCATATCCCATTGT
+TAGGTATAGTAGTGTCCATGCTGGTCCAAAGGCAGATGCAGGGGGGTGGAACTTTGGTTG
+CTTTTTGTTCTCATAATCCTTTCTTGGCTTGTAGGAATTCCCAATGAACCAGCCGCAGGC
+GACTGGAACGAGAGAAGCGGACCACCAATTTTTG
+>TRINITY_DN219_c0_g1_i1 len=363 path=[341:0-362] [-1, 341, -2]
+TCGCTCAAATGATATCCGCGACTTAAAAGTTCAGAGATTATAGCTGAACGAGGCTTGTCT
+TCTTGACGAGCGGCTTGATCGCCTCCAGCACCTCCTTGATCGGTAGTAGAAGCAGCACCA
+CCATCTTCACTGGTGATTTGGATTTTGTTTTGTCCAAGGAGAGCATCTTGCAAAAGTAAG
+GCCGTCTTGGTGGCGCTAGGGCGTTCAAATTGGATTTTCGCGGTTTGGGTTTCTCCAGAT
+TTCTCGGTAGAGATGTTGGACACTTTACCGCAGAAAGAAAAGAAGTCTGAGATTTGTTTC
+TCAGTAACTTCAGGAGAGATGTTCGTTACAATAACTTGGTTGCTCATTACTTTTGTTTCA
+ACT
+>TRINITY_DN219_c1_g1_i1 len=259 path=[237:0-258] [-1, 237, -2]
+CTCTGAACTTTTAAGTCGCGGATATCATTTGAGCGATGTAACTTTGGAAAAGAGTATTCA
+ACTAGACCAAAGCTATGGCGTTTCTTCAAAATTCAAGGGGATCCTCGAGTCTGCTTTGTC
+TGGCGTTCGTTCTGTTAACGAACGTTATCATGTCACCGAAAAGGCCAATGAGGTTGATAA
+TAAATTTGCCATTTCTGACAAATTGAACCGCACCTCTTCTTTGGTTAGCACATATTTCCA
+CAAAGCTCTTGAAACTGCT
+>TRINITY_DN220_c0_g1_i1 len=297 path=[275:0-296] [-1, 275, -2]
+CTCGTATTCATTGTTGATCAACTCGGTCTTTTTGCACAACCATTCACATAGGTTGAGCCT
+GTTGTTTATCTTTGTTATTTTCTGAACTTGTTTTTATATTGCTTTGTTTGATTCAATGAC
+TGCTCTATCAACCAACTCTTCTTCTGGTGGGATCTTCAAGATCGCTATTGTTGGCGCCGG
+TGGCATTAACTTTGGTACCCCCGAGGGACCTTGGAACAATGCCCAGAGAGTTGAAAAGGT
+GTTAGGAAAATCACTTCGAGTAACTGCTCTCATCAACCCCTTAATTAACGAAAGCGA
+>TRINITY_DN221_c0_g1_i1 len=421 path=[399:0-420] [-1, 399, -2]
+CTGCTCTCAACAAGATTGTCAAGCGTTCGAGCTCCCAGCCCACTGAAACCGACCTCCTTG
+TTGCTCAATGTCTCTATGATTTAGAGAGTTCTTCTAAGGACATGGCCAAGGAGCTCCGCC
+CTCTCCAAATTACTTCTGCTCGCGAAGTTGAAGTTGGAGGTGGAAAGAAGGCAATCGTTG
+TTTTTGTGCCCCAACCCCTTCTTAAGGCTTTCCACAAATGCCAAGCTCGTTTGACCCGTG
+AGCTCGAGAAGAAGTTTGCTGACCGTCATGTAATTTTCATCGCTCAACGCCGTATCTTGC
+CCAAGCCTGGCCGTAAGTCTCGTGTTACTCAAAAGCGTCCTCGTTCTCGTACCTTGACTG
+CTGTTCACAACGCTATTCTTGAAGACATTGTTTTCCCCACTGAGATCATTGGCAAGCGTA
+C
+>TRINITY_DN223_c0_g1_i1 len=231 path=[209:0-230] [-1, 209, -2]
+TCGAAAACTGGTGATTTCAGTGAATTCATTAAAATGGCAGAAGAATTGAAAGCCAAGGGA
+AATGCGGCGTTCTCCAAAAAGGATTATAAAACAGCCATTGATTACTTTACTCAAGCAATT
+GGTTTAGATGAAAGAAATCACATTTTGTATTCCAACCGCTCTGCGTGTTATGCTTCTGAA
+AAGGACTATGCCGATGCACTGAAAGATGCCACAAAATGTACCGAATTGAAG
+>TRINITY_DN225_c0_g1_i1 len=210 path=[188:0-209] [-1, 188, -2]
+TTTGTTGAACCTACCGTTTTACTTTCTAAAAACCCTAAACATGATATATTCGTTAACGAA
+TTGTTCGGCCCCGTACTGTCTGTTTATGTATATGAGGATGACAACTTAGACGCTGTTTGC
+GATCTCATCGATACTACCACTCCTTATGGTTTAACCGGATCCATCTTCGCTCAGGACCGT
+GTTGTTGTCAGAAAGTTGACTGACCGTCTC
+>TRINITY_DN228_c0_g1_i1 len=316 path=[294:0-315] [-1, 294, -2]
+TGCTTATTATAAATTAATTAAAATTCAAAAAAAAAGGAAGAAAACAAGTGGGAAAAAAAA
+TCGTTAACAGAAATAGTTATCTCTGTTGATGTAAATAACTATTAAAAACACGAAATGAAA
+AGAAAAGGGGTGAACCACCTATATATTCCTTTCGTAGATTCGCAAGTGAGGCGAAAAGTG
+TTTTGTAGTTGTTAAGTTCCTTAAAAAGACAGAAGTCGGAAGGAACTATGCAGTAGTTCG
+GACGATATTTATGTAATTTTTGAGTAAAGCTAACAACTTCTTATACCGTTGCTACCGAAC
+AAAATGGACGAAACCG
+>TRINITY_DN228_c1_g1_i1 len=201 path=[179:0-200] [-1, 179, -2]
+GGCAAGACGGACTTGCTGTGCTTCATCTCATACTTGCCGTCACCGAGAAGTTGGATCCAA
+CAAACACGCAAGTTGGTACCACCAAAGTCAAGGGCCAAGAAGTCACCAGTTTCAGCGCCG
+GTGGGAAGGGTAGAGATAAAGGCAGGAGCCATAGCAAGCACCTCACCATTCTTTTGTAAA
+CCCTTTTGACGTAATTCGTCA
+>TRINITY_DN232_c0_g1_i1 len=220 path=[198:0-219] [-1, 198, -2]
+CCAGAAACCTGGGCAGCAGAGCCGATCTTTCGTTAGCAGCTTCTGCGTTCACGTCTTGAG
+AAGTATTCATGGTTCTCTACGTTAATTTTTCTTTACTCGGTAACCAAATGGGGATGGTTC
+TGAAGTAAGATGGTTCTTTTTAAAGATAAATAGAAAGGAAAGAAAAGAAAAAGAAACGTT
+CTTCACTAGAAACAGTGGATCACGGGAATTTGAGTAGAAG
+>TRINITY_DN233_c0_g1_i1 len=665 path=[643:0-664] [-1, 643, -2]
+GTAACGTTGGGTTCCATCATGAGTGGTCGCATTGGGGCTTACAATGTGATTGGCAATATC
+ATGATTTCCTTGTTCATTGTTAATAGCATAAGGGGGCCAGTCAATGTTGTAATCTGGCTT
+CAAACCTAATGGAGTAGCAGTTGGTGAAACAATTTGGAACACCGATGATGTTGCAGTGGC
+ATAGTAGTTGCTAAGTGAAGCACTGTAAGCAGAACTATACTCAGTCACATTGGAAACGTT
+AAATCCTTCTGGGATGGAATACTGCTTTGAAATTCCGGTCAAGGGCTCTGCAGGGTTTAA
+GTCAATCATAGCACTCCCACAAGAGCCCACGCAGAACGAAGAGGGTTCGTTCATATCAGT
+CCAAATTCCACTGAATGGAACAGTACCATTCGATCCAAAAGCATAAGTAAGGTTGATAAG
+ACAGTCTTTCCAATAGTCAACCACATCGGGATTGGTGAAATCAGGGAAAGCAGTGAATCC
+TGGCCAAACCGCACCAATGTAGATACTTCCATTAGGATTTTTTAAGAAAATGTCCTTTTC
+AACGCCTGCATAGTATGGATAATAAGAGTCGTCAGTGTGATTGTAGGGGTTTGCGGCATA
+AATCGCAGCATCAATGATTGGAACGTAATGCTGATGATTGCTTACCAAATCACTGAAAAA
+TGTTT
+>TRINITY_DN233_c1_g1_i1 len=393 path=[371:0-392] [-1, 371, -2]
+TACCAAATCACTGAAAAATGTTTGCATATCTGACTTTGAATAAGAAACAGGGTCAACGGT
+AAAATCTCTATATTTCTCCATGTAATCAATATCAGACCAAAAGGTTTCCACTGGAATGTC
+TGCATCAATGTAATTTTGACGAACGTCCATGATTTCTGTGATATTTGTGTAACCCCAACG
+ACATGAGTGGTAACCCAATGTCCAATATTGATGCATAGCAGGCTTTCCAATGGATTGAAC
+GAATTGCTTGACAGTCTCCTTGGGACTCTCAGTGCTACCACTGTATACAAAAAGGTCGAT
+AACACCACCGATCATTCGATACTGAAGATAATCTTGGCGCAAAAGAACATCCATTCCATT
+AGCTGTAAGCATAAGAACACCATGAGAAGAAGA
+>TRINITY_DN233_c2_g1_i1 len=336 path=[314:0-335] [-1, 314, -2]
+GAGAAGAAGAAGTATAAGTGGTTTCGTTCAAAGTTGAATTTATACCATCCGCCTTGTATC
+TTTGTTCTAAATAGTATGGATGACTTCCGTACATGTTTTGGTCCACGGGGCTAGGTTCAT
+CATTAGCCCAAAAGGTACGGGTTAAGTTATTTCCCAGACGTAAACCATGGATGGTTTCAG
+CGAGACCATAAAGATTATAATTTTCAACCATATTAGTAGTTAACTCAATATACTGATCTT
+CGAAAACCAATTTCTGTCCGCGTGTATCAAATAAAACTTCACCATCGCTCTTACGTGTAA
+CCCAAAATTCGAAAGGATTGGCATTGTACGAAAAGT
+>TRINITY_DN235_c0_g1_i1 len=1280 path=[1289:0-132 1290:133-1279] [-1, 1289, 1290, -2]
+GAGGTGGAAGTGATGTAGGAGCTGTTAGGACCGACAGCCATACCGGGAGCATCCCAAGCC
+AATTCGACGCTTTGTCCGGGAAGAGAGAGAGGGAAGGTACGGTTGGTGGAGACAGCGGCG
+GGATACATGTAGGTACCGTTAGGGTACTGAGGGAAAGAGCCGTTGGTGAAATTAGTGTGA
+ACAGGAGGGCTAACCAAATGTAAGGCAGGGAAGTTTTGCCAAACCAACTTTTCGTTTTCG
+GCAGGGCAGCCAACAATGAAAGGGGCAATCAAGGACCAAGCAAAGGATTGAGGAATGCCA
+GTTTCAAACCAGACGGGGTAAGGGAAGAGACCTTGTAATTGACGGAGAGACATTTGTTGA
+CGAGCTTCAGTGGTGATGGATTGAAGCAAAAGAGCAGCTGCTGCGCGAGAGTCAAGGTGG
+GGAAGGAAACCATAGACACCGGATTCACTCCACTTAGTAAGGGTTTGAGCAAAGTCAATG
+AAGGAGCCCACAGTGTCAAAGTTGTACTGGTAAGAGCAAGCCTTGGGGGCGTTGGGGCCA
+AGCATGTTGGTGACAAGCTCGATGTGGCCGATTTCTTGTTGGGCCATGAAGCGAATCAAG
+TGACGGTACTCGGCGTCAATGCCGGCCTCGTCAAACTCGGCATCAGAGAATTTAGTGAGA
+CCGTAGTTGAAGAGGTCGTACTCGATGTACTCGTGGTATAGAGCGAGAGACAAGGACTGG
+TAGTCAAAGTCACTGAAAGGGTGATAAGTAGGGCTGCTATCATTAGTATCGATGCCGCCA
+GCAGGAGTAAAGTTAGCAGGCATGATAGATTGATTAAAGGAACCAGTAGCAGTGTAGTTG
+TATTCGTAAGCGGCACCGCCAATACCAGCAAAGTTAACTGGATCGGCCTTAGCACCGATG
+ATACCGCGCGCCAAGAGAGCGCCGGCCATTAAAGAAGCAGTAAGAGCTTGAACCATTGTA
+TAGATTTATAGATATACAAAAAAAGAGGCGATAGTGTTTTATTAAGGTAAGGTAGAATCA
+ACTAGGTTTTCCACACGCACCGACACGAAAAGAAATTAAAAATATAAAAAGAAGCGACGA
+ACGAGGTCTTTTTCAAAATAGCAATCCAACCAAAAAAAACTACAACTAACAAACGTGGTA
+GTAGTAGTAGTATTAGGAGTAGAGTAGCAGGGAAGCACAGAGAGAGAGAGAGAGAGAGGT
+AGGCTTGATATTTCACAAGACAAGCTCGTTTATTTTTTCTTACTTACTTAAACAAGGGCA
+AAACAAAGTCACACAATTTG
+>TRINITY_DN235_c1_g1_i1 len=455 path=[433:0-454] [-1, 433, -2]
+ACCAAAAGAAGACAGGCCAATAGATAGAATCGTGAACGAGTATGATTTTTGATGAAATAA
+ATCCATGGTAAGGCGAGTCTAATTATTAAGGCTCCAACCTAGCCACATATACAAACGAGC
+TCAATCAACTGAGTCAATCATCTACATGATGTGTACATGTGCAACTAAGGGAGTTTGCCT
+TGATAGAGACGCTTATCCGGACTCGTAAACAAGAGGACCAGCAACAACGTGCTCGTTGAT
+GGCAGTGATGTTGAAGGGAGTGACGGGGATAGCTTCGTCAACGAGAACCAAGAAGTTGGT
+ACCGTTAATGACTTGCTGGGTAGAGTCGTTGTAAAGGTGAGAGCTGGGTTGGTAGGTAAC
+ACCGCTGTTGTTGCCGGTGATGTTTAAGGGAGCGTAAGTAACGTTCAATTGGGAAATCCA
+AGCAGCATAACGAGGAGTTCCGGCAGAGGTGGAAG
+>TRINITY_DN237_c0_g1_i1 len=223 path=[201:0-222] [-1, 201, -2]
+CTTCTTTTTCCAATTTCTCAGTTTTACCTTTCTTTTCCCCATCGGATGGTTTTTCTGATT
+CCTTCTTTGCCTCCGCCTCTTCGGGATGTAGAAAGGCGTCGGCATCTTCCTCATCTAAAA
+CGACAACTTTTTCATTTTTTTGGTAGGGTTCTTCACTCAGAACTTCCTCAACTTCAGGAG
+GCTGTGGTGCGGCTTTTTCTGCTGCTGTTTGTTCAGGAGCATG
+>TRINITY_DN238_c0_g1_i1 len=2114 path=[2092:0-2113] [-1, 2092, -2]
+TTCTAACAAGGAAATTTTCCTTCGTGAGCTTATTTCCAACGCTTCCGATGCCTTGGACAA
+AATTCGTTATCAAAGCCTTTCCGATCCTCATGCCTTAGACGCTGAGAAGGATCTTTTCAT
+TCGCATTACTCCTGACAAGGAGAACAAAATCCTTAGCATTCGCGATACCGGTATTGGTAT
+GACCAAGAATGACCTTATCAACAACCTTGGTGTTATCGCCAAGTCTGGTACTAAGCAGTT
+TATGGAAGCTGCTGCTTCTGGTGCTGATATCTCCATGATTGGTCAATTCGGTGTTGGTTT
+CTACTCTGCATACTTGGTTGCCGACAAGGTCCAAGTCGTAAGTAAGCATAATGACGATGA
+GCAATACATCTGGGAATCCTCTGCTGGTGGTAGCTTCACCGTCACTTTGGACACCGATGG
+ACCTCGCTTGTTACGTGGTACCGAGATTCGTCTCTTCATGAAAGAAGACCAACTTCAATA
+CCTCGAGGAAAAGACTATCAAAGATACCGTCAAGAAACATAGTGAGTTCATCTCTTACCC
+CATTCAATTAGTTGTTACCCGTGAGGTTGAGAAGGAGGTCCCTGAAGAAGAAGAGACCGA
+AGAAGTTAAGAATGAAGAAGACGATAAGGCTCCTAAGATTGAGGAGGTTGATGATGAATC
+TGAGAAGAAGGAGAAGAAGACCAAGAAGGTCAAGGAGACCACCACTGAGACTGAGGAGTT
+GAACAAGACCAAGCCCATTTGGACTCGCAACCCCAGTGAAGTTACCAAGGAAGAGTATGC
+CTCTTTCTACAAGTCTTTGACTAACGACTGGGAAGACCATTTGGCCGTCAAGCACTTCAG
+CGTTGAAGGTCAATTGGAATTCCGTGCCATTCTTTTCGTCCCCCGCCGCGCTCCTATGGA
+CCTTTTTGAGGCCAAGCGTAAGAAGAACAACATCAAGCTCTATGTTCGCCGTGTTTTCAT
+TACCGACGACTGTGAAGAGTTGATTCCTGAATGGTTGGGTTTCATTAAGGGTGTTGTTGA
+TTCTGAGGACTTGCCCTTGAACTTGTCTCGTGAGATGCTTCAACAAAACAAGATCATGAA
+GGTTATTCGTAAGAACCTTGTCCGTCGTTGTCTTGATATGTTCAACGAGATTGCCGAGGA
+CAAGGAGAACTTCAAGACTTTCTACGATGCTTTCAGCAAGAATTTGAAGCTTGGTATCCA
+TGAGGATGCTGCTAACCGCCCTGCTTTAGCCAAGCTTTTGCGTTACAACTCCCTTAACTC
+CCCTGATGATCTTATCAGTCTTGAGGACTACATCACTAAGATGCCCGAACATCAAAAGAA
+CATTTATTTCATCACTGGTGAATCTAAGCAAGCCGTTGAGAACTCTCCCTTCTTGGAAAT
+CTTCCGTGCCAAGAAGTTTGATGTTCTCTTCATGGTTGACCCCATTGATGAGTACGCTGT
+CACTCAACTCAAGGAATTCGAGGGCAAGAAATTGGTTAACATTACTAAGGATGGTCTTGA
+GTTGGAAGAGACTGACGAGGAGAAGGCTGCTCGCGAGAAGCTCGAAAAAGAGTATGAGGA
+GTTTGCTAAGCAACTTAAGACCATTTTGGGTGACAAGGTTGAAAAGGTTGTTGTTTCTAA
+CAAGATTGTTGGTTCTCCTTGCTTGTTAACTACCGGTCAATATGGTTGGTCTGCTAACAT
+GGAACGTATCATGAAGGCTCAAGCCCTTCGTGATACTTCTATGAGTGCCTATATGTCTAG
+CCGCAAGACTTTTGAGATTAACCCCAAGTCTCCCATCATTGCTGAGCTCAAGAAGAAGGT
+TGAGGAGAATGGTGCCGAAGACCGCTCTGTGAAGGATCTTGCTACTATTTTGTATGAGAC
+CGCCTTGTTGTCCTCTGGTTTCACTCTTGATGACCCTAGTGCTTATGCTCAACGTATCAA
+CCGTCTTATTTCTCTTGGTCTTAGCATTGACGAAGAGGAGGAGGCTCCTATTGAGGAAAT
+TTCTACCGAATCCGTCGCTGCTGAAAACAATGCTGAGAGCAAGATGGAGGAAGTCGATTA
+AATCAAATGCATCTAATGTGTCTTTCCAAAATTTATGCATATAATGTTTTTCTTGGATTA
+AAGCAAGTTATCCT
+>TRINITY_DN238_c1_g1_i1 len=318 path=[296:0-317] [-1, 296, -2]
+GTTATTTATAACCCATTTCCCACTAAGTTCCTTTGTTGAACGCTTAAAAGATTGTTCATA
+CGTTTGAACATATTTAAAATCACGTTATAGCTGAGAAGAAAACCCCTTTTCAAGTAATAA
+AAGTATATTTAATTACTTATTTTACCCTTTATATTACGAACTGTACGACTTAACCGGTTT
+TATCTATAAATTCCTTCATTTTTCTTTGTTTTCGTTTTCAATTTGATTTCATTACAAAAT
+GTCGAACACAGAAACTTTCAAGTTTGAGGCTGAAATCAGCCAGTTGATGTCTTTAATCAT
+CAACACTGTTTATTCTAA
+>TRINITY_DN240_c0_g1_i1 len=210 path=[188:0-209] [-1, 188, -2]
+CAACTCTTAATTGACAGGACATCATGAGCGTTGCTAAAGCCAAAGGAGCACAGAAGACCG
+TTCAAAAGGGTATCCATAACAAGGTTGCTAAGAAGGTTCGCACTTCTACCACCTTCCGTC
+GCCCCAAAACTCTTCAGCTTTCTCGCAAGCCCAAGTATGCTCGCAAGAGTGTTGCTCATG
+CTCCTCGTCTCGATGAGTACAAAATCATCG
+>TRINITY_DN243_c0_g1_i1 len=417 path=[395:0-416] [-1, 395, -2]
+GGATATGTTATTTATCGTATTCGTGTTCGCCGTGGTGGTCGTAAGCGCCCAGTTCCCAAG
+GGTCAAACCTATGGTAAGCCTGTTCATCAGGGTGTTAACCATCTCAAATACCAACGCTCT
+GCTCGTTGCACTGCTGAGGAACGTGTTGGTCGCTACTGCTCCAATTTGCGTGTTTTGAAC
+TCTTACTGGGTCAACCAAGACGCAACCTATAAGTTCTTTGAGGTGATTCTCGTTGATCCC
+TCTCACAAGGCTATTCGCCGCGATCCTCGTATTAACTGGATCGTCAACCCCGTTCACAAG
+CACCGTGAGTCTCGTGGTCTTACCTCCATTGGTAAGAAGTCTCGTGGTATCGGCAAGGGC
+CACCGTTATAACAACTCCCCTCAACATGCCACCTGGCTCCGTCACAACACGTTATCT
+>TRINITY_DN245_c0_g1_i1 len=320 path=[298:0-319] [-1, 298, -2]
+TGTGAAACTAGCTTGAATGACGTTACGTTGTCATTATCTACAAATTTTTGGCAACGGCAG
+TAGGGTTAACCTTCTTGCCATCGCGGTTGTAGCGTACACGGGGAGGAGGTGTACGAATAC
+GACGTCCCTCGCGAGAGCGAACACGGACCACACGAGAGTGAATAGCGCAAGAGACACAAT
+ATTGCAACTTGATGTACAACTTGGGGATGGTGTACTCGCTGTAAACGGAAGCCTCAGACA
+AGTCACGAATGGCGGCAGTTTCAACCATGTTACGGATAGTCCAGCGCTTAATGGCTTTGT
+CCTTGGGGACAGCGCGGCTG
+>TRINITY_DN247_c0_g1_i1 len=301 path=[279:0-300] [-1, 279, -2]
+CGCAAGAAGCCAGAGAAACCATTGTCAATGGCAAGAGGAGTGTGACCACGGTTCAAACAA
+TATCGAACGGCAGCACGAGTAGAGAGTTCATACCACCAGCGGGAGCACCAACATGGATGA
+TGGCGACACGCATTCTCTCGTCCTTGGGAACGAAGTGTGACTCATCTTCAATAAAGGTAG
+TACCTTCCCAAGTGTGTAAGTAATCAGCAAATTCGGGGTCACGGAGCTCCATAGCATGAG
+CGAACTGCTTCTTCTCAATAGCATCAGCAACCTCATGAGTCAACTTAACAGCCTCCATCA
+A
+>TRINITY_DN250_c0_g1_i1 len=273 path=[251:0-272] [-1, 251, -2]
+TGCTGAGACTCATGGTTACGTTGGATCTGATTTGGCATCTTTGTGTTCTGAAGCTGCCAT
+GCAACAGATTCGTGAAAAGATGGATATGATTGACTTGGATGAAGATGAGATTGATGCCGA
+GGTTTTAGACTCTCTAGGTGTTACAATGGATAACTTCAGATTTGCCCTTGGTTCCAGCAA
+TCCTTCTGCTTTGCGTGAAACCGTTGTGGAAGTTCCCAATGTTCGTTGGGAAGACATTGG
+TGGATTGGAAGAAGTTAAGCGTGAATTACGTGA
+>TRINITY_DN251_c0_g1_i1 len=241 path=[219:0-240] [-1, 219, -2]
+GTGGAATGTCAGTAGCGGTAGTATGTGCAAAAGAAGAGGCTGTGGGCGCAGGAGCGGCAT
+TTTGACGAGAAACGCTTTTGCAAATACGGATCACATGAGGAGTGATATAGGGACGGATCA
+AGTGTCTGTAGATAATGGTAGCACCGTTGAATTTAGGCAAAGCAAGCCAAATCAAGAAAA
+TAGCCTTGAGTAACCAATACACAGGGACATAGTAAAGGATTAGCTGAGACCAGTACTCAA
+T
+>TRINITY_DN253_c0_g1_i1 len=224 path=[202:0-223] [-1, 202, -2]
+AACGTGTTGAGGGAATCACTCGTGTCGCTATGCGTCGTCCTAAGAACATTTTGTTGATTA
+TCAACGAGCCTATTGTTTATAAGAGTAGCAATAATGCTTACATCGTCCTTGGAAAGGTTA
+CTGTTGAAGATATGGCTGCCCAAGCTCGTGCCTTCAACGAGTCTCAAAAGCAAGCTACTG
+AGACTAAGGAAGAAGCTGCTATTACCGAAGAATCCGGCGATGCT
+>TRINITY_DN254_c0_g1_i1 len=278 path=[256:0-277] [-1, 256, -2]
+AACTCAAAAAATATGATCTCGTCGAGATTCACTAATGTAGTCCGTAGCGGATTGCGTTTC
+CAAAGCAAGGGAGCATCGTTCAAGATTGGCGCTTCCTTGCATGGAAGTCGCATGACCGCC
+CGCTGGAATTCTAATGCAAGTGGTAATGAAAAAGTTAAGGGTCCCGTAATCGGTATTGAC
+TTGGGTACCACCACCTCATGTTTAGCAATCATGGAGGGTCAAACCCCTGAGGTTATTGCA
+AATGCCGAGGGTACCCGTACCACACCATCTGTCGTCGC
+>TRINITY_DN255_c0_g1_i1 len=310 path=[288:0-309] [-1, 288, -2]
+TCCAACCTGAAGAAGGTCACTCTTGAATTGGGTGGTAAGTCTCCCAATATTGTTTTCAAC
+GATGCCGATTTGGACTCAGCTGCTGTCTGGACTAACTATGGTATCTTTTACAACTCTGGT
+CAAGTCTGTTGTGCAGGTAGCCGTGTCTACGTGCAAGAGGATGTTTACGATGAGTTCATT
+AAACGCATGGTTGCCAAGGCCAAGACTTTGAAGGTTGGTGATCCTTTCGCCGAAGATACC
+TTCCAAGGTGCTCAAGTTAGTAAGCAACAGTATGAACGTATTGTTAGTTATATTGAGAGT
+GACATTGCTC
+>TRINITY_DN256_c0_g1_i1 len=243 path=[221:0-242] [-1, 221, -2]
+GGTGTTTTTGACAACCCATGGAATCGTCGTTTGTTTGTCATCGCTAATCATTTGGGTTCA
+GTTGGTTTATGAGAGAAGAAACTAATAATAACATAAAAAAGAATAACGTTAACAACGTTT
+AATCTCTCCGACTTTGCCGAGATGTGATCCGGAATGTTTGGCAATACGTTTGGAACAATT
+AACAAGAACACTTAATGGATAGCAGGTATAGAACGAGCCAATGCTAGGCACTTTACGTTT
+TCA
+>TRINITY_DN256_c1_g1_i1 len=532 path=[510:0-531] [-1, 510, -2]
+ATGCTAGGCACTTTACGTTTTCAAATACACAACAAACCCTGTGTGTATTTTTTCAAAGTA
+TTGCCACATAACCCTAAATGGCGAGAATTGGGGATTTCCAATTTAAAACCATTTTGAGGT
+ACCCTTTTTAAGGGCTTCTGCTTGTTCAGTACCCTTGGCTTGCGCCTCTGACAACACATT
+TTTTACGTTTTCACGAGGTTTGTCGAGTTCATCGACAACCCTCTCCTTCCCACTTTGGAG
+ATAAGATTTTGCCTTTTCAGTGGTTTCGCCAACAGCTTTGTCAAATCGTTGACCCTCATT
+TTCCACGGCTCTGACGATTTCTGCATTCTTCTGTTCCAATCTGGAAGATGCCTGACGATT
+ATGGCGAGTCATATAATAACCAACACCAACAGCAGCGGCCAAGGCTCCAAGAGTAACACG
+CCTATTCATGATGCTCGATTAGGATTTCGTGAATTAACCGAGTAAAAAAAAATTAATAAA
+TCGAAAGGTTATATAAAAGCGGTTTTCTCCGTACAACACAAAGGATTGATAT
+>TRINITY_DN257_c0_g1_i1 len=213 path=[191:0-212] [-1, 191, -2]
+CTACTGACGGTGAAACCCGTGGTGGTTTGCTTTGTAAGGGCGGTAAGCTTTACCGTACTA
+ATACTGCTTACGATAACCTTTGTGAAAACGGTGTTGGCACTGCTTCTGTTCAAAACACAC
+TTGGCCAAGGTGTTGCCATTTGCCAAACCGATTACCCTGGAAGTGAGAACATGGTTATTC
+CTACCTATGTTGGTGGCGGTGCTACCTCTCCTT
+>TRINITY_DN258_c0_g1_i1 len=251 path=[229:0-250] [-1, 229, -2]
+TTGCAAACTTGGAAATCACCGTCCCAAAAAAATAAAACACCTACTTGGCTTCAGTGATGG
+CCTTGGTAAGCTCATAGGTCTTGACGGCATCCAAAAAGTCGGAATGGATAAGGTTCTTGT
+CACCCTTACCTTCAGCAGCATCCAAGAAGATCTTGAACTCACTGTAGTATGGGTCATCAT
+TGGGGTATTTGTAAACCTTTTCTTCGTCCGAATCAGGAGAGCGAACATACAAGACGGGCT
+CTTCATAAAGA
+>TRINITY_DN261_c0_g1_i1 len=560 path=[538:0-559] [-1, 538, -2]
+CTGAACTCGAGGCCAACGCTGCTGACTGCAAAGCTCGTGCTGAGTCTCCCATCACCAATG
+TTGAGGCCGTTCGTGAACGTCAAAGCAAGGTTACTCCCCAAATGCATGAACGTAAGAGTC
+CCTTTGAGACCCGTTATGCCAAGCAACAAGCTTCCCTTAAGCTTCCTCTTTTCCCTACCA
+CCACTATTGGCTCTTTTCCTCAAACCAAGGAAATTCGTGTAACCAGAAACAGATTCGCTA
+AGGGTCTCATTTCTCAAGAGGAATATGATGCCTTCATCCGTAAGGAGATTTCTGATGTTG
+TCAAATTCCAAGAGGAAGTTGGTCTTGACGTTCTGGTTCACGGTGAACCCGAGCGTAACG
+ATATGGTTCAATACTTTGGTGAAAGAATGGAGGGCTTTGTCTTTACTGTCAACGGTTGGG
+TCCAATCTTATGGTTCCCGTTGTGTCCGTCCTCCTATCATTGTCGGTGATGTTTATCGTC
+CCGCCCCTATGACCGTTAAGGAGTCTCAATATGCTCAATCCATTACTTCTAAGCCTATGA
+AGGGTATGTTGACTGCTCCC
+>TRINITY_DN261_c1_g1_i1 len=205 path=[183:0-204] [-1, 183, -2]
+CCTTGATCTTGAAAAGGCTGGTATTAAAGTCATTCAATGTGATGAGCCTGCCTTACGTGA
+AGGTCTTCCTCTTCGTCGTGCCGAGTGGGATGAGTATCTCAAATGGGCTATCGATGCTTT
+CCGTTTGGCTACTGCTGCTGTTCAAGATGACACTCAAATTCACTCCCATTTCTGTTATTC
+TGACTTCAATGACATTTTCGATGCC
+>TRINITY_DN262_c0_g1_i1 len=318 path=[369:0-186 374:187-255 368:256-317] [-1, 369, 374, 368, -2]
+GAGACATCAAAATGGCACTGAAGGAGTATCAAGTCGTTGGCCGTAAGGTCCCAACTGAGC
+ATGAACCTGTGCCTAAGTTGTTCCGTATGCGTTTATTCGCACCTAATGAATCAGTTGCCA
+AGTCTCGTTACTGGTATTTCTTGAAGATGATCAACAAAGTCAAGAAGGCCACTGGTGAGA
+TCGTTGCCATCAATGAGATTTCCGAGCCTAAGCCGTTGAAGGCCAAGGTCTTCGGTATCT
+GGATTCGTTATGACTCTCGCTCTGGTACCCACAACATGTACAAGGAGTTCCGTGACACTA
+CTCGGGTTGGTGGCGTTA
+>TRINITY_DN262_c0_g2_i1 len=318 path=[371:0-186 373:187-255 366:256-317] [-1, 371, 373, 366, -2]
+GAGACATCAAAATGGCACTGAAGGAGTATCAAGTCGTTGGCCGTAAGGTCCCAACTGAGC
+ATGAACCTGTGCCTAAGTTGTTCCGTATGCGTTTATTCGCACCTAATGAATCAGTTGCCA
+AGTCTCGTTACTGGTATTTCTTGAAGATGATCAACAAAGTCAAGAAGGCCACTGGTGAGA
+TCGTTGCTATCAATGAGATTTCTGAGCCCAAGCCTCTTAAGGCCAAGGTCTTTGGTATCT
+GGATTCGTTATGACTCTCGCTCTGGTACCCACAACATGTACAAGGAGTTCCGTGACACTA
+CTCGGGTTGGTGGCGTTA
+>TRINITY_DN264_c0_g1_i1 len=317 path=[295:0-316] [-1, 295, -2]
+CCACAAAGCATTAGAGATCTCAGGATCGACGTTTTGCTTAGTAGTGTTGGTAAAAGGGCA
+ACCGGCCTCCAAAGCAGGGCATTTTTTGTCGGCACCTCCGTGAGCGCCGGAAACTGGGCA
+GACGGGACTGCTTGTCTCGCCAGGTGTGGATTGAGAGGTGTGGTGGGGCTCGGAAGAGGA
+AGAAGAGATGTTTTGAATAACGGGATTCTCAGAGTTGGGGAGAGCAGAGGGAAATGAAGT
+GGCAGAGGGCAATTCGGTGGAAGGGTGAACGGTGTGAGCAGTCAAAGTATTTACAAGGTC
+CTCAGCACCGGATTTAG
+>TRINITY_DN265_c0_g1_i1 len=466 path=[444:0-465] [-1, 444, -2]
+CTTTTGGTTAAGCTTTACCGTTTTTTGGCCCGTCGTACAGATTCCCGCTTCAACAAGGCT
+ATTTTGAAGCGTCTTTTTCAATCCAAGACTAACCGTCCTCCTATTTCTATCTCAAAGATC
+GCTGCTTTAACTAGCCGTAAGAGTGCTTCTTCTCAGAACAAAACCACCGTCGTTGTCGGA
+ACCGTTACCGACGATGAGCGTATGTTGACTGTTCCTAAGCTTTCTATTGCCGCTCTTCGT
+TTTACTAAATCTGCTCGCGCTCGTATTTTGAAAGCTGGTGGTGAAGTTTTAACCCTCGAT
+CAGCTTGCTCTACGTGCTCCCACTGGAAGCAACACTGTTCTTGTTCGTGGTAAGAAGCAT
+GCTCGTGAGGCTTACCGTCACTTTGGCTTTGGTCCCCACAAGCATAAGGCTCCTTATGTT
+CGTTCTGAGGGCCGTAAGTTCGAGAGAGCTCGTGGTCGCAGAAAGT
+>TRINITY_DN265_c1_g1_i1 len=205 path=[183:0-204] [-1, 183, -2]
+GAGCTCGTGGTCGCAGAAAGTCTCGTGCATTCAAGGTTTAAATTACCTTGTTCAAGCTCG
+TTTCCTTTTCTCACACTTTATGGGATCAGCTCTTAGTTGCTTCTCATTTGGTTAGCGTTC
+ATAAATTAGGTTACCGGTGCATTATTGATCCGGCTTTAGTGTACATCAATAGTGTTCGTT
+CCCAGATATGAATACAATGAAAATC
+>TRINITY_DN267_c0_g1_i1 len=250 path=[228:0-249] [-1, 228, -2]
+TGGCAAGGAAGGCTCTGTCAAATCTTGTGCCTCTTGTAATGGTAGCGGTGTCAAATTCAT
+TACTCGTGCCATGGGTCCAATGATACAACGTATGCAAATGACCTGTCCTGATTGTAATGG
+TGCAGGTGAAACCATCCGCGATGAAGACCGTTGCAAAGAATGTGATGGTGCCAAGGTCAT
+TTCTCAACGTAAAATCCTTACCGTACATGTTGAGAAGGGTATGCACAATGGTCAGAAGAT
+TGTATTTAAG
+>TRINITY_DN269_c0_g1_i1 len=325 path=[303:0-324] [-1, 303, -2]
+TGGCTGCTGAAATTCTCGAATTGGCTGGAAACGCTGCTCGTGACAACAAGAAGACTCGTA
+TCATTCCCCGTCATCTTCAACTCGCCATCCGTAACGATGAAGAGTTGAACAAACTTCTTG
+GTCACGTTACCATTGCTCAAGGTGGTGTTGTTCCCAACATCAACGCCCATCTTTTGCCCA
+AAACTTCTGGTCGCACTGGAAAGCCTAGTCAGGAGCTGTAAAGTCAGTCGTCAAGTAAAA
+CATTTTGAAAGAGGATGAAGGGAAAGACATTGAAAAGTTGTAAAGGACCTTTCTTTTTTT
+ACAACCCCGCAATACTTTTTTTGGT
+>TRINITY_DN272_c0_g1_i1 len=239 path=[217:0-238] [-1, 217, -2]
+CAAGTGCATTGTAAGCATAAGGTAAAGGGGGAAGAGTAGCCTTAGTATGAACTCCCCTGG
+CAATTGAGACGTTCCTAATAGCGGCTACAGAGTTCTTAGACAAAAAGCGAAGCATCGTTA
+AAATGAGATCAAAAGTAAAAAAGTAATAGCAACCAAAGTGACCAACGAACAAAGTAAACC
+GAAATGTTTTCTTTGTTAAATACCTTAACTTATAACTAAATTGTACGGTTTGATTGAAC
+>TRINITY_DN273_c0_g1_i1 len=465 path=[443:0-464] [-1, 443, -2]
+CAAGAAGAATGATGCCATCGTCGCAGTTTTCGATTTGGGTGGTGGTACTTTTGATATTTC
+TATTTTGGAGTTAAACAATGGTGTTTTTGAGGTTAGAAGTACCAACGGTGACACTCATTT
+GGGTGGTGAGGACTTTGATGTTGCTCTTGTTCGTCACATTGTCGAGACCTTTAAGAAGAA
+TGAGGGTTTGGACTTGAGCAAGGACCGTCTCGCCGTTCAACGTATTCGTGAGGCTGCTGA
+AAAAGCTAAGTGCGAACTTTCCTCTCTTTCCAAGACTGATATCAGTCTTCCTTTCATTAC
+TGCGGATGCTACTGGCCCTAAGCATATTAACATGGAAATCTCTCGTGCTCAATTTGAGAA
+ACTTGTTGATCCTCTCGTTCGTCGTACCATCGATCCTTGCAAGCGTGCCCTTAAGGATGC
+TAACTTGCAAACCTCTGAAATCAATGAAGTTATCCTTGTCGGTGG
+>TRINITY_DN273_c1_g1_i1 len=270 path=[248:0-269] [-1, 248, -2]
+TATCCTTGTCGGTGGTATGACTCGTATGCCTCGTGTTGTCGAAACTGTCAAGAGTATCTT
+CAAGCGTGAACCCGCTAAGTCCGTCAACCCTGATGAAGCTGTTGCCATTGGTGCTGCTAT
+TCAAGGTGGTGTCTTGTCTGGCCATGTTAAGGACCTTGTTCTTTTGGATGTCACCCCCTT
+GTCCCTCGGTATCGAGACTTTGGGCGGTGTTTTCACTCGTTTGATCAACCGTAACACTAC
+CATTCCTACTCGCAAGTCTCAAGTTTTCTC
+>TRINITY_DN274_c0_g1_i1 len=322 path=[300:0-321] [-1, 300, -2]
+AAAGAAAAGAAGGAAAGAAATTCAGAAGACAGGAATGGAGAAAGCATGCTGCACAGCTTT
+GCTACTGACGGCCAATTGTTGCATTGAAATATCATTGATATAGACAAAACGTAGTGCTTC
+TCTTAGAACCAAACTAAGGAAGAGAGAACATAGCATCCATTCACATACCTTGTTAATCAT
+TGAAAAAATAGTAGCAAACAAGCTTTCAACAACAACAATGAAATCAGCGGGGAATACGAG
+AGGAAAAGGGGATGGGAGACTTGCAAAGCAATTGAAAAGAAAAGACATTAGGGCAATTAG
+AACTTCTTGCCGAACATCAAAA
+>TRINITY_DN274_c1_g1_i1 len=358 path=[336:0-357] [-1, 336, -2]
+TGGTCATAAATGGAAAGGACACCAGCTCCAGCAACACCACGAAGAATGTTGGCACCGGCA
+CCCTTGAAGAAAGAACGAGCACCTTCCTTGGCGAGGATTTGACGACCACATTCAAAGGAG
+GAGCTATACTTGACGGCTTCACCAGATGTCATCATCATACGACGACGGATGGTATCAAGA
+GGATAAGAAGCAACACCAGAACCAGTGGTAACGGCCCAACCGAGAAGGAAGGAGGCCAAG
+AAGTTGCCCTCCAAAGGACCAACCAAAACGACGGGTTTCAAGGTATCATACATACCGAAG
+TACAAACCACGGTAAACAACAATACCGACAACAGAAGGGCCAAAACCACGGTACAAAC
+>TRINITY_DN274_c2_g1_i1 len=428 path=[406:0-427] [-1, 406, -2]
+GCCAAAACCACGGTACAAACCACGTAAACCATCAGAACGATAGGTCTTACGATAGACATC
+GACCAAACCGTTAAATTGACGTTCACCTCCCTTCTTGGCGGATTTGGCATCATTGGCAAG
+ACGGGTACGGGCATAGTCAAGAGAGTAGACAAACAAAAGGGAAGCGGCACCAGCAGCACC
+ACCAGAGGCTAAATTACCGGCAAACCATTTAGCATAACCATCCCTTTCCTTCTTGTAACC
+AAACATCTTCTTAAATTTATCCTTGAAAGCAAAGTTCAAGGCCTGAGTGGGGAAGTAACG
+TAAGACATTAGCGGTATTACCTCTCCAAAGGGAAATAACACCTTCTTCAGCAGCAGTACG
+CTTGAAACACTCACCAATACCCTTGTAGCGGTGAGAAAGACGACCAGCACGAATCATTTC
+GTCTTGGT
+>TRINITY_DN274_c3_g1_i1 len=299 path=[277:0-298] [-1, 277, -2]
+GCACGAATCATTTCGTCTTGGTTTTGAATGAGAAGCTTGACACGCTCAATGGGAGCGGCA
+GCGGTTTTAGATACAGCAGCAGAAACACCACCCATCATGAAATCAAAGAAGAAAGTAGAG
+TTCTTTGTTTCAGTGATGGTGTTTGCATTCACGGGGGTGCTAGCAGCAGCGGCAGCAGAT
+GAAGTAGCCATTTTTCACTAATTCTGGTAAATAGATAAGTTCAAATGTACGAAAAAAAAA
+GAGATAAAGAGATGAAGCCTTAGCACAACAACAAGAAAATGATGATATGAAAGGAAAAC
+>TRINITY_DN275_c0_g1_i1 len=207 path=[185:0-206] [-1, 185, -2]
+TCAATTCCAACGAAATCACCCCCCAAGCCAATATGACGATACGATCCAGTTACATTGGCA
+ATATGCATTATATGCTCAACGACGGTATCAATTGTAGCATTTTCAGGGTGTGGACTAATG
+AATGCAGGGTAAAAATTCACCATAACAACGCCATCAGTTTCCTTGACGCGAATCAGAACA
+TCGTCAGGAACATTTCTGGGATGATCA
+>TRINITY_DN276_c0_g1_i1 len=259 path=[237:0-258] [-1, 237, -2]
+CAAAACCCTCGAGCTTGCCCGTAAGCCCAAATATGCTCGTAAGAGTGTTCCCCATGCCTC
+CCGTCTTGATGAATACAAAATTATTGTCAACCCAATTAACTCGGAATCTGCTATGAAGAA
+GATTGAGGATGACAATACTCTCGTCTTTCATGTGCATTTGAAGGCTAATAAGTTTACTAT
+TAAAAATGCTGTCAAGAAACTTTACAGTGTTGATGCTGTTAAAATTAACACTTTAATTCG
+TCCCAATGGTACCAAAAAG
+>TRINITY_DN277_c0_g1_i1 len=248 path=[226:0-247] [-1, 226, -2]
+CTGCTTTGGAGGTTGTTAAGGAAGAAAAATTAACTGAACGTGCTGCTGTTTTGGGTGAGA
+AATTCCGTACCGCTCTTATTGAATGCAAGTCTCCTATTGTTCAAAAGGTTCGTGGTCGCG
+GTCTTCTTAACGCTGTCGTTATCGATGAGTCTAAGACCAATGGCCGTACTGCCTGGGATC
+TTTGCTTGATCATGCGCTCTCGTGGTGTATTGGCCAAACCTACTCATGGTAACATCATTC
+GTTTCTCT
+>TRINITY_DN278_c0_g1_i1 len=534 path=[512:0-533] [-1, 512, -2]
+CCTCAACGCAAAATGAAGTTAAACATTTCTTATCCAGCAAATGGTACACAAAAATTGATT
+GAAATCGACGATGATCGTCGTCTTCGAGTCTTTATGGAGAAGAGAATGGGACAAGAGGTT
+CCAGGTGACTCTGTAGGCCCGGAGTTTGCTGGATATGTCTTCAAAATTACCGGTGGTAAC
+GACAAACAAGGATTTCCCATGTTTCAAGGCGTCTTGCTTCCTCACCGTGTTCGTCTTTTG
+CTTCGTGCTGGCCACCCTTGCTATCGCCCACGCCGTGATGGTGAGCGCAAGCGTAAATCT
+GTCCGTGGTTGCATCGTCGGCCAAGATTTGGCTGTCCTTGCTCTTGCCATTATTAAACAA
+GGTGAACAAGATATCCCTGGTTTGACCGATGTTACCGTCCCCAAGCGTCTTGGTCCAAAG
+CGTGCCTCTAAGATCCGCCGCTTCTTTAACTTGTCCAAGGAAGATGATGTCCGTCAATTC
+GTTATTCGTCGTGAGGTTGTTCCCAAAAAGGAAGGAAAGAAGCCTTATACCAAG
+>TRINITY_DN279_c0_g1_i1 len=362 path=[340:0-361] [-1, 340, -2]
+CCGCCCTCCTATCTCTATTTCTAAGATTGCTGCTCTTACTAGCCGTAAGAGCGCTTCTCT
+CGAGGGTAAAACTACCGTTATCGTCGGAACCGTTACTGATGATGAGCGTTTGTTGACTGT
+CCCCAAGCTTTCCGTTGCCGCCCTTCGTTTTACCAAGTCTGCTCGCGCTCGCATCTTGAA
+GGCTGGTGGTGAAGTTTTGACTCTTGATCAACTTGCTCTCCGTGCTCCCACTGGAAGCAA
+CACCGTCCTCTTGCGTGGTAAGAAACATGCTCGTGAAGCTTACCGTCACTTCGGTTTCGG
+CCCCCATAAGCACAAGGCTCCTTATGTCCGTTCTGAAGGTCGTAAGTTTGAGAGAGCTCG
+TG
+>TRINITY_DN280_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2]
+TGATCCAAAAAGATAACTGAAGCATTGGAGTTCCAACTGTGAGGGTTATATTCGGGTTTA
+AGAGTCTCAATGTTGATTGAAGAAGGACCTAATTCCATGAACAAACCAGTAAGGGAAGAG
+CAACCAGGACCACCGTTCAACCACAACACGACGGGATCATTCTCGGGATCATTTCTAGAT
+TCAAAGAACCAGAAGAAAAGATGTCTGTCATCTTCGACATCTAAGTAAC
+>TRINITY_DN280_c1_g1_i1 len=211 path=[189:0-210] [-1, 189, -2]
+ACGCGAAGAGTGTGATCAGGGAAAGCCTTTAAATTTACATGTTCACCATTCTCTTCTTGT
+GAAAAAACAGCGTAGGGACGTGAAGAATCAGCAGGTTGAGCATTAGATGGCTTAGCAGGA
+TGACTCTGGTCACGGAAAGCAGTCATAGGATCAATACCTTCAGCCTTGAGCATTTCAAGG
+TAGGCAAATTGTTCAGGAGTGAGATCACTCA
+>TRINITY_DN281_c0_g1_i1 len=244 path=[222:0-135 223:136-243] [-1, 222, 223, -2]
+GGTAGGCGAAAAGAGTTTCTTCAAATACGTAATGACGTTGTTACGATCAGCCGGTTTCTT
+GAAGCCAGCAAAGGCCATCTTAGTACCGGGGATATACTTCTTGGGGTTTTCGAGGTAGGC
+GAAAAGAGTTTCTTCATCCCAAGTAATACCCTTATCGCGATTGGCTTCGGTGTAAGAGAA
+ACCCTCAGCTTGACCGGTCTTACGGCCAAATACACCGTGCAAATTGGGACCGACCTTGTT
+GGCG
+>TRINITY_DN281_c0_g2_i1 len=249 path=[224:0-135 225:136-248] [-1, 224, 225, -2]
+GGTAGGCGAAAAGAGTTTCTTCAAATACGTAATGACGTTGTTACGATCAGCCGGTTTCTT
+GAAGCCAGCAAAGGCCATCTTAGTACCGGGGATATACTTCTTGGGGTTTTCGAGGTAGGC
+GAAAAGAGTTTCTTCAAATACGTAATGACGTTGTTACGATCAGCCGGTTTCTTGAAGCCA
+GCAAAGGCCATCTTAGTACCGGGGATATACTTCTTGGGGTTTTCGAGGTAGGCGAAAAGA
+GTTTCTTCA
+>TRINITY_DN281_c1_g1_i1 len=508 path=[486:0-507] [-1, 486, -2]
+ATAGGCATCAATGAAAATCAATTCGAAACTGAATCTTGCTCAAATGAATTGACCAAGATA
+CACCAAAATATGCAGGAAGCTAAAAATTCAAAAAGCAGAGGGGAGTTGATGGGGAAGAAC
+CCGGTGGGCCCAGGAAATAAGCTTTTGGGAACTCCGAATAAAAAAACTGGTTCACGGTAT
+AGGAATTGCGGAATTTTTTTTTTTTTTGAAAAAGGTTGTCTAATAGAAAAAGAGAATAGA
+AAAGGAATAAATGAAAAGAAGGAGACCAATTCCAAAGTAAGAATTTATATCAAACAATTC
+ATGTTCCTATGCTGCTCGTTTCCATGTTGTTTTATTTTTTTTTGGTAAACGCAATCAATC
+AATCAGTAACGTGACAGACACAAAAGCAAATTGGGAATTACGAATTCATAAAGCATATCC
+CAACGGCATTACGCCAACACTTGCAACTGTCGTTGACGGCCATCACCCCATTTACTCAGA
+GGTGGCCTTCTTCAAATACGTAATGACG
+>TRINITY_DN281_c2_g1_i1 len=205 path=[183:0-204] [-1, 183, -2]
+GGACCGACCTTGTTGGCGCCGCCTTTTTCAACGGTATGACATTGAGCGCAACGAGTCTTG
+AACAGGGAAGCACCCTTCTTTTCGTCTCCAGGAGCGTAAGGCATTTTGAATTAATAAATT
+GCTAAGGAAAGGAAATAGGCTTAAGAGTTTAGTATTTGTAGAGAAGAAGATTTAAAAACC
+ACAAATTCACAGCGAAGTTAGTGAG
+>TRINITY_DN284_c0_g1_i1 len=294 path=[272:0-293] [-1, 272, -2]
+AAAGGCGGCTCGAAAGTTGCTACGCAGAATACTTGTCTCCGATTCACCCAATATGCAGCT
+TGTAGTGCCAAATAATTTCCAGCAAATGTTTATTCATCATCCAGTCGTAGACACAATATA
+TTCTCCTGAAGAGTCTTCGGAATCCCAAGCTGAAGTCGCTGACCAACAAACTGGCCCATA
+CTCTACATCAGAGTACGCAGGTGCTCAACAATCTCAACCATTTCGCATATTTATTCAAAA
+CGACAATGCACCTGAACAACAAAGTGGCCCAGACGTTGCTGAGCTTAATACGCT
+>TRINITY_DN287_c0_g1_i1 len=244 path=[222:0-243] [-1, 222, -2]
+ATCAGAATCTTAGAGCCGTTGTCAATGAGCTTGTTGGCCGTATTAACGGTCGTTTTGGTA
+CTGTTGAATATACACCTATTCATTTCTTACATAAAAGTGTTCGCTTTGAAGAGCTGGTTG
+CTCTGTATAACGTTTCAGACGTTTGTTTAATTACCTCAACTCGTGATGGTATGAATCTTG
+TTTCATACGAGTACATTTGCACTCAACAAGAGAGACATGGTGCCCTAATTCTTAGTGAAT
+TTGC
+>TRINITY_DN287_c1_g1_i1 len=216 path=[194:0-215] [-1, 194, -2]
+CAACAGTACCAAAACGACCGTTAATACGGCCAACAAGCTCATTGACAACGGCTCTAAGAT
+TCTGATACTCTTCGACATCTTGACGAGAAGGAACGGCAACTTGAACCAACACGACCTTTC
+CAACCCATTCAGGGTATTGTTCTAAGAACACTTCAAAGGCATGGAATTTTTGGGGAACAC
+CCTTAATGTAGTCCAAACGATCGACACCCACAATCA
+>TRINITY_DN294_c0_g1_i1 len=289 path=[267:0-288] [-1, 267, -2]
+GCCTTGCCAGTCCACCAGTGGAGCATTGGGCCAAGGTATTGCAGGATCGATTCAGAGGTA
+AACATATTATCCTTTCTCACGACAAGCTTGACCCCATTCGTGGTTTGCGCTCCAAGTTAA
+TTTCTTTTGAGCGATTTTTACAAAAGTACCCCGAGTATCGTGAAAACACCATTTTACTTC
+AGGTTGCCCTCGAATCCCTACAGGACAGTGAGCATCTTCCTCACATCTCCGACATTGTCA
+CCCGAATAAACTCTGCCTATTCCAACATTGCCTCTCGTCACGTGCCCGT
+>TRINITY_DN294_c1_g1_i1 len=228 path=[206:0-227] [-1, 206, -2]
+GCCTCTCGTCACGTGCCCGTTATTTTGCTGAGACAGAAACTTGGTTATGCACAGTTTTTG
+GCTTTAATGATGATATCCGATGCCTTAATTGACAATTCCTTACGTGAGGGAATTAGCTTG
+ACTAGCCATCAATTTATTTATGTGCAGCGCAAGAGACACAGGCCATTAATTCTTAGTGAA
+TTCGTTGGCAGCGCCTCTATCTTGAATGACAATGCCATTATTGTCAAC
+>TRINITY_DN298_c0_g1_i1 len=272 path=[250:0-271] [-1, 250, -2]
+GCCTTCTCAGGAAGCCTCAGTTAAATCCGTCGAGAAGGCTCCTAAAGGTTTAGAAGGTGC
+TAAAAAGGAGAAGCAAAATAAGAAGGAAAAGAAAGACAAAAAAGATAAAAAAGATAAAAA
+GGAGAAGGCTCCCAAGGAACCTCCTAAAGCTGCTACTCCTGTCCCTTCCATGATTGATTT
+CCGCATTGGCTTTATTGAGAAGGCAGTCAAACATCCCAATGCTGACAGTTTGTACGTTTC
+TACCATACATTGTGGTGATGCTGAGGGACCAA
+>TRINITY_DN299_c0_g1_i1 len=232 path=[210:0-231] [-1, 210, -2]
+GATCCCGTCCTAGTCAACCCCCCGCTCAAAACGAGGTTATCACTCGACCCCTTAACGTGA
+GCCTGGAGGATCTATTTACCGGATGTACCAAGAAGATGAAAATATCTAGACACATAATTG
+ATGCTTCTGGTCAATCGGTGAAAGCGGACCGAATTTTGGAGATCAAAGTAAAGCCTGGAT
+GGAAAGCTGGCACTAAAATCAAGTTTGCTGGTGAGGGTGATGAGAAACCGGA
+>TRINITY_DN299_c1_g1_i1 len=495 path=[473:0-494] [-1, 473, -2]
+ACAAAAATCCTAATGGTGAGAAGAAATTTAAAGAAATTTCTCTTGCTTACGAAGTATTGA
+GCGATCCCCAGCGCCGTAAGCTTTATGACCAATACGGTATCACAGAAGGGAATGCTGCTC
+CACCACCACCGGGTGCTGAAGGTGGCCCTGGTGCAGGCTTTGGCGGCTTCCCAGGCGCCG
+GACCTGGTGGAGCTCGAACATTCCACTTTAATATGGGTGGCCCAGGTGGAGCTCAATTTT
+TCAGTGCCAGTGATCCGAACGACATTTTTGAAAGAGTATTTGGTCATGCCTTTGCTGGCG
+GTGGAGGCATGGGCGGAGGAATGGGTGGAATGGGTGGTATGGACGATGATATGGACATGG
+ATGGAGGTTTTGGTACGCGGACTCGTGGAGGTGGTATGCCTGGCGGATTCGCTAATATGT
+TTGGCGGTGGTGGAGCAGGTCCTCACGCCAGACGTAGCCATCCATCTTTTGGTGGATCCC
+GTCCTAGTCAACCCC
+>TRINITY_DN299_c2_g1_i1 len=470 path=[448:0-469] [-1, 448, -2]
+AGAAACCGGACGGAACTGTTCAAGACATTCAGTTCGTGCTAGCTGAAAAACCTCATCCTG
+TTTTCACACGCTCTGGTGATGATCTCCGTATGCAAGTAGAGCTATCCTTGAAGGAAGCAC
+TTCTGGGCTTTTCAAAGCAAATTTCAACTATTGATGGAAAGAAGCTTAAAGTATCTTCGT
+CTTTACCAACTCAACCTGGTTATGAAATTACGTATCCTGGATTCGGTATGCCCTTGCCAA
+AGAATCCTTCTCAACGTGGTAATATGATCATTGAGTGCAAGGTTAAATTTCCTACCGAAC
+TTACGCCTGCTCAAAAGACTGCTGCAGAAGCCTTTTAAATTGAGTAATCTTTTCCTATCT
+ATGCCCTCATTGCATTTATGACCTTCTTTCAATTCTTTTATAGTTGACTTGTTAGGATGA
+CAACATATATTTTGGGTTTTATGATTCCTGACATTGTTTAGATATGCCGG
+>TRINITY_DN300_c0_g1_i1 len=532 path=[510:0-531] [-1, 510, -2]
+GTTATAGTAGCATTGTTGGCACTCGGGGCTAGCAGTGATGTTGTTACGCTCCAAAGTACG
+CTTAACAACGGCACAGGCAAAACATTGACCAAAGTAGGTGTCATTGTCAACGGTAGAGGA
+AATAAGGCCGTTGGTAAGAAGTTGTTGAATCATGTCTTCAGTGTAGTAGGTGCGATCAGT
+GGAAATGTTAGTGAAGTAGTTGTAAGGAACGTTGGGAAGATAGATAACCAAAGGAGGAGT
+GTCACGGGTAACAGTGTGGTTACCAGCAGTGGTGTTACGACCATCACAACCAAAGAAGAC
+AGGGCGATCGTTGAAGTGAAGACTGACAAAGGATTGTTGGCTAGGAACGTAGGGGAAACC
+CTTAACATTGGTGTTTCCGGCAGCTTGGGCAGCAACGACACGCTCATAAGTTTGGACAAG
+AGAGTTACCGTTGGGCCAGAGCCATTCACTGTCATCACCATTGTCAACGGCAACGATAAC
+ATCGACATCACGACCCTTTTGCAACAAAGGCCACAAAGGAATCTTCTCACCA
+>TRINITY_DN300_c1_g1_i1 len=1205 path=[1183:0-1204] [-1, 1183, -2]
+TTTGCAACAAAGGCCACAAAGGTGTCTTCTCACCAGTAAGGAAGGTATCAACTAAGTTAA
+GGGAAGAGCTGGAACCCAAGTTGTTGGCAGCATCAGAATTAGCACTCTCAACACCTTGGA
+AGGGGTTGGGAATGGAGATGATTTGTTGACCGTTTTCAGAAAAGTTACCTTTCAAGTATT
+GTTGGATGATACGACCGTTCTTGGTAGAAGAGTCATTGAAGTTACGCATTATCTTGTTGA
+AGTAAGTAGAAGAAGCACCCATCATGAAACCAAAGTTGTCATAGTTGATAACGCAAGAAC
+CATTGCTGCTAGCACCATTGTTTAAGGTAGTACCCAAGTATTCGGTAGGAATAAAGGAGT
+TGATTCCATGGTCAAAGGTACCGAAAACGTTGGGGGAAGCTTCAAAGAAAGTAGTGTTAA
+CATTGCTAATATCCTCACCATAGTTTTGGGTAGCAAAGGTAATGATGGGGTAAGGGAAGT
+TGGCATTGCGGTACCATTCTTGGGAAGTAATACTAGACAAAGAGACATTAGGGAAACCAT
+AAGTAGTGTCACCAAGGGTACGAGAAATCACACGTCCCCAGTAATCGGAAAGACTGATGT
+TAAAGCCAGCATTGGCCTTTTCGGCAACTTCATTCATAATAGAACTGTAGAAATGAGCGT
+TGAAAACAATAGCACTCTTGGGATACATCAAAGGGTGGTTGAAAGCCCAAAGTTTGCTAA
+AGTCGTTAATGGTACTGAAATTGTTGAGAGCAATGCCACCAACAGTCCAGGCACTACCAT
+CAGTACCAACGAGATAGTCAGAGGCTTGAAGGAGACCAGTCAAAACAGTGTGGTTGTCGT
+GACGAGCATCCATGGCAGAGAGGGCACCAGAACCCAAAATCATGGCACGTAAACCACCAC
+CGGACAAGGCAATACCGATAGAAGGACCTTCAGAGCCAGAAAGAGTATCGGCATTCAAAC
+CAGGCAAGTTGGCGTTACGAAGGAAGTCCTTCATGGCAGTGTTGGTAATAGTAGAACGAG
+TGCTCAAGTATTCAGACTCGGCGCTAGGAATCTCATTGCTGGAGAGACTCTCGACAATGT
+TATCAGAGGGACAGTCCACATAATAAGGAGCGTAACTGGGTCCCTCTTGCTTAGTGCTAT
+GCTTCTTGGCACGCTTGAAGACCTTGACAGAACCATCGTCTTCAGCAGCGGGAAGAGCAA
+GGGCA
+>TRINITY_DN300_c2_g1_i1 len=300 path=[278:0-299] [-1, 278, -2]
+AAGCGGAGTGAACGTTCAGTTTAATAATCCGTTAACAAAAACCCATATCGCGTAATTGGA
+TTGATTCACATATATGGCTAGGTTTGATTTATGCTAAGACAGCAGACATTGTATAGATTT
+TTTTTAAAAACTTTTTTCCAGGCATAAGCATTGCCCTCTATCTTTTGCTTGTGAGCAACA
+GATATGTCGTATAAATACTGAAGAGAGAAAAGTTTGCATGCGCCTTTCCTTAAATGCCTT
+CACCAAGACGGCAAGTAGGATTGTAGACAATATCATCATTAGCAGCGCTGTCATCATAAA
+>TRINITY_DN302_c0_g1_i1 len=424 path=[402:0-423] [-1, 402, -2]
+CAATACATCGATCCAACCCAGCTTCTTTAGAGCAAAATCAACCAAATCCCTACAGTTATC
+AGACTTGTCAAGTTTTCCCTCCCATATCCAACAATTTCTTCCTTCACGTTCAATTAAATC
+TCTCGTAACTTCTGCATCGTCTCTTTCTTCTGGAAGGCATGATATAACGAGATCAGATCC
+CTCTCTGGCAAACATCACCGCTGCTGCTTTACCAATACCAGAGTCTCCTCCTGTGAGCAA
+TGTCTTTTTCTCTGCAAGTTTCCCTGATCCGACATGTACCCGTCCATCACAATATCTGAG
+AAGTGATGGTTCAGGATCTAAGTCGGCATGCTTGCCAGGCCATTTTTGAGTTTGTGTGCT
+AGGAACAGGATCCATTTTATTAATGTTTTTTTAATAAAGTCGCAGTTATTTAGTTAGTTA
+GTCA
+>TRINITY_DN302_c1_g1_i1 len=413 path=[391:0-412] [-1, 391, -2]
+GCATTGTCTTCATGAGAATGAACATCTCAAAAGTATATGAAAGTACAACTTCAACAATCA
+TCCGGATCAGCAAAATTAAATTGCTGCATTATTCATTTCAAACCAAAAAAGTAATAGACG
+ACAGTAAATGAACATCGTCTTCCTTTAAAATTTAATTGTTAATCACAGTTCCACCGTTAG
+GATGAAGAGTTTGGCCTGTCATGTAACCACCATCTGAGCATGCAAGGAAAAGGTAGCAAG
+AAGCAACCTCAACAGGCTGTCCCATACGTCCAAGAGGAACTTGGTCAGAAAGTTCAATCT
+TCTCCTTGGGAAATGTGGAGCTAACGAGAGGTGTGTAGATGGGACCAGGAGCAACGGCAT
+TCACACGAATACCATGCTGCGCATATTGATTGCTCAACCCCCGAGTAAATGCG
+>TRINITY_DN302_c2_g1_i1 len=252 path=[230:0-251] [-1, 230, -2]
+CCCCCGAGTAAATGCGGTAATGGCACCCTTAGTGGATGTGTAGTCTAGTAAATCAGGTCG
+TCCTACATAAGCGTTGATGCTGGAACAATTGACAATTGAACTTCCGCTCTTCATATGCGA
+AATAGCGGCCTTGGTGACCCAGAAAAAGGAGAAGATGTTCGTTTTAAAAGTGAGATCCCA
+TTGTTCATCGTCGATATCTTCAATGGATTGAGCGACCTGTTGATATGCGATGTTGTTCAC
+CAATACATCGAT
+>TRINITY_DN303_c0_g1_i1 len=203 path=[181:0-202] [-1, 181, -2]
+AGGGTTTTGAATTGGAAGAGAACAAGCCTTTCTCGCCGTGGGCAAACCAAGTTTAACGGT
+TTGCACGATCAGTTGGGTACTATGTCTGAGGCTCATAATGAAAGGACAAGGATAATAATC
+GACAAGTTAGATTTAATAGAAGAAGAAACAAAAATAAATGCGTTTGATCTTCAACAAATA
+TATATATTCAATGTTCACAAAAG
+>TRINITY_DN304_c0_g1_i1 len=262 path=[240:0-261] [-1, 240, -2]
+CATTTTCCAACTCTTCATAATCATAACGACTGTAGAATGTACGGCCATAAATATTGTAAA
+AATCTTTCTTAACATCGATCAACGTCTTGATCTTGGGGTTTTGCGCGTTCAATCCAGCAA
+GAATGTTCAACCAACACAAGATTCCCCAAACGCCATCCTTCTCTCGAATGTGATCACTAC
+CGGTTCCAAAAGACTCTTCACCGCAGATGGATAAACGCTTAGCATCAAACAAGTTGCAGA
+AGAACTTCCAACCAGTAGGAAC
+>TRINITY_DN305_c0_g1_i1 len=237 path=[215:0-236] [-1, 215, -2]
+GAGAGAAGTAAAGACAGACAGACAGAGAGATACAGGCAGCGGAGAGCAAAGAATAAGGCT
+AGAACGGGATACCGAAACACTGTACCAGAGTCAACTTCGGATAAACCAAGTGAATGGATG
+GATGAGTGGATGGATGCAAATTAGCTTGATTTTGCAATAAAAAACAAGCAGGGGTAAAGC
+AAAGGCGAGCGTGCTGCGCTAAGCTGAGAATAACGAAATTAGTTACGAAAGAAAAAC
+>TRINITY_DN306_c0_g1_i1 len=298 path=[291:0-106 292:107-297] [-1, 291, 292, -2]
+AAGAACTCTCGTGAAGTTGCCTTTACCATTAATGGTATGAACTTGAAGAAGGCCTTCATC
+TTTCTTGACAACGTCAAGGAGCACAAGCAAGCCGTTCCTTTCCGTCGCTTCAACGGCGGT
+GTTGGCCGTACTGCTCAAGGTAAGGAGTTTGGCGTCACCCAAGCTCGCTGGCCCGTCAAG
+TCTGTTAAATTCTTCTACGACCTTTTGAAGAATGCCGAGGCTAATGCTGAGGCTAAGGGG
+TTAGACATGGACAAACTCATCATTAAGCATGTCCAAGTCAATGCTGCCCCTAAGCAAC
+>TRINITY_DN307_c0_g1_i1 len=386 path=[364:0-385] [-1, 364, -2]
+GGCCTTCAGTACGCAGTTGCAAGCTCAAGGAAACTCTTCCAATTCTCCTCCTGATCCTAA
+AGACCTTGATCCCTCAGTTTTAGATCATATTTTTGGAGCAAACCCAGCTGATGAAATGAG
+GAAAGCGATGGACGCAATTGAGGATCCATCGGTACCTTTAGATTAGAAAGAGATAGCTTT
+TGACAACTTAGAAATGCTCGTAGAGCATATTGACAATGCAAATAATTTGGTTCCCCTGCA
+ATTGTGGCCTCGCCTATTGAAACAGCTTGAGAGTCCGGAATCTACCTTGCGCAGATTAGC
+TGCTTGGACGATCGCAACTGCCGTTCAAAATAATCCTAAATCTCAACAAGCGCTTATAGA
+AAATGATGGATTGAAGATTCTCTTCG
+>TRINITY_DN307_c1_g1_i1 len=202 path=[180:0-201] [-1, 180, -2]
+GATGGATTGAAGATTCTCTTCGGCGCCCTAAAAAAAGAGGATTCGGATGAAACAAAAAAT
+AAAGTCCTTTATGCAATAACTAGTGAGCTTAAACTTAACGAAGCTGGAATTGCTTTATTA
+GATAAAATCCCAAACTCTTGGGAAATGCTGATTGAAATCTTGGAGCTTAAACACTCGGTT
+ATGACAAAACGAGTTATCTTTT
+>TRINITY_DN308_c0_g1_i1 len=203 path=[181:0-202] [-1, 181, -2]
+TGTAAGATCGATTTCATTGCTTGCCATTGGTATGGTATTGACTTTAGCAATTTGCAAGAT
+TATATTAACTCTCTCGCCAATTACGGTCTCCCTATTTGGCTTACTGAATTTGCTTGCACC
+AACTGGGATGATAGCAATTTACCTTCATTGGATGAAGTTAAGACTTTGATGACCAGCGCT
+CTTGGCTTTTTAGATGGACATGG
+>TRINITY_DN309_c0_g1_i1 len=422 path=[400:0-421] [-1, 400, -2]
+CTGCCACTACTACTAAAACTACCACATATGTTGGACCCAGTCCTTCTGCTTCTAGCGTCG
+TTGCTTATACCACCAAGTGTATTGTTGTCCCTGTTATCACCACTGCCGCTAGCCAAAGTG
+AAGCTGCAACTCCATCACCTTCTGCTGCTGTATATCCTTTGTTCCCCCATGGCATTCGTT
+TAATTGATTCGACTAAGCCTGAAGCTAACTCCGGTAATGTTTACTCACCCGTCGTCTTTC
+AGAAGCAAAACAATCATACCAACACGATTTTCACATTTGATGTTCCTCAAGTTTCCGGCA
+GTTGCGAACTCAACCTACATCTCGATACTAGCGGTTTCCCAATCACTGTTGAAGGCAGCA
+ATGGTGTTGGTCAATTCATTCTTTTCAACCTCTCCTCCGTCGCCAACGATTCTACTGTTT
+AC
+>TRINITY_DN309_c1_g1_i1 len=213 path=[191:0-212] [-1, 191, -2]
+CGGAAATGGTAACCCCAATTGTGCAGGTATTGCTATTGAGGCCTTCGTGTCTCCATCCTC
+TTCTTCTTCTTCTTCTAGTTCAGCTGCTACTTCAACTTCAACTCGCGTTTCATCGTCTGC
+TAAAGCAAGCACTTCTAGTGGGGCAATTGCTTACACCACCAAATGTGTTGTTGTTCCTGT
+TACAGCATCGGCTACTGCCACGGCAAAAGCCGC
+>TRINITY_DN310_c0_g1_i1 len=221 path=[199:0-220] [-1, 199, -2]
+CGTAAAGTAGAGCGGCCAGCAGGGCGCAACAGTTGAGCAGCCGGACGGAATAAAGAAGAG
+CTTAGGCAGAATGAGCGAGTTGCGAACATGGTCAAATTGGGTCGCAAAAAAAAAGGGGGA
+TAATTCAAATTTTTAAAAGAATACTTATTCAATAGTTGTACAGTGTAAAAAATGGATGCA
+GACACAAGTTTTCAACTGATTAATTATATGTGTACTGCAAC
+>TRINITY_DN310_c1_g1_i1 len=225 path=[203:0-224] [-1, 203, -2]
+CAAGTAGCCCATAGCGAAAGCATAAAGAGTACCGGCGACAACACAACCAGTGATACGATG
+TAAACTGGATAGATACCAAGTCAATTGAGGTTCATAGATAGTCAAATGAGGAGAATTTGG
+ACGGTGAACACGCTGGGAAGCAAGACGAGAATTAGCCTCCGTCTGGGTCAAATGTTCGGT
+TGCAATAGAGCGTCTCCAAACATTTCGTAAAGTAGAGCGGCCAGC
+>TRINITY_DN311_c0_g1_i1 len=546 path=[524:0-545] [-1, 524, -2]
+CGCAATAGCCTGACGCTCAGCAACACCAGTCCAATGATCGGTATAAATTAAAACAATGCG
+CTCTTCCGGAATGGTGTCGTTGGAAAAGAGACCGGAAGAATTATGAACATCGACGACTGC
+ACTGCCACTAAATGGGAGGGACAAAACTCCGTTTTCATGTTCATCGGGGTAGATGGCAAT
+AGGATAATTCTCCCAATGGATTAAATCCTTGGAAACTGTGTGACCCCAATGAACTTCGCC
+GGCTGTTAGAGTTTTTGGTGAATATTGGAAGAACATGTGATAGACGCCGCCAGTATATAC
+CAATCCGTTTGGATCATTCATGAAACCGGAAGAAGGAGTAAAATGAATTTTGGGACGATC
+GGTAGCATTGTAATATCCTGAAGGAAGATACTCGTTATAGTTACCCAAACAAGTCCCATT
+AGGGGCCGTTGTATTTACGAATGGAGGAGGAGGAACGGTGGTAGAATTGCTGACTTCAGT
+GATGTTGGAAGCATTATAAATGACAGGATAACGTTTTACATATAAGTGACGGGGAGCCGC
+GTTTGT
+>TRINITY_DN311_c1_g1_i1 len=692 path=[670:0-691] [-1, 670, -2]
+CGTTGGCAAAAGAAGGCGTGAAAAGTGAATTAAACCATCCCATCTGAGCTTTGGCACGAT
+TAATGACTAAAGTGCTAGCTGCAAAATCAACGTCCACGGAGATGGATTGTAATCTGTATG
+GATCATCAGAATCAATGATAATACGCCCCAGACAATATCCTGTTGTGCAGCCTTCTGTGT
+AATTGATACTGAGTGTGACATTGAACTCGAATGCGGTATTGCTTGGAAGAGTAATCGGAG
+AGCCCGAAAGACTACTTGAACTATTGATAACGGGTGCGGTAAATAGTGTTTCATCTCGTA
+AGAGAGAAACATTCAATGGGGTTTGAATGAGAGAAGTAAGGTTGGTCATGGGGTTCTGAG
+GAACGTCGCGAAGAGTGAATTTTCGTGCAACTGTCATAGCACTGCGGAAAACTTGAGTAG
+GAGCTTGGTTGGTGTATTGCCAGTTGCTAGCCCATCCAACTCCAATAACATCGGCATTGG
+CGGAAGACGAGTGATACAAAGCGCTGGCGTAAAAGTCCTTACCCAAGTCTACGAATCTAG
+TTTGGCCATCATCGGGGACGAAGTTTGTACCATTCCAATCGCCAACAAAGTATTGGACAA
+CGGATCCTCCCAATGGAGCGCCAGGATTGATGGAGATGAAGAGTACCCATTTGTATTCAT
+CGGTGCCTTCAACGGGCACACGAGCCACTCCA
+>TRINITY_DN311_c2_g1_i1 len=473 path=[451:0-472] [-1, 451, -2]
+TTACATATAAGTGACTGGGAGCCGCGTTTGTAGATGATAAGAGAGAGACGAGGCAAATGC
+CACTAGCTAAAATATATTTCAAAAACATTGTAGCAAATCTTCAAAGTTAGCGATTATAAC
+GTATTAATTGGTTGGTTCCAAGAAAGATTATTTACAAAAAAGACGATAATCGGTGAACAG
+AAAATTAAATAGGGACTATCAATAAATAGTCAAAAGTGGAGAATTGGCAGTTGTGAGTAT
+AAAATTTAACAATCGTAAAACAAAAAAGAGACCGGCCAACAACGAAGAAGCTTGAGTCTT
+TTTTTTTGGTGAGAATAGATTTAATGTTTCAGCTTTTGATAGGTGTTAATTGATTTAGAG
+TATTCAACAAATTATCATATTCCGTTGAAAGGGAGACGAATTTCTGTAATATTCAAGCAA
+GCGAGCAAAGGATGAATGATCAAGAAAAACAAAATAGTTTTAGAATTTTTTTC
+>TRINITY_DN311_c3_g1_i1 len=269 path=[247:0-268] [-1, 247, -2]
+ACCGGGCACACGAGCCATTCCAGGGCATTCATATTGCAACCCCAAATAACCAGAAGTGGA
+GAAAACAGATAACTCGGTCCAGTGAATCAAGTCATAGGAGGAATAAAAGGCAATTCCATA
+ATTTTGAGACATAGCTACAATCATCACCCAACGATTAGCATCGAAATCCCATATTACCTT
+GGGGTCGCGGAATTGAAGTGAATTAATGTCAAGAACGGGATTTCCTGAATATTTTTTGAA
+AGTATATCCACCATCAGTGGTATACGCAA
+>TRINITY_DN312_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2]
+CTGTCCGCCACACTCGCCAAATGCAAGGTGAACTTCGTCGTGTGAAGTCTATGTCTCCCG
+ATGAGTTGTACACCTATGCCAAGGAGATTGCCGCCCCCATTGATTTGGTTAAGGAGTGTG
+CTCAATTAGGCCGTTTGCCTGTTGTCAACTTTGCTGCTGGTGGTGTTGCCACTCCTGCTG
+ATGCTGCTCTCATGATGCAACTTGGCTGTGATGGTGTTTTTGTAGGATC
+>TRINITY_DN313_c0_g1_i1 len=258 path=[236:0-257] [-1, 236, -2]
+GGCTGTTTTGTCACTGAGAAAGAGAGTGGAGGACATACACAAATCACTGTCACACGAAAA
+CCCCAAAAAAAAGTTTCTTCCATGCTAAACAGGGGATTTGCGCACACCTCTGTACAGTCG
+AGATTAGTTGGAAAAAAACATATCGCTCAGCTAATCTCCAAAAAAAATTAACTGATCAAC
+AGTCATTTCCAAAAAATATAAAAGTAGAGTAATCTCAAAATAAAAACTCAAACGAGATTT
+CGAACAACACCATACCTC
+>TRINITY_DN313_c1_g1_i1 len=223 path=[201:0-222] [-1, 201, -2]
+TGTAATTGGAAAATATCCTTTAAAAGCTTTCAACCTTTAAAATTGCATTACGAATAAAAA
+ATGCAGCAGGAGAGGAAGAAAAAATAAAAGAGAAGAACATTTCAAAGATTTTTATTTTTT
+CTGATCATTATAGGATTAGAAAAAATAGAAATTGTCAAATATCAAAATCAGCAGCAAAGA
+AGTCAAAATCATAGAACGCTATATTAATGCGATTCAAGGGCTG
+>TRINITY_DN313_c2_g1_i1 len=331 path=[309:0-330] [-1, 309, -2]
+GGAAAGAGGATTTGATGAATATTCGAAATCGGAACGGTTAACATCACGTTCTAAACACAA
+TAGACGACCGCATGGACACTGGAGAAGTTGGAGCGAAGAGCAAGAGTAGGAGAAAGAAAG
+TGTCGTAAAGGTCTTTGGAGGAGTCGTTGGAGGTATGGTGTTGTTCGAAATCTCGTTTGA
+GTTTTTATTTTGAGATTACTCTACTTTTATATTTTTTGGAAATGACTGTTGATCAGTTAA
+TTTTTTTTGGAGATTAGCTGAGCGATATGTTTTTTTCCAACTAATCTCGACTGTACAGAG
+GTGTGCGCAAATCCCCTGTTTAGCATGGAAG
+>TRINITY_DN315_c0_g1_i1 len=427 path=[405:0-426] [-1, 405, -2]
+GTTCGTGTCACTCCATCCCGCTCGGAAATTATTATCCGTGCCACTCACACTCAGGATGTT
+CTTGGAGAGAAGGGACGCAGAATCCGTGAACTTACCGCTTTAGTTCAAAAGCGTTTTAAG
+TTTGCTGAGAACACTGTTGAGCTGTATGCCGAGAAGGTTCAAAACCGTGGTCTCTGCGCT
+GTTGCCCAATGTGAATCCCTTCGCTACAAGCTTTTGGCTGGTTTGGCTGTTCGTCGTGCC
+GCCTATGGTGTCCTTCGTTATGTTATGGAGGCTGGTGCCAAGGGTTGTGAGGTTGTCATC
+TCCGGTAAGCTCCGTGCTGCTCGTGCCAAGTCCATGAAATTTGCCGACGGTTTCATGATC
+CACTCTGGTCAACCTGCTGTTGATTTCATTGACTCTGCTACTCGCCACGTTTTCCTTCGT
+CAAGGTG
+>TRINITY_DN316_c0_g1_i1 len=304 path=[282:0-303] [-1, 282, -2]
+ATACACCTTGAGTTTTGATTCCTGATCTTCTGTCGGCTTGGAAGAATCTTTTTCTATCTC
+AGATTTGGCTTCCTTATGTATTTCGTACCATTCTCTATCGACTTGTTCAAAAGCATGACG
+AATTGAAAGCTCCATGGACCTTGCTACGGTAGATCTCACGTATGTCATGAGTGAGGGCTT
+TAAGAAAGCGAGTAATAACCTGTGCCTTGATTTACGAATTTTTAGCTTAATGTGATGTAT
+GTCCACCTTCACGTCCTCCACCTTAAAAAAGGAATCCGGAAGTTCGTTTTCAAACATAGT
+ATTT
+>TRINITY_DN319_c0_g1_i1 len=417 path=[395:0-416] [-1, 395, -2]
+GCATCGCGTAGGGCTCTGCGTGCAACCTCTACGTCGTTGACATACTGGGATGGCTCGGCA
+GTGCGCAAGTCAGTCAATTTGCTTTCCTCGAGAGTCAAACGCTCCTGTGCCCGTTGAATG
+GCAGAGCTATAGTCGAGGTTGGCGGGTTGAGGAGGATGAGAGCGTTTAGCGTTAAGGTCT
+TGAGTGATGCTTTCGGCCTTGCTATACAAGTCCTTGGCCTCATTTTCCTTAGCTCTAGCA
+GCCTCGGCAATGGTTTCATTGCGCTTCTCAGCGGCCTTGACGGCATCATAGGCTTGAGTG
+GCACAACGAGTGATTTCCTCTTCACGTTGATGACAGCTGATGCGATACTTCTCTTCGGCA
+TCCTCAGCGTCACGGACCTTCTTGGTGAGCATGGCGAGCTGTTGACGAGAATCAACG
+>TRINITY_DN319_c1_g1_i1 len=571 path=[549:0-570] [-1, 549, -2]
+GAAGGTTACGTCCAAAAATTTTGATATTGCAAGTATTCCCTTTACTTGTTGGACATACCC
+AAGGCATGACGAACATTGTTCATCAAGCCATGACCGCTGCTGGTGCTGCTTCTACGTTCC
+TTGCGGGAACTTTTGCTTTCAGATTTGCCCAAACCGGTGGTACCCTTGTCGCTATCCGAA
+GAAGCAGAAGAAACATCATCACGTACAGCAGTAGATTTGGCAGCCTTGGGCTTTTTAGTG
+GTAGTAGTAGCAGCAGCATTTGTGGAAGCTGAAGTAGGCAAGGTGCTGGGAGTAGATTCA
+ACAGCCTTTGTCGTACTAGGAGTTTTAGTGGCACCGCCAACATAAGCAGGAGTGGTGGCA
+GAGCGGGCTGCTTTGCTTGAAACAGTCTCAGTGGTGGCAGGATAGTGATAGGCGGCGGAC
+TTGCTCTTAGTACTAACATCAGTAGGTTCATTAGTGGTAACGGCGTGTGGATGAACGGGT
+TCGGTGGTATACAATTTGCTACCCTTAACACTGTTGTACTCGCTCTCCACCTTGCTTTGT
+TCAGCTTGAGCATCGCGTAGGGCTCTGCGTG
+>TRINITY_DN322_c0_g1_i1 len=211 path=[189:0-210] [-1, 189, -2]
+TTCACATCAAGAAGTTTGGCACCATTCCTCGCTGCGGTGATACTGGCGTCCCTTTGCAAG
+GTATTCCCGCTCTGCGTCCTCGTGAGTTTGCTCGTCTTTCACACAACAAGAAGACTGTCC
+AGCGTGCTTATGGCGGTTGCTTGAGTGCCAATGCCGTTAAGGATCGTATTGTTCGTGCCT
+TTTTGATTGAGGAACAGAAGATTGTCAAGCA
+>TRINITY_DN323_c0_g1_i1 len=327 path=[305:0-326] [-1, 305, -2]
+GGGATTTGGCGGAACCACAAAGGAGCCAGACCACGGTATAAAGTACCGAAACCTTCATTA
+GTGACAATTTTAGACCACGCTTCACGAGTGGTGTTGGCAAAACGAGGGTTGGAAGTTTGA
+ACACGGACCTTGATAGCCTCCATAGGGCAAAGCATTATATCAGCCAACAATTCAGCAGAG
+GCAGAAGCAGCCAAGTAAATGCTTGTACGGTATTCATGTGCCTTTTGAGCACCAACCAAA
+GTAGAGTATTTGTGTTTGAACAACTCATAAAAACCGTACTTACCGCAGCCTTGAAGAGAA
+TAACCAATCAAGGTGGGCATACCACCA
+>TRINITY_DN323_c1_g1_i1 len=242 path=[220:0-241] [-1, 220, -2]
+AGCAGCAGCGCCAGCGCCCTCACCAGCCTTTTTGTTGGAATTCAACTTGGAAACCATAAC
+ATCAGCAGGATGACTGATAATGGCGCAAAGAACACCGGCCATGTAACCACCAGCAAAAGA
+AATACCAATCTTTTCGGCCTTTGAATACATGTTCTTGGGCTTGCCAATGTAGGTGTACAA
+AGCTTCGACAATGCGCTCAAAAGAAGCAAATTTCATCATGGTGTAAGGGATTTGGCGGAA
+CC
+>TRINITY_DN324_c0_g1_i1 len=755 path=[733:0-754] [-1, 733, -2]
+TTCATCTAAAAGATACATGTATTCATATACAAATATTATATATATATACATATATATGTG
+AGAAAAATAACCTAATTGGAGATCCATGTTTATGATGATGCAGAGAATAATTGACAAAAG
+TTTCAGTTTCTGCATTATTGGAATGGAATAACCATGTTTGGTGATAAGAAGATAAAAAGT
+AACGGAGAGGACTTCAAAGAACTAGGAATTACTATTTTATGAAATTAATATATTCCTCGA
+CTTCATGTTTACTTCCAAGCCAAATACTGCTTTTTCCGTGTAATGTTTTGGGTACCAAAT
+CCAGAATGCGATCTCCTTTGTCGTTTACCGCAATACCTCCTGCTTGTTCAACAAGGAAGG
+CCATGGGGAAACATTCGTAAAGAAGTCTCAACTTTCCGTTATTTCCTTTTGAGCATGGAT
+AAGCAAACAACCCACCATAAAGAATGGTACGGTGCATATCGGCGACCATAGAACCAATGT
+ATCGAGCAGAGTATGGTTTTTTGTCTGGTGTGCTTTCTTTGAGATGAGCAATAAAACGAG
+CGATTTTTTCATCCCAAAATGCAGTGTAACCCTCATTAATGGAATAAATACTATGTTGCA
+AAGGCATTTTCATGTTTCGATGGGTCAAGATGAATTCGCCAATATCAGTGTCCAAGGTGA
+AGCCATTGACACGATGACCTGTGGTAAGCAATAAATGAGCCGAAGCACCATACATAGTAT
+AGCCAGCAGCAACCATTTCTTTACCAGGCCTTAAG
+>TRINITY_DN324_c1_g1_i1 len=405 path=[383:0-404] [-1, 383, -2]
+TCCCGATAAACCAATGAGATTTACCAACTCTGCTTTACGAATGGTGTTGGCGATGAATTT
+GAAGCTGAATTGTAAACTGTTTAGCAGTAATGACAATTCCCCACTAGCCTCTTGAATAAT
+GCAAGGTTTTCCTTCTTCATTTTTATGCTTCTGATTGTATCGGCGCTGTTCCTGCAAAAT
+AAAGGAGGAAAGTGTGACAATGTCAGTGTCGATTTCGTCGAGATCTTTTTTCATGATGGA
+GTAAACGAAACCTGAATCAACAAGAAACGGGGAATGAAGTTGAATAAGCTGGCCAGGTGA
+ATCCTAGCTGAAGTAAGTTTTTAAGAAAGAGGAGCAAATCGGTTCTAAGTAGAACTGAGT
+TGAGCTGAGTTAAGTTGGGCTAGAAACCGAGTGGTGAGATGAGAT
+>TRINITY_DN325_c0_g1_i1 len=234 path=[212:0-233] [-1, 212, -2]
+CTTTTGGTCACGCCGTTGTCGCTGGTGTCGAGCGCTACCCCTTGAAGGTCACCAAATCTA
+TGGGTGCTAAGCGCATTGCCAAGCGTTCTAGAGTGAAGCCTTTCATCAAGGTCATCAACT
+ATAACCACTTGATGCCTACCCGTTATGCTCTCGAACTTGACAATTTGAAGGGACTTGTCA
+CTCCTACTACTTTCAGCGAGCCTTCTCAACGCTCTGCTGCAAAGAAGACTGTCA
+>TRINITY_DN326_c0_g1_i1 len=313 path=[291:0-312] [-1, 291, -2]
+CGCTTCAACAAATCTAAGGCTGTTCATTCCATTATGCGCCATATTGCTGAGAAGCATAAT
+GTTCCTTTGGAGACCATGTATACCACAATTGGATGGCCATTATACCGCAAATATGGACAT
+GCTTATGACGCCTTTAAGCTTGCTATTAGTAACCCAGATCATGTCTTTGAGGGTTTAGAA
+CCTCCCAAATCGGGTGTTATTAATGATTTGTTGGCTCAAATCTCTCGTCGTCTGACGCCT
+CAGCCCATTAAAATTCGTGCTGACGTTGAAGTCACTTGCTTTGGCTACGAAGGTATTAAC
+GCTATCAAGGCCG
+>TRINITY_DN327_c0_g1_i1 len=320 path=[298:0-319] [-1, 298, -2]
+CATGTGTCTCAAAACCTTTCTGACACCGGGCATAACGTCTTGACCGTTAACTTTCATGGG
+CTTCTCGGAAACGTTGCGAAGAGCGGGGTGAAAGACGGCACGGTCTTCGGTAAAGTTGAT
+GTGCTCACCAGCAAATAAAGCATCACGAAGACCCTCAACATTGGCTTCTTTGGCTAATTT
+AACCAAAAGCTCAACGGTCTCTTCGGTGATCAAGTTCTTGGAGAAATCGAACAAGATAGG
+TCCATCTTCTTCTTTTAATCCGTTAAAAGTAAAAGAAAATTTCTCAAAACGGGATGAATC
+ATTGGCGAACAATTCCTTGA
+>TRINITY_DN328_c0_g1_i1 len=211 path=[189:0-210] [-1, 189, -2]
+TCTTAACCTCAACAGCGACTTGGACGACTGGGGAGACGGAAAACTTCATAACCTTCATGT
+TGTGGGCAACTTCGGAAGTGGTCAAAGTACCAGATTTGACCAAAAATTGATCAACACCGA
+CCAAACCAATAATGTTACCAGCAGGACAATCCTCAATAGGCTCAATTCTGGAACCCATCA
+TAAGGACGGTACGTTGGATAGCCTTGATGAA
+>TRINITY_DN328_c1_g1_i1 len=206 path=[184:0-205] [-1, 184, -2]
+CGTTGGATAGCCTTGATGAAGAGATCGTCCTTCTTACCGGGAACATAGTTAGGGCCTTGA
+ATGCGGACCTTCAAACCAGAACGGACAGTACCGGAGAAGACACGACCAAAAGCATAGAAA
+CGACCACGATCAGATGTGGGAACCATCTTAGAAACGTAGATCATAAGAGGAGCATTGGCA
+TCACAGTTACGGATACCAACAGCACA
+>TRINITY_DN329_c0_g1_i1 len=233 path=[211:0-232] [-1, 211, -2]
+TCACTGGTATGTTTAGGGCCTTGCGAAGTGCGAATTTGGTCCAAAAATTTTAGAGAATCC
+AATCCGGCATCAGCTGCAAGCGGTTTATGAGGGGTATTGGGTTCAAGCGTATCCTTAATA
+TGTAAAGCACAGGCACGTCCAAAAACAACAATGTCCAGAAGAGAGTTGGCACCAAGACGG
+TTACCTCCATGGACAGATACACAAGCAGCTTCACCAGCAGCATACAATCCAGG
+>TRINITY_DN330_c0_g1_i1 len=256 path=[234:0-255] [-1, 234, -2]
+ACATTATCAACTTAGGCAAGACTTGGGAAAAGCTTGTTCTTGCTGCTCGTGTAATTGCTA
+CCATTGAGAACCCAGCTGATGTTTGTGTTATTTCTAGCCGGCCATATGGACACCGTGCTG
+TCTTGAAGTTCGCTGCCCACACTGGTGCTACTGCCATTGCTGGCCGTTTCACTCCCGGTA
+ACTTCACCAACTACATCACTCGTACTTACCGTGAACCTCGCCTTATTATTGTTACTGATC
+CTCGTGCTGATGCTCG
+>TRINITY_DN330_c1_g1_i1 len=231 path=[209:0-230] [-1, 209, -2]
+CAAGCTATCAAGGAAGCTTCCTTCGTCAACATTCCAGTTATTGCCTTGTGTGATACTGAC
+TCCATTTTGAACCATGTTGATGTTGCTATTCCTATCAACAACAAGGGTTACAAGTCCATT
+GGTTTGGCCTGGTATCTTTTGGCTCGTGAAGTCCTTCGTCTTCGTGGTAACATTTCTCGC
+ACCACCGCTTGGGAAGTCATGCCTGATCTTTACTTCTACCGTGATCCTGAA
+>TRINITY_DN331_c0_g1_i1 len=444 path=[422:0-443] [-1, 422, -2]
+CAAAGATCCAATAAGGATGATGCTGAAAAGAACGTAATTTACCTCACCGTTTTAATTCCG
+GATGCTGTTGACCCAAAAATTAATTTGACACCTGAAAAACTAGTTATCGATAGCAAATCT
+GGAGCCAACGCTCATTACGCAGTTCAAATTGACTTTTTTAAGGACATTGATGTCGAGAAA
+AGCAAGTACTCTGTTACCGGCCGCTACATCTTTTTCGTCTTATACAAGAAGGAATTACAA
+GAAGAGTTTTGGCCTCGTCTTACTAAAGAGAAACTTCGATTACACTGGCTCAGAACGGAT
+TTTGATCGTTGGGTTGACGAGGATGAGCAAGAAGCACAACCTGAAGTTAGTCCATTTGGC
+GCAGGTGGCATGCCAGATTTGAGCGCACTTGGAGGTATGGGCGGTATGGACTTCAGTCAA
+TTTGGTAACCTTGGAGGTATGGAC
+>TRINITY_DN331_c1_g1_i1 len=244 path=[222:0-243] [-1, 222, -2]
+GTTGGCTCCAGATTTGCTATCGATAACTAGTTTTTCAGGTGTCAAATTAATTTTTGGGTC
+AACAGCATCCGGAATTAAAACGGTGAGGTAAATTACGTTCTTTTCAGCATCATCCTTATT
+GGATCTTTGTGCCCATAAAACTTCAGGAATTTGTGTATTTAAACTCATTCTTTAATGATA
+AAAAGTATAGGTAAATAATAGGTTCAATATGGTAATTTTATGTTGAAACTTTTCAACTGT
+GAAC
+>TRINITY_DN332_c0_g1_i1 len=266 path=[244:0-265] [-1, 244, -2]
+GTCAAGTTTTTGACTGTCATGCAAAAGCATGGCTACATTGACGAATTCACGGAAATTGAC
+GACCACCGTTCTGGCAAAATTGTTATCCAGTTGAATGGTCGTATTAACAAGTGCGGTGTT
+ATCTCTCCCCGTTTCAACGTTAAGCTTAAGGATATTGAGAAGTGGGTCAACCAACTTTTG
+CCCTCTCGTCAAGTCGGTGTCATTGTTTTGACCACCTCTCGCGGTATCATGTCCCACAAC
+GAAGCTCGTGCTAAGGACGCTGGTGG
+>TRINITY_DN333_c0_g1_i1 len=436 path=[414:0-435] [-1, 414, -2]
+TTCTTCATTTGTTAAACCCTTGGTTCCTTGATTAGTAATGAAATGCCATTTGCAATAGTA
+GAATTCACCCTTATCATTAACAAATTTGTAGGTATGACTGGAAAAGCCATCCATGAAACG
+GTAGCTATAAGGGGTACCACCCAAGTCAGAGAAAAGAATCATAACTTGATGGATGGACTC
+TGCGTTTTGAGAAAGGTAATCCCAAAACATAGTAGCATCCTTCATATCATTTTGAGGGTT
+AAGCTTCTGAGTATGGATGAAGAGAGGGAATTTAGCGGGATCACGAAGGAAGAAGACAGG
+GGTATTGTTTCCAACCATATCGAAAATACCTTCATCGGTGTAGAACTTTAATGCGAACCC
+ACGAGGATCACGAGCAGTATCAGGAGTACCCCTTTCACCACCGACGGTGGAGAAACGAGC
+AACAATAGGGGTTTTC
+>TRINITY_DN333_c1_g1_i1 len=259 path=[237:0-258] [-1, 237, -2]
+CCATATGAGAAGGAGAGAACCCAGCCTGCTCGATATCTGCAAAGAAATTGGTAGGATTCT
+GATTCAAGGTAAAGCGTCCAACCCTTTGCATTGGTACGTCCTTATGAGGCCAGACCTTAG
+TAAGATCGAAAATGTTGTAGCGATATTTTTCAGCCTCCTGAGGGGTCATAACTTGAACGT
+AAAGCGTCCAACTGGGGTAATCACCACGTTCAATAGCTTCGAAAAGATCTTGACGAGCAT
+GGTCGGGATTGGATCCATC
+>TRINITY_DN335_c0_g1_i1 len=413 path=[439:0-306 441:307-348 434:349-412] [-1, 439, 441, 434, -2]
+AAAACTATCCACGAGCCAACATGCAGTCTGTTCAGTGCTTTGGAAAGAAAGGCAATGCCA
+CAGCAGTCGCCCACTGTAAGGTCGGCAAGGGCTTGATCAAGGTCAACGGTGCCCCTCTCT
+CTCTTGTTCAACCCGAAATTTTGCGCATGAAGGTCTACGAGCCTATCTTGGTCGCTGGTG
+CCGATAAGTTTGCCGGTGTTGACATTCGTGTCCGTGTCTCTGGTGGTGGTCATGTTTCTC
+AAATCTATGCCATTCGTCAAGCCATCTCCAAGGCCATCGTTGCTTACTACCAAAAGTTCG
+TTGATGAGCACTCTAAGGCTGAACTCAAGAAGGCTCTCATTACTTATGACCGTACTTTGT
+TGGTTGCTGATCCTCGTCGTATGGAGCCCAAGAAGTTCGGTGGTCATGGTGCC
+>TRINITY_DN335_c0_g2_i1 len=413 path=[435:0-306 442:307-348 438:349-412] [-1, 435, 442, 438, -2]
+AAAACTATCCACGAGCCAACATGCAGTCTGTTCAGTGCTTTGGAAAGAAAGGCAATGCCA
+CAGCAGTCGCCCACTGTAAGGTCGGCAAGGGCTTGATCAAGGTCAACGGTGCCCCTCTCT
+CTCTTGTTCAACCCGAAATTTTGCGCATGAAGGTCTACGAGCCTATCTTGGTCGCTGGTG
+CCGATAAGTTTGCCGGTGTTGACATTCGTGTCCGTGTCTCTGGTGGTGGTCATGTTTCTC
+AAATCTATGCCATTCGTCAAGCCATCTCCAAGGCCATCGTTGCTTACTACCAAAAGTTCG
+TTGATGAACACTCCAAGGCTGAGCTTAAGAAGGCTCTCATTACTTATGACCGTACTTTGT
+TGGTTGCTGATCCTCGTCGTATGGAGCCCAAGAAGTTCGGTGGTCATGGTGCC
+>TRINITY_DN336_c0_g1_i1 len=254 path=[232:0-253] [-1, 232, -2]
+TCAAAACCTTGCTGTCATCCAAGAGGTTAAGAGGTTCAAGGAAGATGGCGGAGTCATTAA
+TTTCCGTGCACCTACCGTTCATTCCTCGCTTCCTAATGAAACTACAGCTATCTATGGTAA
+AGCAGAGGAAAAGACTTTGTCTGAGATTTTGCCTGGCATTTTGAACAACCTTGGTCCTGA
+ATCCTTGACTGCCCTTCGTCAAATGGCTGAGCAATTAAAGGTCAGTGAAGGTGAAAAGGG
+AGCTGATGCACAAG
+>TRINITY_DN338_c0_g1_i1 len=268 path=[246:0-267] [-1, 246, -2]
+TCTACCGCCGCCAACCCTGAAGTTTGTCTCGAAACTTTGAAGGCTGTTCTCGGTGAGATC
+AAGGTCCCCACCAACGAGGAGGTTATTGCTAAGTACGTTGCTAACATTGCTGCCCAACTC
+GTTGAAGAGAAGGATAACGAAAATGAGTCCTGGGTTCTCAACATCACTCCTTACTTGACT
+GCCTTCATTGACGAGGCCCACATTCACAAGATCGTTGAGCAACTCCGTACCCGCTCTATC
+GCCAAGATTCCTGGTGGTGCTTCTCATG
+>TRINITY_DN339_c0_g1_i1 len=443 path=[421:0-442] [-1, 421, -2]
+GTGATGCCAAGGCCATCGTTGTCTTGTCCACCAGCGGTAACACTGCTCGTCTCTGCTCCA
+AGTACCGTCCTTCTATCCCCATTGTTATGGTTACTCGTTGCCCTCAAAGAGCTCGTCAAT
+CTCACCTCAACCGTGGTGTCTACCCCGTCATCTACGAGAAGGAGCCTCTTTCTGACTGGC
+AAAAGGATGTTGACGCTCGTGTTGCCTACGGTTGCCAACAAGCTTACAAGATGAACATCC
+TCAAGAAGGGTGACAAGATCATTGTCCTTCAAGGTGCCGTTGGTGGTAAGGGTCACACCT
+CCATCTTCCGTCTTACCGTTGCCGAGTAAGCTGATTATGACGATCCAGTGATTTGCGAAG
+CCAGGATTTCTTAGGGCTTTGGAATGTAAGCTTCAATTTTCGAGTGTGGGCCGTGCTGGT
+ACAGGTGATTTCTTCTTTTTTTT
+>TRINITY_DN339_c1_g1_i1 len=249 path=[227:0-248] [-1, 227, -2]
+TTCCGATGTTGGTAACGCCGTTCTCGATGGTGCTGACTTGGTCATGCTTTCCGGTGAGAC
+TACCAAGGGTTCTTACCCCGTTGAAGCCGTTACCTACATGGCTGAGACTGCCCGTGTTGC
+TGAGGCTTCCATCCCTTACGGCAGCCTTTACCAAGAGATGTTCGGCCTCGTCCGTCGTCC
+TCTTGAGTGTGCTACCGAGACCACTGCTGTCGCTGCCATCGGTGCCTCCATTGAGAGTGA
+TGCCAAGGC
+>TRINITY_DN340_c0_g1_i1 len=245 path=[223:0-244] [-1, 223, -2]
+TTCCTTCAAAGCCACCCCAACTTCCTCTTCGTTGCCATATACTTCCGCGCAGTCGATATG
+AATGAAACCAGCAGCAAGTGCATTCTTTACCGAATCTACAATGGTTCGATTGATTTCTCC
+CTTTTCTTTCTTAAACAAAGCTGTACCAACCCCATAAGCAGGGACGGGAATCTTAGGGCC
+CATAGCAGCGATAAGCATGTTGAAAATGTTAAGAGTACGAAAGAACTTGAAAGTAGAAAA
+AGAGT
+>TRINITY_DN341_c0_g1_i1 len=440 path=[418:0-439] [-1, 418, -2]
+TGGCAGAGGAAAATCACGACGAGGCCGTTCGTGTCGCTGAACTTAGGAAGAAGAGAACCT
+TCCGTACCTTCGCCTATCGTGGCGTCGAGCTTGAACAACTTTTGGACCTCTCTGCTGAGC
+AGTTGGTTGACTTGTTCCATGCTCGTGCTCGTCGTCGTATGCTCCGTGGCCTTGGACCTA
+ATGCTTCTCGTTTTATCAGAAAGCTTCGTAAGGCCAAGTCTGAGGCTCCTCTCAATGAGA
+AGCCTGCAACCGTCAAGACTCACTTGCGTAACATGATCATCCTTCCCGAGATGGTTGGTT
+CTGTTGTTGGTATCTACAACGGTAAGCTCTTCAACCAGGTCGAAATTCGCCCTGAAATGA
+TCGGCCACTACTTGGGTGAGTTTTCCATTACCTACAAACCTACCAAGCACGGTCGCCCTG
+GTATCGGTGCTACTCACAGC
+>TRINITY_DN341_c1_g1_i1 len=327 path=[305:0-326] [-1, 305, -2]
+GTTTGACCATCACCAACTACGGCATAAAATCCAATACACAGCATGGCCGAAGAACATGAT
+GAAGCCGTTCGCGTTGCCGAACTGAGAAAGAAGAGAAGTTTCCGTACTTTTGCTTACCGT
+GGTGTTGAGCTTGAGCAGCTTTTGGATCTCTCTGCTGAGCAATTGGTTGATTTGTTCCAT
+GCCCGTGCTCGTCGTCGTATGCTTCGTGGTCTTGGACCCAATGCCTCTCGCTTCATCCGT
+AAGCTCCGCAAGGCTAAGACTGAAGCTCCTCTTAATGAGAAGCCCGCCACTGTTAAGACC
+CATTTGCGTAACATGATCATCCTTCCC
+>TRINITY_DN342_c0_g1_i1 len=278 path=[305:0-45 306:46-277] [-1, 305, 306, -2]
+CGTCCTTAAAACAAGTCTATCACCCCCGATGAGGCTGTCGCCTACGGTGCTGCTGTTCAA
+GCCGCTGTCCTCACCAACAAGGCTGACTCTGACAAAACTCAAGATTTGCTTTTGTTGGAT
+GTTGTCCCCCTTTCCTTGGGTGTTGCCATGGAAGGTAATGTTTTCGGTGTTGTTTGCCCT
+CGCAATACTCCCATTCCTACCATCAAGAAGCGTACTTTCACCACTGTTGCTGACAACCAA
+ACCACCGTTACTTTCCCTGTTTACCAAGGTGAACGTGT
+>TRINITY_DN342_c0_g2_i1 len=302 path=[303:0-69 304:70-301] [-1, 303, 304, -2]
+CTCGTTTCTGATTTCATTGATGGCCGTGCTTTGAACAAGTCTATCAACCCCGATGAGGCT
+GTCGCCTACGGTGCTGCTGTTCAAGCCGCTGTCCTCACCAACAAGGCTGACTCTGACAAA
+ACTCAAGATTTGCTTTTGTTGGATGTTGTCCCCCTTTCCTTGGGTGTTGCCATGGAAGGT
+AATGTTTTCGGTGTTGTTTGCCCTCGCAATACTCCCATTCCTACCATCAAGAAGCGTACT
+TTCACCACTGTTGCTGACAACCAAACCACCGTTACTTTCCCTGTTTACCAAGGTGAACGT
+GT
+>TRINITY_DN342_c1_g1_i1 len=264 path=[242:0-263] [-1, 242, -2]
+CGTGGTCAAGCTGAGTTGGAAGCTACTTTCGAGTTGGATGCCAATGGTATCTTGAAGGTT
+ACCGCTGTTGAAAAGACCACTGGTCGCTCTGCTCACATTGAAATCACCAACTCTGTTGGT
+CATCTTTCTTCCACTAAGATTCAAGAGATGATTGAAAACGCTGACAAGTTCAAGCAACAA
+GACAAGGATTTCGCCAAGAAATTAGAGGCTAAGAGCCAACTCGAATCTTACATTTCTAAC
+ATTGAGACTACCATCTCTGAGCCC
+>TRINITY_DN343_c1_g1_i1 len=274 path=[252:0-273] [-1, 252, -2]
+CTCTATACTACAAAATGGGAAAACCCGCAGGATTGAACGCCGCTCGTAAGCTTCGCAATC
+ATCGCCGTGAGGAGCGTTGGGCCGATGCTCATTACAAGAAGCGCTTATTGGGAACCGCTT
+ACAAGTCATCACCTTTCGGTGGATCGTCTCATGCTAAGGGTATCGTTGTCGAAAAGATTG
+GTGTAGAAGCTAAGCAACCTAACTCTGCTATTCGTAAATGTGTTCGTGTTCAGTTGATCA
+AGAATGGTAAGAAAGTTACCGCTTTCGTTCCCCA
+>TRINITY_DN344_c0_g1_i1 len=276 path=[324:0-275] [-1, 324, -2]
+CTCGAATAACTTCAAAATGGGTCGTGTACGTACCAAAACTACCAAGAGAGCTTCCCGTGT
+GGTAATTGAAAAATATTACCCTCGTCTCACTCTTGATTTCCAAACCAACAAGAGAATTGT
+TGACGAAGTCGCTATCATCGCCTCTAAGCGTCTTCGTAATAAAATTGCCGGTTACACGAC
+TCACTTAATGAAACGTATTCAACGTGGTCCCGTTCGTGGTATCTCCTTCAAGCTTCAAGA
+AGAGGAGCGTGAACGCAAGGATCAATACGTTCCTGA
+>TRINITY_DN344_c1_g1_i1 len=202 path=[180:0-201] [-1, 180, -2]
+CAAGGATCAATACGTTCCTGAAGTTTCTGAGCTTGAGGTCGATCGTGTTAACGTTGACCA
+AGACACCAAGGACATGCTTAAGTCTCTTGGCTACGATCAAATTCCCGTCCGTGTGCTTGC
+TCCTGCCCCTCAAGAGCGTTTCCGTCGCAGACAGTAAATGAAATTTCGGTCGTAATGGGT
+CCATTTATACTTTTCAGTGCAG
+>TRINITY_DN345_c0_g1_i1 len=281 path=[259:0-280] [-1, 259, -2]
+GTTGAATGGTAACACGCTTGCCATGGATAGCGCAAAGATTGGTATCTTCGAAGAGAGAGA
+CAAGATAAGCCTCGACAGCTTCTTGAAGAGCACCAATTGCGGAGGATTGGAAACGCAAGT
+CAGTCTTAAAATCTTGGGCAATTTCACGGACCAAACGTTGGAAGGGAAGTTTGCGAATCA
+ACAATTCAGTAGACTTTTGGTAACGACGGATTTCACGAAGAGCGACAGTACCAGGACGAT
+AACGATGAGGCTTCTTGACACCGCCAGTAGCGGGAGCGGCC
+>TRINITY_DN346_c0_g1_i1 len=289 path=[267:0-288] [-1, 267, -2]
+TAGTCCTCCTGGATATATTGGTTATGAAGAATCTGGAGAGTTGACTGAAGCTGTGCGTCG
+CAAACCATACGCCGTACTTTTGTTTGACGAATTAGAAAAAGCGCATCATGATATTACCAA
+CCTTCTTCTACAAGTACTAGACGAAGGATTTTTGACCGATTCACAAGGACGTAAAGTGGA
+TTTCCGATCTACCTTGATTGTTATGACCTCGAATTTGGGAAGCGATATCTTGGTTGCTGA
+TCCTAGTACTACTGTCACCCCCAAGATCGGAAGAGCGTCGTGTAGGGAA
+>TRINITY_DN346_c1_g1_i1 len=207 path=[185:0-206] [-1, 185, -2]
+GGTTGTTGTATCAAGGGCGACAGGAATTCCTACCACTAATTTAATGCGTGGTGAAAGAGA
+CAAGCTCCTTAATATGGAACAAACTATTGGCAAGAAGATTATTGGTCAGGACGAAGCTTT
+GAAAGCGATAGCCGATGCAGTTCGTTTATCACGCGCAGGTCTCCAAAACACCAACAGACC
+TTTGGCATCATTCCTTTTCCTTGGACC
+>TRINITY_DN347_c0_g1_i1 len=565 path=[543:0-564] [-1, 543, -2]
+GTCACCGTTATCGAAACTCCCCCTATGGTTGTTGTCGGTGTCGTTGGTTATGTCGAGACT
+CCTCGTGGTCTTCGTTCTCTCACCACCGTTTGGGCCGAGCACTTGTCTGAAGAAGTCAAG
+CGTCGCTTCTACAAGAACTGGTTCAAGAGCAAGAAGAAGGCTTTCACCAAGTATGCCAAG
+AAGTATGCTGAGAGCACTCAATCCATCAACCGTGAGCTCGAGCGTATCAAGAAGTACTGC
+TCTGTCGTTCGTGTTCTCGCTCACACTCAAATCCGCAAGACTCCTCTTGCCCAAAAGAAG
+GCCCATCTTATGGAAATTCAAGTCAATGGTGGATCCGTCGCCGACAAGGTTGAATGGGCC
+CGTGAGCACTTTGAGAAGACTGTTGACATTAAGTCTACCTTTGAGCAAAACGAAATGATC
+GATGTTATTGGTGTCACCAGAGGTAAGGGTAACGAGGGTACTACTGCCCGTTGGGGTACC
+AAGCGTCTTCCCCGTAAGACTCATCGTGGTCTTCGTAAGGTTGCTTGTATAGGTGCTTGG
+CACCCTGCCAACGTCCAATGCACTG
+>TRINITY_DN350_c0_g1_i1 len=233 path=[211:0-232] [-1, 211, -2]
+CTGGACTTCAGCTCAATGAAGAAAAAGAAGAAGAAGAAGAAGAGTGCAGATTTATCTGCT
+TTTGAAAAAGAATTAGAGGCTTCTTCTACGGGTGATGCTACTTCGGACCTTAGTAAGCAA
+ACTTTTGATTCTGAAAATATGGGTGAACACGCTTGGTTAAAGTCGGATCGTGACTACTAC
+TATCCTGAGTTACTGAATCGCTTTTTCACTTTATTGCGTACCAACAATCCCGA
+>TRINITY_DN351_c0_g1_i1 len=278 path=[256:0-277] [-1, 256, -2]
+CTATTTTACGAAAATTAAAGCCATTGCTGAAGCCGAATTGATTGGTTCTGTTAGTGATGT
+TGTTATTTCTATCCCTGCTTGGTTTACTGATATTCAACGCCGTGCTTTATTAGAAGCCGC
+CAACATCGCTGGTCTCAATCCTTTGCGTTTAATGAATGACAACGCTGCTGCTGCCCTTAC
+TTATGGCATCACCAAAACTGATTTACCTGAGCCTGAAAGCCCTCGTCGTGTTGCCATCGT
+TGATTTTGGACACTCTAACTACTCTGTCTCCATCGTTG
+>TRINITY_DN352_c0_g1_i1 len=893 path=[871:0-892] [-1, 871, -2]
+GGGTGCTCGAAACCGGTCATGTCGTGAACAACACCATTGATGAGAACCAAGGGACGAGTC
+TTGCTTTGCTCCAAAAAGTCTTCGAATTCCATGACGGGAAGTTGTTCAAGAGGAATACCC
+CAGTTAAGCTTGGCACGCCAGCGGTCCAAAACCTTTTGCTTTTGTTGAACAATACCCTTT
+TGGATTTCGTTGTCAGGGAAAGTGTTGAGGTTGTAGGCAAGACCAAAGAGACTGGCAATG
+TAGATGAAGATCTTGGTGGGATCATATTCGTACCATCTAAGACCGTTACGGTAATCGTTG
+GGGAAAGCATGGTGGTAGTTGTGGTTGCCCTCACCAAGAGTGACCAAGGCGGTGATGAAG
+TGGTTACGGGCACTGTTGGTGTCGTCAAAGGGTTGGCTACCGATCAAGTGAGCAAGAGAG
+TTAACACAGAAGGTAGCGTGGTGAACAAAGACCAAACGGCAGACACCGGCATAGAAATAA
+CCACCACGGTAATCACCCCACAACAAACCGCAGAAGAGAGAAGGGAAGATGAAGGCCATG
+AAGCTAGCAATGGGCAAGAAGTGACGGTGGTTGAACATGACAAAGGGATCCGAGTTCAAA
+TCGGAGACATCGGAGCGACCAATACGACGGGGGTTTTGCAAGATGATCATCCAACCGACA
+TGAGCATACCAGAAACCCTTCTTGACGTTGTAGGGATCCTTGTCGGTATCGGTGTAACGG
+TGGTGAGCACGATGGTCACGAGACCACCAACGAATGGAGCCCTCAAAGGCAGCAGCACCA
+CCGGCAGCCAAAAAGTATTCCAAAGGCTTCTTAGCCTTGTAAGCACGATGAGACCAGAGA
+CGATGGTAACCGGCAGTGATACCCAAACCAGAGTAGGCGTAGTATATAATGGC
+>TRINITY_DN352_c1_g1_i1 len=223 path=[201:0-222] [-1, 201, -2]
+ACAATCTTTTGTCCTTGGGTATCCTTCATAGGGAGTTGGGCACCGGCACCAGACTTCCAC
+ACCTCAACCTCCATACCACCGCGAACAACGGCGACACGATAAGTGGAAAGCAAGTTGTGG
+GCACCATTAGTGTGGTCATAAACACCACCGTTGAAAGCAGCAGTGGCATCCTTACCGAAA
+GCAGAACGCAAAAGGCCTTGACCACCTGGGTGCTCGAAACCGG
+>TRINITY_DN354_c0_g1_i1 len=983 path=[961:0-982] [-1, 961, -2]
+TCGTGGATACGGGCAAAAGATTTGGTGATAACAGCGGCGCCTCCCAAATAACGAGGTTCG
+AGAGCAGCATGCTCACGAGAAGATCCTTCACCAAAATTTTGTTCACCCAAGGTAACCCAA
+CGGATTCCATGATCACGATAATCAATAGCAACGTTGGGGACAGTCTTGTATTCACCGGTG
+AGTTGATCCTTCAACTTATTTGCTTCACCGTTTTCAGCATTAATAGCACCAATCATATAG
+TTATTAGAAATGTTTTGAAGATGTCCACGGTACTTCAACCAAGGACCAGCGGCAGAGATA
+TGATCAGTAGTACACTTGCCCTTAGCCTTGATAAGGATTTTCAAACCCTTCATATCCTTT
+CCATCCCATTTCTTGAAGGGAGTAAGGCGTTGTAAACGCTTCGAATGAGGATCAATGGCG
+ACATCCTTGACATTGACCGAGCTAGGTGCAACATAAGTGTTGCTTCCTGGGTCGTAACCC
+TTGGAAGGAAGACCAGCACCGGTAGGAGGTTCAAACTTAAAGTCGTTTCCATCCTTATCT
+TTCAAAGTATCAGTAAGAGGGTTAAAGTTCATGTCACCAGAGAAAACCATGGCAGTAACA
+ATATCGGGGGAGGTTACAAAAGCATGAGTGGCAGGGGTAGCATCGTTACGACCAGTGAAG
+TTACGGTTGTAAGAGGTGACGATTGAGTTCTTCTCTCCCTTCTTAACATCGGTACGCTTC
+CACTGACCGATACAGGGACCGCAAGCGTTAGCCAAAACAATACCACCAGCCTTTCTCATT
+GTGTCCAACTGACCATCGCGAGTCAAAGTAGCACGAACTTGTTCGGAACCGGGTGTGATG
+GTAAACAAAGATTTGGTTTTAATGCCCTTGTCGATGGCTTGTTGGCAAATGGAGGCAGCA
+CGAGACATATCCTCATAGGAGGAGTTAGTACAAGATCCAATCAAACCAACTTTGAGCTCT
+TGAGGCCAATCATTCTTCTTGAC
+>TRINITY_DN354_c1_g1_i1 len=271 path=[249:0-270] [-1, 249, -2]
+CTCATTTCGTAACTTTATTTATTTATTAATTTATTAGTTAGGATCATTGTCTTTCATCTT
+TTTAAAAAAAGTTCATTTCCTAAATCCTGCTTTTCAAACCAGCTATGAGTAAATACATAT
+AACGACGTTCTTTAATGACACAGCGACAACGCTTTCAAATAGACATTACCATAATCATCA
+CGACCTGTCATACAAAAAAGGAACCTTAAAACCTCTCATCGTTACAAACCGGAAGGCTTA
+TAAGTCCTTTACTTTTGCTTGTGCATGTTTG
+>TRINITY_DN354_c2_g1_i1 len=474 path=[452:0-473] [-1, 452, -2]
+GCCACCTTCGTAGGCTTCGATCAAGTGGTCACAATGGACAGTGACGGGGACAGCGACCTC
+CGGCATACCCGCGGACATAAATTGAAGGATAGCCATTTGTGCAGTGGCATCCTGACAAGC
+AACACGATCAGGACGAAGCTTCAAGTAAGAGACACCACGTTCAATATCCTGATTTACGGG
+ATCGTCCAAGTGACCGTAAAGGATTTTTTCTGAATATGTGAGAGGACGGTTTAAGCGCTT
+CTTAACAATCTCGAGATTGTCTTTGATGCGCTGATAATTAATAAATTTATTTTTTTCAAA
+GTTGCTCATGGCAACCTTTTTAGCGTCAATGTTGGCTGCGACAGGAGCGCATGAAAAGCT
+TCTGAGGGTGGATTGCGTAAAAATACGCGAGCCCATCCGAGCAGGAGCTCTTGAAATTTT
+GCAAAACATAGTTAATGAGTCAAGAACAAACACCCCAAACTTGTCGTTTCAAAG
+>TRINITY_DN354_c3_g1_i1 len=539 path=[517:0-538] [-1, 517, -2]
+CAATCATTCTTCTTGACGGCTTCCTTGAACTTGGAAATTGGGGTAGCCAAATCGGGGGTA
+AAGGGACCGTTCAAATGGGGTTCCAATGTGTTCAAATCAATTTCAATAATTTGGTCATAG
+TGAGCATTTTCATCAGCGGCAATGATAGGGGCGAATTCTTCAGCATAATCAGCAATAGCG
+GAACGGTTGGTGGCACGAAGGTACTCGGACATACGAGGGTTAAATGGGAAGATAGAGGTA
+GTAGCGCCGATTTCAGCACCCATGTTACAGATCGTACCCATACCAGTGCAAGAAAGAGAT
+TCAACACCGGGACCAAAGTACTCAACAATGGCACCGGTACCACCTTTGACGGTAAGAATA
+CCAGCAACCTTTAAGATAACGTCCTTGGGAGAAGTCCAACCCTTTAATTGACCAGTGAGC
+TTAACACCGATGACTTTAGGACACTTCAACTCCCAAGGCAAATTGGCCATAACATCGACA
+GCGTCAGCACCACCAACACCTATAGCGACCATTCCGAGACCACCGGCGTTGGGAGTGTG
+>TRINITY_DN354_c4_g1_i1 len=277 path=[255:0-276] [-1, 255, -2]
+TGTGCATGTTTGCCATGTGATTCAAAGCACTACCGGCCTTGAACCATTCAATTTGATCCT
+TGTTAAAGGTATGGTTAAGTTTGGTAGACCACTCAGCAGATCCATCAGCAGGGTGAACAA
+CCAAAGTTAAAGGCTTACCGGGAGCAAAGGTAGTGAGACCATCGATATCGACGGTGTCGA
+AAGGAGAAATCTTGTCATAAGCTGCGGGATCGGCAAAAGTCAAAGGCAACAAACCTTGCT
+TTTTAAGATTGGTTTCGTGGATACGGGCAAAAGATTT
+>TRINITY_DN355_c0_g1_i1 len=543 path=[521:0-542] [-1, 521, -2]
+CTAAATTGTGCCATAGTCTCTTCGTCCAAATCCGCAGGGTGAATAAGTGTAGGAACCATA
+TGCCAGAGACCAGTGAGCTCTGGTTTAATCTTTTCATCTCTCGCGATATGACTCAAAACG
+GAAACAAAGTTTCCGCCAGCAGATGCACCTCCTAAGAAGAAACCACGTTTGGGATTTGCA
+CCGAGTTTTTCAATGTTGCTGGCAACCCATTTAAAGGAGTCAATGGCATCATTGTGGGCA
+ACGGGGAATTTGCTTTCGGGTGCTAGACGGTAATCGACTGAAACACAAACGCATCCAAAC
+TTTGGAGTCAGAATTTTGAAAAGTGAGTCATCATCACGAACACCACGCATACACCATCCA
+GAGCTATGATAGAATACCATCAGAGAACGATAATCTGCAGGTACTGACACTGGAGTAAAC
+ACCCTACCATCTATTTCCGTTCCATCTCGTGTAGGAATCAAAATATCGGTGACTGAAACA
+TCATCAGGAAGAGGCAAGATTGTCTCAGCAAGTTGCTTACGACATTCCTCATCCATTGCT
+CGC
+>TRINITY_DN356_c0_g1_i1 len=507 path=[607:0-89 620:90-254 610:255-278 622:279-404 618:405-447 615:448-506] [-1, 607, 620, 610, 622, 618, 615, -2]
+CCACTTCTTTAACTAGTAATTCAAGATGGCACGTAGACCTGCTCGTTGCTACCGTTACTG
+TAAGAACAAGCCTTACCCCAAGTCTCGTTACAACCGTGCCGTTCCCGATTCCAAGATTCG
+TATTTTCGACTTGGGTCGTAAGCGTGCTGGTGTTGACGAGTTCCCTCTTTGCATCCACTT
+GGTCTCTAACGAATACGAGCAAATCACCTCAGAGGCTCTTGAAGCTGCTCGTATCTGTGC
+CAACAAGTACTTGGTTAAGATTGGTGGTAAGGATAGTTTCCACCTTCGTGTCCGTGCACA
+CCCCTTCCATGTTGTTCGTATCAACAAAATGCTTTCATGTGCCGGTGCCGATAGATTGCA
+AACCGGTATGCGTCACGCCTTTGGTAAGCCCAATGGTTTGGTCGCTCGTGTAAACATCGG
+TCAAATTTTGATGTCTGTCCGTACCAAGGATTCTAGCCGTGCTACTGCTATTGAGGCCCT
+TCGTCGTTGTCAATACAAGTTCCCCGG
+>TRINITY_DN356_c0_g1_i2 len=490 path=[603:0-72 620:73-237 610:238-261 622:262-387 619:388-430 613:431-489] [-1, 603, 620, 610, 622, 619, 613, -2]
+TTTTCACAATGGCACGTAGACCTGCTCGCTGCTATCGTTATTGTAAGAATAAGCCTTACC
+CCAAGTCTCGTTACAACCGTGCCGTTCCCGATTCCAAGATTCGTATTTTCGACTTGGGTC
+GTAAGCGTGCTGGTGTTGACGAGTTCCCTCTTTGCATCCACTTGGTCTCTAACGAATACG
+AGCAAATCACCTCAGAGGCTCTTGAAGCTGCTCGTATCTGTGCCAACAAGTACTTGGTTA
+AGATTGGTGGTAAGGATAGTTTCCACCTTCGTGTCCGTGCACACCCCTTCCATGTTGTTC
+GTATCAACAAAATGCTTTCATGTGCCGGTGCCGATAGATTGCAAACCGGTATGCGTCACG
+CCTTTGGTAAGCCCAATGGTTTGGTCGCCCGTATAAACATCGGTCAAGTTTTGATGTCTG
+TCCGTACCAAGGATTCTAGCCGTGCTACTGCTATTGAGGCCCTTCGTCGTTGTCAATACA
+AGTTCCCCGG
+>TRINITY_DN357_c0_g1_i1 len=306 path=[284:0-305] [-1, 284, -2]
+GAGGGGCGACGGCAGGGCCACTTCCCTTTCCACGACCACGACCACGGAAGGTGTAGTTAG
+GAGTGTCGTTCTTGGCAATGAAGATTTGAACAATGAAGGAAGCAACATAGAGACCAAACA
+TAAACCAAAGGAAGAAACACAAGGCCTTCAACTCTTGGCAACGTCTCATGGAACCTTGGG
+TGTAGTGGTTGCGGTCGAGATATTTTTGATTGTCGCAAGCATGGACACGAATGGCGACGG
+CGATACAGCAACCACCGGTGAGTGCAAAGACCCAGTTGACAAAGTTGTAAAAGGCAATCA
+ACCAAG
+>TRINITY_DN358_c0_g1_i1 len=474 path=[452:0-473] [-1, 452, -2]
+ATCCAAAAGGCGCTAGCATATTTAAAGACGAATTAGGATTGATCAAAGTTGATAAGAGGT
+CGATCCAAATCGATCAGAGTCGATCATAATAATCGGACACATGGCTATGTTTCGATCGCG
+CCAAATCAATAAAAACCCAGGTGGTTTTAGATGGTACGACGAACGGTAGGATCGATATGA
+ACATTGGGGTCTGCGAGCAATTTCTTGCCCATGCTATATGTAGCAAAGCCAACAGCAGTA
+GCTACAGCAGCACCTAAAGGATAGAGTTCGACGGGGACTTTACGAAGAGCAGCACGGAAA
+GGCATGATGAATGTAAAAAAGTAAGAATGTAAAGAAATGAGAGTTTTTTTAGAAAATCAA
+GAGAATTTGTAAAAAATCGTAGACTATAAGGTATTCGGTAGAGTACGTTATAGAGACTAA
+CTATATGAAAAGTTTGACTTGACTTAAACCAAGTGAAGTGAATGTAAAGATGGG
+>TRINITY_DN358_c1_g1_i1 len=242 path=[220:0-241] [-1, 220, -2]
+TTTTTTTTTTTTTAAGAACAAACAAGTATGAAGAATGGAAATTCAAATGCAAAACAGAGC
+AATCAAACAGACAAGGGGGTTGATGAAATGGTTTTCACAGCAATGATGAGAGAAATGAAT
+GTGAATTATAAACAAACGAAAAAAAATTCCAATCGCAATAATTTTTCTTTTCATTGCAAA
+ATGGTTTTAATTCTGTCATCAAGAGAAGCTGTAAAGCAATTTATTTCAATGCATAAAATT
+TC
+>TRINITY_DN359_c0_g1_i1 len=281 path=[283:0-153 284:154-280] [-1, 283, 284, -2]
+ATTTTTGCTTGCTTGCTTGTTTGTTTTTCTTAAAAAGGGTATAAGATTTCTTTTTTTTTC
+TTTTAAAAAAGATGTTTGGAATTAAAAAGGCAAAAAAAAAAAGAAACGACAGATGAGTTT
+AAGAGAAGGGTATATAGAGAGGGAGAGCGAATACGCAAAATACAAGACTCAAACAAAAGG
+AATGAGAGAGAATGAATGGAAATTTGGAAGATGAACGATTCCTTACAAATCGAAAAAGGC
+ACAAAACACAAACTACTCGAAGCAAAATAAAGCAATCGAGA
+>TRINITY_DN359_c1_g1_i1 len=232 path=[210:0-231] [-1, 210, -2]
+TGGAACCGGTATCGGCGCCAAACATCCATCCGGCCATGGACACGAAGACCAACATGACAA
+TGGTCAAATTTTTTCCCATTTTTGAAAATTACGATTAAAAGGGTAATATAATGGAAGGAG
+AAAAATTAATAAAAAAAGATATAAAGGGTTTGATTGTAAATAGGGTTAAAAGACAACAAA
+AAGCTTTCAATGACAAGACAAAAGCCCAAAATAGAACCGAAACCGAAGTTTA
+>TRINITY_DN360_c0_g1_i1 len=282 path=[260:0-281] [-1, 260, -2]
+GATGAGGCTGATGAAATGTTGTCCCGTGGTTTCAAGGACCAAATTTACGACATTTTCCAA
+CTTTTGCCTCCTACTGCTCAAGTTGTTCTTCTTTCTGCCACCATGCCTCAAGATGTTTTG
+GAAGTCACCACCAAATTTATGCGTGATCCCATTCGTATCCTTGTTAAGAAAGATGAGCTT
+ACCTTGGAAGGTATCAAGCAATTCTATGTTGCCGTTGAAAAGGAAGAGTGGAAGCTTGAC
+ACTCTTTGCGATCTTTATGAAACCGTCACTGTTACTCAAGCC
+>TRINITY_DN360_c1_g1_i1 len=264 path=[242:0-263] [-1, 242, -2]
+TGATATGGACCAAGCTCAACGTGATACTTTGATGCATGAGTTCCGTACTGGTTCTTCTCG
+TATTCTTATCACCACCGATCTTCTTGCTCGTGGTATCGATGTCCAACAAGTCTCCTTGGT
+TATCAACTATGACTTACCTGCTAACAGAGAAAACTACATTCACCGTATTGGTCGTGGTGG
+TCGTTTCGGTCGTAAGGGTGTTTCCATTAACTTTGTTACCAACGACGATGTTCGCATGAT
+GCGTGAGATTGAACAATTCTACAA
+>TRINITY_DN360_c2_g1_i1 len=201 path=[179:0-200] [-1, 179, -2]
+AATTCTACAATACACACATTGAGGAAATGCCTATGAACATTGCTGACTTGATTTAAAAAA
+TACAAAAGTCCTTTCTTCTCTTTGTTCTAGATATGGAACGCTCCGTGATTGCTCTTCTCG
+CAACCCGGCAAACCTCCCGCAACTTAATTTATCTGCTTTTCTTTGCCCATGTTTTTAATG
+CTTCTTTTATCTGTGCCGGTT
+>TRINITY_DN361_c0_g1_i1 len=674 path=[726:0-178 729:179-217 719:218-241 728:242-337 722:338-361 723:362-673] [-1, 726, 729, 719, 728, 722, 723, -2]
+GCTACGTCGAGTCTCACCCCGGGCGTCTCTCTTGATGAGAATGGCAGCATCAAACTTTTC
+AACAAGTTCCCTTTTGAGGGCGTTGAAGTTAAGGACATCTCCTTGGTTGATTACATTACC
+ATTGGCAATGGTCAACCTCTCCCTCACACCGCTGGCCGTTTCCAGACCAAGAGGTTCCGT
+AAGGCCCGCTGCTTCATTGTCGAACGTTTGACCAACAGCTTGATGATGAACGGCCGTAAC
+AACGGTAAGAAGCTCTTGGCCACTCGCATTGTCAAGCATGCTTTTGAGATCATTGCTCTC
+TTGACCGACCAAAACCCTCTCCAAGTTTTGGTTGATGCCGTTGCTGCCTGTGGTCCTCGT
+GAAGACTCCACTCGTATTGGTAGTGCTGGTACTGTTCGTCGTCAAGCCGTTGATGTTTCT
+CCTCTTCGTCGTGTCAACCAAGCTCTTGCTCTTATCACTATCGGTGCTCGTGAGGCTGCT
+TTCCGTAACGTCAAGTCCATTTCTGAATGCTTGGCTGAAGAAATCATCAATGCTGCTAAG
+GGCTCTTCCAACTCTTACGCCATCAAGAAGAAGGATGAGCTTGAGCGTGTTGCCAAGAGT
+AACCGTTAAAGACTTATTTGTATTAATGGATTTTGTTACTCCCTTGCATTTAATCTTTGT
+GCTTTAACTTCTCG
+>TRINITY_DN362_c0_g1_i1 len=274 path=[252:0-273] [-1, 252, -2]
+ATAGTTACCTCACCAATGACATCTTGGCCATGTTCTGCGCGAAATTTTTTGATTTCTGCT
+TGTTTTTCAGGAATAAGCTCAGCTAACCGATCCTTTAAGGAAGAGGAACGAGTTGAGTAA
+GAAGATGTGAAAAGGGGGTTTAATTGACGGGAACGAAGCGACGCTTGAGAAAGTAACGAC
+GAAGCAAGTCGTCGAGTACTAGCTAATCTTGTGTTTGTCATAAAACGAGGTGCGTTTAAT
+ATAATCATCATGAAAAAGGGTATTACAATGCACC
+>TRINITY_DN362_c1_g1_i1 len=394 path=[372:0-393] [-1, 372, -2]
+ACCAGAATTCAAAAGCTTCCAGAGATAAGACTTGATTGTTTCTTCAGATAAATCATCACC
+GATTTCTTTCTTCATTGTAATCAAAAAGTTCAAAACTTCTTGGTTGGCAAGACCATGAAG
+GGGACCAGCAAGTCCATTTAAGGAGGCAGCCATCGACAAAAAGGGTGAAGAAAGAGCAGA
+ACCTACCAAATGACCGGTGTGAGCAGATACATTACCACCTTCATGGTCAGCATGGATGGT
+CAAATAAAGACGCATAAGCTCCACAAATTCCTCATTGTTAGCAAAGCCCAGAACATTAGC
+AAAATTGTACGAATGGTCCTTATCCATTTGAATAGGAGCAACAACACCATCACGGTACAA
+ATTGCGGTAGATACGACCGGCAATTGGAACGGTC
+>TRINITY_DN363_c0_g1_i1 len=267 path=[245:0-266] [-1, 245, -2]
+GTGGTAACGATAAGCAAGGTTTCCCAATGTTCCAGGGTGTTTTGCTTCCTCACCGTGTCC
+GTCTTTTACTCCGTGCCGGTCACCCTTGCTACCGTCCTCGTCGTGATGGTGAGCGCAAGC
+GTAAGTCTGTCCGCGGTTGCATCGTTGGTCAAGATTTGGCTGTCCTCGCCCTTGCCATTG
+TTAAGCAAGGTGAGCAAGACATCCCTGGTTTGACCGATGTTACTGTTCCCAAGCGTCTTG
+GCCCCAAGCGTGCTTCTAAGATTCGTC
+>TRINITY_DN363_c1_g1_i1 len=351 path=[329:0-350] [-1, 329, -2]
+CGTGCTTCTAAGATTCGTCGTTTCTTCAACTTGTCCAAGGAAGACGATGTTCGCCAATTC
+GTTATTCGTCGTGAGGTCGTTCCCAAAAAGGAGGGCAAGAAGCCCTATACCAAGGCTCCC
+AAGATTCAACGTCTTGTCACTCCCAGAACCCTTCAACACAAGCGTCACCGCTTTGCCCTC
+AAGCGCAGACAAGCTGAGAAGAACCGTGAGGAAGCTGCTGAATTTGCTCAACTTATGGCT
+AAGCGTGTTGCTGAGGCTAAGCAAAAGAAGGAGGTTGTCAAGGCCCGTCGTGCTTCTTCT
+ATGAAAAAATAAGTTGTTTGCCTGTTTGTAGTACTTTTTAAACGAGTCCCT
+>TRINITY_DN363_c2_g1_i1 len=241 path=[219:0-240] [-1, 219, -2]
+ACAATGGCAAGGGCGAGGACAGCCAAATCTTGACCAACGATGCAACCGCGGACAGACTTA
+CGCTTGCGCTCACCATCACGACGAGGACGGTAGCAAGGGTGACCGGCACGGAGTAAAAGA
+CGGACACGGTGAGGAAGCAAAACACCCTGGAACATTGGGAAACCTTGCTTATCGTTACCA
+CCGGTAATCTTGAAGACATAACCAGCAAACTCAGGTCCTACAGAGTCACCTGGGACCTCC
+T
+>TRINITY_DN364_c0_g1_i1 len=217 path=[347:0-46 348:47-216] [-1, 347, 348, -2]
+GCAATCTTCTCAGCCTTCTTAACTGCGTCGTCAATGCTACCAACCATATAGAAAGCAGAT
+TCAGGTAATGAATCGTGCTTGCCTTCAAGAATTTCCTTAAAAGAGCGGATAGTATCTTTC
+AAGGAAACAAGGCGTCCTTCAATACCAGTAAACACTTCGGCAACTGCAAATGGTTGGGAC
+AAGAAACGTTGTACCTTACGAGCACGCTCAACTGTCA
+>TRINITY_DN364_c0_g2_i1 len=343 path=[345:0-172 346:173-342] [-1, 345, 346, -2]
+TTCTTGACCAAGCGGTAAGCAAATAACCGCTGAAGAGAATTTCTGGCTTGAACAAGATTG
+ATGACAAGTTTTGTGCAAAAAACATCAAAAAGTCTTAGCAAATTGATTTATGCAGCCAAT
+TCTTGTGCAATCTTCTCAGCCTTCTTAACAGCGTCGTCAATGCTACCAACCATATAGAAA
+GCAGATTCAGGTAATGAATCGTGCTTGCCTTCAAGAATTTCCTTAAAAGAGCGGATAGTA
+TCTTTCAAGGAAACAAGGCGTCCTTCAATACCAGTAAACACTTCGGCAACTGCAAATGGT
+TGGGACAAGAAACGTTGTACCTTACGAGCACGCTCAACTGTCA
+>TRINITY_DN364_c1_g1_i1 len=307 path=[285:0-306] [-1, 285, -2]
+ATCCATACCAAGAATGGCAATGATATCTTGTAGTGATTTGTATTCTTGAAGCATTTGTTG
+AACAGAACCTGCAAGGTTATAGTGCTCCTCACCAAGAATACGAGGATCCATCATACGAGA
+CTTGGAGTCAAGAGGATCGACAGCAGGATAAATACCCAACTCGGAAATACTACGAGATAA
+CACAGTAGTAGCGTCCAAATGGGCAAAGGTAGTGGCAGGAGCAGGATCAGTTAAATCGTC
+AGCTGGAACATAGACAGCTTGGACTGAGGTAATAGAACCTTTCTTAGTAGTGGTAATACG
+TTCTTGC
+>TRINITY_DN365_c0_g1_i1 len=524 path=[502:0-523] [-1, 502, -2]
+GAACTTTATGCTTCAAGGTGGTGACTTTACTCGTGGTAATGGAACGGGTGGAGAAAGCAT
+CTACGGCGAGAAGTTTGAGGACGAGAACTTTGAGCTCAAGCATGATAAGCCTTTCTTGCT
+TTCCATGGCCAATGCCGGCCCTAATACCAATGGATCTCAGTTCTTCATTACTACTGTTCC
+CACCCCTCATTTGGATGGAAAGCATGTTGTTTTTGGCAAGGTAATTCAAGGAAAATCTAC
+TGTTCGTACCATTGAAAATTTGGAGACCAAAAATGACGATCCGGTTGTACCTGTTGTTAT
+TGAAGAATGTGGAACTTGCACAAAGGATCAGATTGAGGCACCAAAGCCAGACGTTACTGG
+TGATTCTCTGGAAGAATTTCCTGATGATTACGAGGGTGATAAGTCCGAGACTGCCATTTT
+CAAAATTGCTAGCGACTTAAAGGGAATTGCTAACAAGCAATTTGCTCAGCAAAATTTGGA
+TACAGCCGTTGCCAAATGGCAAAAAGCTTTGCGCTACCTAATGG
+>TRINITY_DN367_c0_g1_i1 len=239 path=[217:0-238] [-1, 217, -2]
+AAACTTCGCCAACAGTAAATTCGGCCAAATAACGATAGTAATCACCCTTCATTTTATAGT
+AAAATACCTTGGATTCACCGGTTGTAGCGGCAGGAATCAAATGCTTTTCAAGGACGGAAA
+GGACGTCATGACAAATATCGGATAACTCATCTTCAATCTTCTTACGGTACTCTTTAATCA
+ATGCGGCTTGTCGAGTGTTGCCCCTCATTTCCTCCCTTTGCTCCATCGAGGGAATTATA
+>TRINITY_DN368_c0_g1_i1 len=243 path=[310:0-85 316:86-199 309:200-242] [-1, 310, 316, 309, -2]
+TGAGCAATCCTGCATACATTATTCCAATTTAAAACTTAAGTAATTTCTTTATCAAGCATG
+TCTGGAGGTAAATCTGGTGGTAAGGCTGCTGTTGCCAAATCTGCTCAATCCCGTTCTGCC
+AAGGCCGGTTTGGCTTTCCCCGTTGGTCGTGTCCATCGTTTGTTACGTAAGGGTAACTAT
+GCTCAACGTGTTGGTGCTGGTGCTCCCGTTTACTTGGCTGCCGTCTTGGAGTATTTAGCT
+GCC
+>TRINITY_DN369_c0_g1_i1 len=234 path=[212:0-233] [-1, 212, -2]
+TTTCACTTGGAATCCAATCACCATCTTCTTCATCATCCCAATCCTCAGGCTTCTGAGCTT
+CAGGATCAGGAATGTAAAGAGGTTCATCCTCTAACCAATCCTCAGGTTTCACTGCGTCAG
+GATCAGGAATCATACGGGGAGCGTCTTCATCCCAATCATCAGGCTTAACCGCATTGGGGT
+CAGGAATTTCAGGTTCGTCAACCCAATCAGCAGGCTTGATATCTTCGGGATCGT
+>TRINITY_DN370_c0_g1_i1 len=434 path=[292:0-178 296:179-205 298:206-226 297:227-250 295:251-406 285:407-433] [-1, 292, 296, 298, 297, 295, 285, -2]
+TCTTCAAGTTGCTTACCAGCAAAAATAAGACGTTGTTGATCAGGAGGAATGCCTTCCTTA
+TCCTGAATCTTGCTCTTTACGTTATCAATGGTGTCAGAAGACTCAACTTCCAATGTAATG
+GTTTTACCAGTCAAGGTTTTGACAAAAATTTGCATACCGCCACGAAGACGAAGAACAAGA
+TGTAGAGTAGACTCCTTTTGAATGTTGTAATCTGAAAGAGTACGTCCGTCTTCAAGTTGC
+TTACCAGCAAAAATAAGACGTTGTTGATCAGGAGGAATGCCTTCCTTATCCTGAATCTTG
+CTCTTTACGTTATCAATGGTGTCAGAAGACTCAACTTCCAATGTAATGGTTTTACCAGTC
+AAGGTTTTGACAAAAATTTGCATACCGCCACGAAGACGAAGAACAAGGTGAAGAGTAGAC
+TCCTTTTGAATGTT
+>TRINITY_DN370_c1_g1_i1 len=479 path=[229:0-250 230:251-478] [-1, 229, 230, -2]
+TTTTTGTCAAAACCTTGACTGGTAAAACCATTACATTGGAAGTTGAGTCTTCTGACACCA
+TTGATAACGTAAAGAGCAAGATTCAGGATAAGGAAGGCATTCCTCCTGATCAACAACGTC
+TTATTTTTGCTGGTAAGCAACTTGAAGATGGACGTACTCTTTCAGATTACAACATTCAAA
+AGGAGTCTACTCTTCACCTTGTTCTTCGTCTTCGTGGCGGTATGCAAATTTTTGTCAAAA
+CCTTGACTGGTAAAACCATTACATTGGAAGTTGAGTCTTCTGACACCATTGATAACGTAA
+AGAGCAAGATTCAGGATAAGGAAGGCATTCCTCCTGATCAACAACGTCTTATTTTTGCTG
+GTAAGCAACTTGAAGATGGACGTACTCTTTCAGATTACAACATTCAAAAGGAGTCTACTC
+TTCACCTTGTTCTTCGTCTTCGTGGCGGTATGCAAATTTTTGTCAAAACCTTGACTGGT
+>TRINITY_DN371_c0_g1_i1 len=523 path=[501:0-522] [-1, 501, -2]
+AGCCAAGGGAGAGTACTGAGGTTGTTTAAGAAGCTCAGTCAAGCGAAGACCTCTATCTAA
+AGTGGCACGAGTACCGGCATCCAAATCAGATCCAAATTGAGCAAATGAAGCAACTTCACG
+GTATTGGGCAAGGAAAAGTTTAATTTGACCAGCAACTTGTTTCATGGCCTTGACTTGGGC
+GGCGGAACCGACACGAGAGACTGAAAGACCAACGTTAATAGCAGGTCGGATACCCTTAAA
+GAAAAGTTCAGATTCCAAGAAAATTTGGCCATCAGTAATAGAAATAACGTTAGTGGGAAT
+ATAAGCTGAGACATCACCACCTTGAGTTTCGATAACGGGTAAGGCGGTTAAAGAACCACC
+ACCGTGTTTAGGAGACATCTTGGCAGCACGTTCCAAAAGACGGGAATGAAGGTAGAAAAC
+ATCACCAGGGTAAGCCTCACGACCAGGAGGACGACGTAATAGAAGAGACATTTGACGGTA
+AGCGACAGCCTGCTTGGAAAGATCATCATAAACAACCAAACCG
+>TRINITY_DN373_c0_g1_i1 len=1220 path=[1198:0-1219] [-1, 1198, -2]
+TCCGCGTTGAAATTCGTGCTTTAGAGCGTGAGAAGGACGAAGCTTCCAAAGAACGTCTCA
+AGGCTGCTCGTAAAGAGGCTGAACAAGTGGAAGAAGAAACAAGACCTATTCGTGAGAAGT
+ATGAATTAGAAAAGTCTCGTGGAAGTGAACTTCAAGATGCTAAGCGTCGTCTTGATGAGT
+TGAAGGCTAAGGCTGAGGATGCCGAGCGTCGTAATGATTTCACTCTTGCTGCTGATTTGA
+AATACTATGGTATTCCTGATTTGCAAAAACGTATTGAATATTTAGAGCAACAAAAAAGAA
+AGGCTGATGCAGAAGCGATTGCAAACGCTCAACCAGGCTCAGAACCTTTACTTATTGACG
+TAGTTGGGCCCGATCAAATCAACGAAATCGTTGCAAGGTGGACTGGTATTCCGGTTACTC
+GTTTGAAGACAACTGAAAAGGAACGACTCCTTAACATGGAGAAGGTTCTCAGTAAACAAG
+TAATTGGTCAAAATGAAGCAGTTACTGCAGTTGCAAACGCCATTCGCTTATCTCGTGCTG
+GTCTTTCTGATCCTAATCAACCAATCGCATCTTTCTTGTTTTGCGGTCCTTCCGGTACTG
+GTAAGACTTTATTGACAAAGGCATTGGCATCATTTATGTTTGATGATGAAAATGCAATGA
+TTCGTATTGACATGTCTGAATACATGGAAAAACACTCTGTTTCACGTCTCATTGGAGCAC
+CACCCGGTTATGTTGGACATGAAGCTGGTGGACAGCTTACTGAACAACTTCGTCGACGAC
+CTTACTCCGTCATCTTGTTTGACGAGATTGAAAAGGCTGCTCCAGAAGTATTGACTGTAC
+TTTTGCAGGTACTAGATGATGGACGTATCACTAGTGGCCAAGGCCAGGTTGTTGATGCCA
+AGAATGCTGTTATCATTATGACTTCTAACTTGGGCGCTGAATACTTGACAACAGACAATG
+AGTCTGATGATGGAAAGATAGATAGTACCACTCGGGAAATGGTTATGAACTCGATTCGTG
+GCTTCTTCCGTCCCGAATTTTTGAATCGTATCTCTTCAATCGTTATCTTTAATCGTCTGC
+GTCGTGTGGATATCCGCAATATTGTCGAAAATCGTATATTAGAGGTTCAGAAACGGCTTC
+AATCCAATCATCGCTCAATTAAAATCGAGGTTAGCGACGAAGCTAAAGACCTTCTTGGAA
+GCGCTGGTTATTCCCCTGCT
+>TRINITY_DN373_c1_g1_i1 len=219 path=[197:0-218] [-1, 197, -2]
+CTCCATTGCTGAAGGACTTGCTCGTCGTATAATTGACGATGATGTCCCCGCTAATCTTTC
+GAATTGTAAGCTTCTCAGCCTGGACGTCGGAAGCTTAGTTGCCGGCTCCAAATTTCGTGG
+TGAATTTGAAGAGCGTATCAAATCTGTTTTAAAAGAAGTTGAAGAAAGTGAAACTCCCAT
+TATTTTATTCGTAGATGAAATGCATCTTTTAATGGGCGC
+>TRINITY_DN373_c2_g1_i1 len=284 path=[262:0-283] [-1, 262, -2]
+TCGAACGTAGATTCCAAATCATCTTGGTAAAAGAGCCTTCTATTGAAGATACGATTTCTA
+TCCTTCGTGGTCTTAAAGAAAAGTATGAGGTTCATCATGGTGTTACTATCTCTGACCGTG
+CCTTGGTTACTGCTGCCCATCTCGCTTCCCGGTACCTAACTTCTCGTCGTCTTCCAGATT
+CTGCCATCGACTTGGTCGATGAAGCTGCGGCTGCAGTTCGTGTTACTCGTGAATCTCAGC
+CCGAAGTTCTTGATAACCTTGAGAGAAAGCTTCGACAACTCCGC
+>TRINITY_DN374_c0_g1_i1 len=238 path=[216:0-237] [-1, 216, -2]
+CTTGCTTTCCATTCATTTCCTCAATAGCTCTGGATTGATCCTCAGCATTAGCAAAAGACA
+CAAATCCAAAACCACGACCACGACGTTGCTCACCACGTAATTTTATACGGCGAATAATAT
+AAGGAGGAAGGGAACGAACAGCAATACGAGCACGAGTAGGATTGTAAGCATCGAACATTT
+CTTTAAGGCCTTCATTTGTTAAAGTAACGGAGAGGCCTGAAACATAAATAGAGTTGGG
+>TRINITY_DN375_c0_g1_i1 len=262 path=[240:0-261] [-1, 240, -2]
+TTTCATTGGTACTGATGAAGCCTTAGGTGTCCACCATTGTGACAACGCTATGCTTTATGT
+TATTGCCTCTCCCGTTGGCCCCTACTACAGCTCTGGTTTCAAGGCCGTTAAGCTTTGTTG
+CTCCGAAGAATCCGTTCGTGCTTGGCCTGGCGGTACTGGTCACTACAAGCTTGGTGGTAA
+CTATGCTCCTAGTGTTTTGCCTCAAAAAGAGGCTGCCAAGAAGGGGTATGCTCAGATTCT
+CTGGCTTTATGGAGACGAGGAC
+>TRINITY_DN375_c1_g1_i1 len=274 path=[252:0-273] [-1, 252, -2]
+ATCTTACCTGGTGTCACTCGTGATTCTATTTTGGAAATTTGCCGTGAACGTCTCGCACCT
+AAAGGCTGGAAGATTACTGAGGGCAAGTATTCCATGAAAGAGGTTGCTCAAGCTTCTAAG
+GAAGGTCGCCTTTTGGAAGTCTTTGGAGCTGGTACTGCTGCCCTTGTTTCCCCCGTCAAG
+GCTATTAACTACAAGGGTACTGAGTATGAAATTCCCATGCCTGAGGGTCAGGAAGCTGGT
+CCCATCACTTCTGAAATCAGCAAATGGATTTTGG
+>TRINITY_DN376_c0_g1_i1 len=575 path=[553:0-574] [-1, 553, -2]
+TCCAAGAGGAAAGGAAGCACACGAAATAAAAGACTACTATAGAAAAAAAAACACTCAGGA
+CATTAATGATCAATGAAGAAAACCCGCTTAAAAATTTCTTTTCTTCTTTTGGATTTACTA
+GGGAAAATTGAAGCTGGGGATAAAAATAATGCCTATGGATGAATGTCGGTCAAGTGAGGA
+CTATGACGAGAAGGGGGTAATCTAAAACGCTCGGTCCATCCAGTTTGTTCTTGCCATTTT
+TGTGAATAGGAGTCAACGGCTTTAATAGCGTCAGCAATTTGAGATGGATTGAACTTCTTT
+GACATGTTGTGAATACTCTCATCAGGTCGCAAAGTAGCTCTACCTACCATCAATAACTCT
+TCATCGGTTACGTTGGGAATACCAAGTTCCTCAAGGGTAATGGGAAGATGACATTTTGCC
+ATAAAAGAAGCAAGATTATTGAAGTCTTCCAACGGCCAATCCTCCAAAACAACTTGAACT
+AAGGTACCGTAAGCAACCTTTTCACCATGCATTAAACGATGAACGGGACCGTGGATGGCG
+GTCATACCGTTATGGATGGCATGAGCAGCAGCAAG
+>TRINITY_DN376_c1_g1_i1 len=400 path=[378:0-399] [-1, 378, -2]
+TTTTGAGAAAGAGAATCGACAATTTTATTGGCACAAATGTTCCATACGTTCTGGTCGGCA
+AGCACGACAGCTGATTTAGTGGCCCATTTTTTGACATACATATAGGATCTAGTGAAGGCA
+TGACGACCCTGAACATACTTTTGAGGAGAGGTGAAAATGCGATCTTTGGATTCTTCAAAC
+TCTACACCAACTTTGTGAGGCGTCTCCGTTTCAATAGGAGCATAAAAGCGTTTGCCCCAA
+CGTTGTGCAACGGCATTGGAAGAGGCGAGCGCAAATACTTTAGAGTTCCTGTGGGCGAGG
+GAAACGAGAGGGAAGCGAGGGGTTGCAGCGCAAAGACGAGGACCAATCATTATGAAGGAA
+GTTCAAAGACTAGCTAAGCGTTACGAATAGAAATCGAATC
+>TRINITY_DN376_c2_g1_i1 len=264 path=[242:0-263] [-1, 242, -2]
+GGACAAAGCATCACCAATGCCACTAATAAGGAAGCGGACGGGAGCGCGAACAATCACATC
+GGTATCGATGAAAATGAGGTTGGGATTAAGGGGGTAAAAGCTGTATTTTTGGAATTGACC
+GTCAGGAGTGTAAATGACGGAAAGAGAGGAAGTAGCGGCATCAGAGGAGGCAGTAGTAGG
+ACAAATGATGGATGGAAGATTCATGGAATGAGCAATATACTTTGCGGAATCCATGGTTTT
+ACCACCACCAACTCCAATGATGAC
+>TRINITY_DN376_c3_g1_i1 len=246 path=[224:0-245] [-1, 224, -2]
+AATAGACAGTCGAAAGATCACGAAAGTTCCAAGAATGAACGGGATATATGATCTCGGCTG
+GCCAAAAAAAAAGGGATCGACGTAGTCAATGGTGATTGTCAAAACTAGAATCAGCCGATC
+GACGGTAAACGGGAAGAGTAGGAAGAATGAAAAGAGAAAAAATATTTAAAAATTAAAGCA
+ACGAAAGTTGATTAAAAAAATAATTAAAGAAAAGAAAAAAAAACCCCAGTGGTAGTGAAA
+ACTTGC
+>TRINITY_DN377_c0_g1_i1 len=601 path=[579:0-600] [-1, 579, -2]
+GCTTTGAAGAACTACCCTGGTCCCAGATCTATGCTTACCAAGTACAAAGTTATTGAATTC
+CAACCTTTCGATCCCGTTTCCAAGAAGGTTACTGCCTACGTTCAAGCTCCTGATGGAACC
+CGTATTACTTGTGTCAAGGGTGCTCCCCTTTGGGTTTTGAAGACCGTCGAGGAAGATCAT
+CCTATCCCCGAAGACGTTTTATCTGCATACAAGGACAAGGTCGGTGATTTGGCTTCTCGT
+GGTTATCGTTCTTTGGGTGTTGCTCGTAAGATTGAGGGTCAACATTGGGAAATTATGGGT
+ATTATGCCTTGTTCCGATCCTCCTCGTCATGATACTGCTCGTACTATTTCTGAAGCCAAG
+CGTTTGGGTCTCCGCGTTAAAATGCTTACTGGTGATGCCGTCGATATTGCTAAGGAAACT
+GCTCGTCAGTTGGGTATGGGTACTAACATTTACAATGCTGAACGTCTTGGTCTTACTGGT
+GGTGGTAACATGCCCGGTTCTGAGGTTTATGACTTCGTCGAAGCTGCTGATGGTTTCGGT
+GAGGTGTTCCCCCAACACAAGTATGCTGTCGTCGATATTCTTCAACAACGTGGTTATTTG
+G
+>TRINITY_DN377_c1_g1_i1 len=430 path=[408:0-429] [-1, 408, -2]
+GCGTGGTGAAGGTTTAATGGTTGTTACTGCTACTGGTGACTCTACTTTCGTCGGTCGTGC
+TGCTTCTTTGGTTAATGCCGCTGCTGGTGGTACTGGTCACTTTACCGAAGTTCTTAACGG
+TATTGGTACCATTCTTTTGGTTCTTGTCTTGCTCACTTTGTTCTGTATCTACACTGCTGC
+CTTCTATCGTTCCGTTCGTCTTGCTCGTCTTTTGGAATACACTCTTGCTATTACCATTAT
+TGGTGTCCCTGTCGGTTTGCCCGCTGTCGTTACCACCACTATGGCTGTCGGTGCTGCTTA
+CTTGGCTGAGAAGCAAGCTATTGTCCAAAAACTTTCTGCTATTGAATCCCTTGCTGGTGT
+CGAAGTTCTTTGCTCTGACAAGACTGGTACCCTTACCAAGAACAAGTTGTCTCTTGGTGA
+GCCCTTCACT
+>TRINITY_DN378_c0_g1_i1 len=420 path=[679:0-249 680:250-419] [-1, 679, 680, -2]
+CACAATCATGCAGATTTTCGTCAAGACTTTGACCGGAAAGACTATCACCCTTGAGGTGGA
+GTCCTCTGACACTATTGACAATGTCAAGAGCAAAATCCAAGACAAGGAAGGAATTCCTCC
+TGACCAACAACGTCTTATCTTCGCTGGAAAGCAATTAGAGGATGGCCGTACTCTTTCTGA
+CTACAACATTCAAAAGGAGTCTACCCTTCATTTAGTTCTCCGTCTTCGTGGTGGTATCAT
+TGAGCCCTCTTTGAAGGCATTGGCTTCCAAGTACAACTGTGAGAAGCAAATCTGCCGTAA
+ATGCTATGCTCGTCTTCCTCCTCGTGCCACTAACTGCCGTAAGAAGAAATGTGGTCATAC
+CAACCAACTCCGTCCTAAGAAGAAGCTTAAGTAAAGCATAATCGTGGCCGTAATCAAGAA
+>TRINITY_DN378_c0_g2_i1 len=531 path=[681:0-249 682:250-530] [-1, 681, 682, -2]
+CACAATCATGCAGATTTTCGTCAAGACTTTGACCGGAAAGACTATCACCCTTGAGGTGGA
+GTCCTCTGACACTATTGACAATGTCAAGAGCAAAATCCAAGACAAGGAAGGAATTCCTCC
+TGACCAACAACGTCTTATCTTCGCTGGAAAGCAATTAGAGGATGGCCGTACTCTTTCTGA
+CTACAACATTCAAAAGGAGTCTACCCTTCATTTAGTTCTCCGTCTTCGTGGTGGTATCAT
+TGAGCCCTCTCTAAAGGCTTTGGCTTCCAAATACAACTGCGAAAAGCAAATCTGCCGTAA
+GTGCTATGCCCGTCTTCCTCCCCGTGCTACCAACTGCCGCAAGAAGAAGTGTGGTCACAC
+CAACCAACTTCGTCCCAAGAAGAAGCTCAAATAGATTATTTCTTTTGGGGTATTTCGTGT
+TCTTGTTATTTCTGTCTTGGTAACTTTACAGATAAAGAAATATTAAGAATATTTTGGATT
+ACACGGATGTAAACATGTGAAATTCACTGTAGTGTAGCAAAATTCGAGCAA
+>TRINITY_DN379_c0_g1_i1 len=671 path=[673:0-66 674:67-670] [-1, 673, 674, -2]
+CAACAATGGCAGAAGAAGAACACGTCGATTTCGAGGGTGGTGAGGCCGGTGCCTCTTTGA
+CCTTCCCCATGCAATGCTCTGCTTTGCGTAAGAACGGCCACGTCGTGATTAAGGGACGTC
+CTTGCAAGATTGTCGACATGTCTACCTCCAAGACTGGCAAGCACGGACACGCCAAAGTTC
+ACATTGTTGCCCTTGACATCTTCAATGGCCGCAAGTACGAGGATATGTCTCCTTCCACTC
+ACAACATGGACGTTCCTGTTGTTAAGCGTGATGAGTACCAATTGGTCAACATTGATGATG
+GTTACTTGAACCTCATGACCACCGATGGTACCACCAAGGATGATGTTCGTCTTCCCGAAG
+GTGAGCTCGGTAACGAAATTGAGGAGGGCTTTGATGAGGGCAGAGACTTGATCATTACCG
+TTGTCTCCGCTATGGGTGAAGAGACTGCCCTTGCCTGCCGTGATGCCCCCAGCTCTTAAA
+CTTTTGAAACTTGACTGAAATCAGTCATTGTGCTCCATGATGATGTGGACGGTTTTAAAG
+GGAAAAAAGTAATAATAATTTCGTTTATCAGCAACAGATTTTAGCCTTGTTGCCTTATCC
+AACGTTCCACTAGGCGAAAAGCAAATGATTGTCTCGTAATACGGATTTAATTGTTTTTTT
+TTTAAAAAAAG
+>TRINITY_DN380_c0_g1_i1 len=537 path=[515:0-536] [-1, 515, -2]
+CGCACCATTGCTGCCCCCAGCATGCGTTTTGCGCCTCGCATGACCGCCCCTTTGATGCAA
+ACTCGCGGTATGCGTGTTATGGACTTTGCCGGTACCAAGGAGAACGTTTGGGAGCGTTCT
+GACTGGCCTCGTGAAAAGCTTGTTGACTACTTCAAGAACGACACTCTTGCCATCATTGGA
+TACGGATCTCAAGGACATGGTCAAGGTTTGAACGCTCGTGATCAAGGTTTGAACGTTATT
+GTCGGTGTCCGTAAGGATGGTGCTTCCTGGAAGCAAGCTATTGAAGACGGTTGGGTCCCT
+GGTAAGACTTTGTTCCCCGTCGAGGAGGCCATCAAGAAGGGTTCTATCATCATGAACCTT
+TTGTCCGATGCCGCTCAAACTGAGACTTGGCCCAAGATTGCTCCCCTTATTACCAAGGGT
+AAGACTTTGTACTTCTCTCACGGTTTCTCCGTCATCTTCAAGGATCAAACTAAGATTCAC
+CCCCCTAAGGATGTTGATGTTATCCTTGTCGCTCCCAAGGGTTCTGGTCGTCCCGTT
+>TRINITY_DN382_c0_g1_i1 len=559 path=[537:0-558] [-1, 537, -2]
+GGCGAAAATGTGTTGCAAGGCAAAGAGGTGAATAAACATTTGTCCAATACCGATTGAAAG
+GAAAAGGTATGCGCTGACGAGGGAAAGAGCCCAGTCATGGAATCCTAAAATAGGAACAAG
+ATACATGGCGGCAAAGAACCAGATAAACACATTAGAAAAGACGCGGCAACCAATGCCGGT
+GCAGTGTAAAGCGGCAGAGAAGGCATAAACAACGAACCAAAGAGACTTGCCAAAAACAAG
+TTTCGAGGGCAACTTCATGCTAATCATCTCAACAAAACCATTTCTCAAGCGAAGCGATTG
+GCCGTACATGGTGAAAGAAGATGAGAATAGACACAAGGAAAAGAATGCAGTCCAGTACAG
+CTTCTCACGGGTAAATGCCCAGACGGTAAACACGACAAATACATTGTACCAGATAGATGT
+GTGAATAATGGAGAAGGTAAAATCGTTTACCTGATCACCAAGCATTAAAAGGGGCACAAT
+CATCAAAAGGAAAGACAAGTATTCGACCAAGAGGTAGCCACCAAGCATGAACTTGTTGGC
+GAAAAATGGAGTGGCATGG
+>TRINITY_DN382_c1_g1_i1 len=337 path=[315:0-336] [-1, 315, -2]
+CCAATAATGTATTTTGACTCACGAGTAATTTGCATATTGAACAATTAAGTAGTAGGCGAA
+AGAATAAGAAGAAACTAGCGGTAATATTAATAGTACGAATTGGAAGAAGAAGAAAAAATT
+AAATTACAGGTCTTCTTTCCCGGAGATAGTAAAAGTAGCGAAGCGGCAATTTTCAACCAC
+TTTTGGAATTTGGTTTGTTTGTGTTTTTTTAGATATTAACTAGGTTCCGGCAATACGCAA
+GGAATTGACGATAAACTAAGCAACAGCCTATGAAAGTCAAACTTTTTAAATTGAATAAAA
+TCGTTGGTAAATACGACTTAAAAAAATTGAATTCTTC
+>TRINITY_DN383_c0_g1_i1 len=476 path=[454:0-475] [-1, 454, -2]
+CTTCTGAGGGCCCCACTAGTGCTCGCATTACCCAAGTCAATAGCTGTGAAGGAGATGTCG
+ATGTCTCTATGCGCAAAAGAAAGGTCATTACTATTTTTGATTTGAAAATACAAATGGAAT
+TTAAAGGAGAAACTAAGGATGGAGTTGAAGCTACTGGCTCCATTACTTGCCCCGAGCTTT
+CTTATGACTTAGGATACTCTGATTACGTGTTTGACATCGACATTTACTCTGCTTCAAAGG
+AAAAAGAACCCATTAAAGAGCTTGTTCGTGAGAAAATTATTCCTCAAATTCGTCAGCTTT
+TTTCTGGATTTTCCCAAGTTTTGTTGCAAACCCATGGTGACGATGTTTATCTCTCCACTG
+AAGAACATAACGGTAACGCTGCTCGTGGACTTCCCGTGCATAGTAGCTTTAAGCAAAACA
+ATTCTTCACAGACTTCGTCTAACAAAGGTACTACCACGGTGGCCGCTGGATCTGGC
+>TRINITY_DN384_c0_g1_i1 len=463 path=[441:0-462] [-1, 441, -2]
+GAACCTGTTAAGATGCGCAAGGTTAAAAAGTTGGTTAAGGTTGCTGACTTAAGTGTTTCT
+GTTCAAGAAGATCGTCTTCCCACTGAAGTCCTTGAGAAGTACCGTGAAGCTGAACATCAA
+ATGATTGCTACCGATAAGCTTGTTGCTGAGACTGTTGATCGTAAAAATGCCCTTGAGGAA
+TACATTTACGATACTCGTGCTAAGCTTGATGATATCTATGCTCCCTTCACCAACGAAGAG
+GAGAGCTCTAAGTTTAAGGAGATGCTTACCAAAGCAGAAGATTGGCTTTATGAAGAAGGT
+GAGGACACCACTAAGGCTGTTTATACTGCTAAACTCGAGGATCTCATGCGCGTTGGTGGC
+CCTATTCGTCAACGCTATCTAGATGCGGAGGAAGCTAAAAGACAAAAGGTCCAGGCTGAG
+AGAGAAGCTGCCAAGGCCGCTACTAAATCCGAAGCTGAAAAGC
+>TRINITY_DN385_c0_g1_i1 len=241 path=[219:0-240] [-1, 219, -2]
+CCCAAAACAACTATGTTCTTTTTCGGAACACCAGATTTTCCTTTTGGCGAACTGTTGTTC
+AGTCTTCGTAAGGATTGGAAGAGGGCTACGGCACCCAACATGGACAAAGAAGAAGTAACT
+TCCGCCATTTCAAGTGCTCGAGAGAAAAATGATTTGTTACGGGGTGTAGGAACATTCCCA
+CTGTTCTTTACAGCACAGGATACATGAAATGAACGAACCATCGTTTTTGAATATGGCACT
+G
+>TRINITY_DN385_c1_g1_i1 len=234 path=[212:0-233] [-1, 212, -2]
+AGACCGACATTTTTTAAGAAAAAAGAAGTAAACAAATTTCCCCTTAAATAGGACTAAGTG
+ATAAGTGGTAGGGAGGCGTGAGTAAAAAAATGTATGAGATAATGACAAATGTTAAAGAGC
+AAGCAAACTAAAGAGATAAACCCATTCAAAATTGAGCTATTTTACGATATTAATAGACAG
+TAATAGAAAGAGAGAACGACAACCTTGAGTCCTCTCCTAAATACACAGTGAATT
+>TRINITY_DN386_c0_g1_i1 len=957 path=[935:0-956] [-1, 935, -2]
+TAATGTTCTGTAGACCGGTAATTAGCAATTCCTCAGTATCGTTAGAGTACTGGAAGGAGG
+AGACGTTTTGTCCATTCAAGGTGATTGAACTAGGGGATTCAGTGAGACCAAGGATCGTTA
+CGTTGGCCAAGGGTTGGCTAACTTCGTAGCTGCCAGTTGGAACGGCACTCAAAACACCAT
+CACTAAATGTGAAGCTAACGGAAAGTGTAGCGTTTAGCTCAATGGAAACACCATCATCAA
+GGTAAAGCTCACCAGTAGCAGAACCATCTCTATCCAAAGCGACGAGGAGGTTGAATGGAT
+TTTGACGACTTTCATAAGTAGTGAGCGAAGGTTGTTGCATGGGAAGAACACTACCACCAC
+GAATAGCGACATTGATGTGTTCCAAAGGAGCGTACAGAGTAACATTTTCGTTGTATTGAC
+GAACAATTTCAGTGTGGTTGTACCAGTCATACCATACAGTGCTGTTGTCACCAGGGAAAA
+CACCTTGAACGTATTCAACATTAGGCTCCAAGACAGGTGTCACCAATAGAGAGTCGCCTA
+CCATGAATTGACGGTCAACGTCTGCTAGAGTAGGATCGTTGGGGAATTCAACGAACAAAG
+CACGTAGGGCAGGTGTGCCATCTTGGGATGCCTTAGCCATGATAGTATACCAGTAAGGGA
+GTAAAGAATAACGAATGTACATAGCACGACGTGAGGCCTCAGCAACAGAAGACCATGTGT
+AGGGCTCTTGTGAGATTTGGTAAATGTTGTTATGATTTCTATAGAATGGCGAAAAAGCAC
+CCATAGCCATCCAACGAGAGCAAAGTTCTTCATCTGAATCACCAAGGAAACCACAAACAT
+CAGCTCCTACCATTGGAATACCCATCATGTTAAAAACGATCATTCCAGAAATGGAGAAGA
+ACATGTTAGACCATAGAGAATGATTATCACCCAACCAATGTGCACCATAGACTCCAG
+>TRINITY_DN387_c0_g1_i1 len=260 path=[238:0-259] [-1, 238, -2]
+TGCTGCTAACCCTGATGTTGCAGAGAACGAAGGTAACACTCCCTCTGGAGCCCAAACTCC
+TGCTGCCGAGGAGGAAAATGTTAAGACTCTTGATGAATATCTGTCTGAACGCAAGTCCGC
+CGCAAAGCCTGTTGGTCGTACTGTTGAGAAACTTGAAAACGCTACTAAGGTCGAGAAGAG
+TGCCCCCGAAGAATTGTTTGCCTCTCTTAAGAAGAGCGCTTCTCAAAAGAAGTCTGCTGC
+CAAGGAAAGCAAGCCAAAGA
+>TRINITY_DN387_c1_g1_i1 len=232 path=[210:0-231] [-1, 210, -2]
+CCGTCAAGCTCCTCAAGGAAACGAAGCCTTTGCTCGTGAAGGCAAAGAAGCTCGTGCTAA
+CAACGCTGCCCATCCTGTGGATGCCACTGGCGCCCCCTCCAACCGCCGCAATGCTCGTGC
+TCGCCGTGGTCGTGAATTTGACCGCCATAGCCAAACTGGTAGAGTTGATACCAAGAAGGC
+TACTGAACGTGGCTGGGGCGATCTCGTAAACTCTGCTGCTAACCCTGATGTT
+>TRINITY_DN388_c0_g1_i1 len=384 path=[362:0-383] [-1, 362, -2]
+CCTTGGATATGCTTGGGGGCCTTGGGATCCCATTTGCGTTCGGGAACGCTGGGGACGACA
+GGAATAGTACGCTTGCGCATAGAAGCGTTACCCTCAGTGGTGGGCTGAGTGGTAGCGGAG
+GAGAAAGCAGTTGCAGAAGGAGCAGTCATATTGTGAAGAAAAAATAATAATAAAAAAAAA
+GGAAAGTGAGAAGAAATATAGAAAAAAAAACTAGTTCCAAACTTGGTTCTTTATAAACAA
+AGACTTGGAAAAAGGTCTACAGGCACCACAAAACAAAAAAAGAAGAATTCTAGAAAAAGG
+AAGAATTCAAGAAGTTAAGCGATGTTTCCAGACGTACAAGTAGTATAAGGGTTTTTTACG
+TATTCTCGCAAAAAAACCTAAAAC
+>TRINITY_DN389_c0_g1_i1 len=334 path=[410:0-255 411:256-333] [-1, 410, 411, -2]
+CCAAGAATGAAATTCGTGAGAAGTTGGCTCAAATGTACAAGACTGATTCCGAATGCGTTC
+AAGCCTTTGGTCTTCGCACTCATTTTGGTGGTGGCAGATCTACCGGCTTCGCTTTGATCT
+ATGACTCTACTGAGTCCATGAAGAAGTTTGAGCCTCACTACCGTCTTGTTCGTGTTGGTC
+AAGCTGAGCCTATCCAAAAGGTTGCTCGTCAACAACGCAAGCAACGTAAGAACAGAGGCA
+AGAAGGTCTTTGGTACTGGCAAGCGTCTTGCCAAGCGCAAGTCTAAGCAACAAGACTAGG
+CAATCTTATTTTTTCTTGGTTCAGAAAAATAATT
+>TRINITY_DN389_c0_g2_i1 len=352 path=[408:0-255 409:256-351] [-1, 408, 409, -2]
+CCAAGAATGAAATTCGTGAGAAGTTGGCTCAAATGTACAAGACTGATTCCGAATGCGTTC
+AAGCCTTTGGTCTTCGCACTCATTTTGGTGGTGGCAGATCTACCGGCTTCGCTTTGATCT
+ATGACTCTACTGAGTCCATGAAGAAGTTTGAGCCTCACTACCGTCTTGTTCGTGTTGGTC
+AAGCTGAGCCTATCCAAAAGGTTGCTCGTCAACAACGCAAGCAACGTAAGAACAGAGGCA
+AGAAGGTCTTTGGTACAGGCAAGCGTCTTGCCAAGAGAAAATCTAAGCAACAAGACTAGA
+GTAGATACTTACTTTAGGTTCCTTTCTCGCCAAAAACTCAATACATTCTGTC
+>TRINITY_DN391_c1_g1_i1 len=247 path=[225:0-246] [-1, 225, -2]
+CAAGTCGAATCGAATCAATCTAAAAGCAAAAAAAAAGATAATCAAACCCAACGTTTAGTA
+ACTTTTTTGTAAAAAAAGTAGGGCGATAGGTTGGAAAATGGATCGATTTTCTCGTGGGGA
+TGGAATCAATCGACTCGTTTCTTTTGCAATGTGGGGAGACTTACTAAGGCGGATGTGGGG
+GGAGGACAAAAAAACAAGTAGCAAAGAATCAAAACTTAACAAAATAAATTAAAGGTGTGG
+AAGGTTT
+>TRINITY_DN391_c2_g1_i1 len=239 path=[217:0-238] [-1, 217, -2]
+TTGTGACTCAGATATGTTAACAGCTTGATATCCTTGACAATTTACACCGCGATATGGGTC
+ATATACGGATAAGCGTTGAGGGATACCATTGGTAGGGATAGTGACATTGCGATCACCAAT
+GACATTGAAAGTTTGGTAGACGTTACCGACAGCAATCGAGATTGCTGAAAACAGAGCAGT
+TAAAAATAGAGATTGGTAGGCAGTAGAAATCATCATCGTTAAAAAAAAACAAAAAAGAG
+>TRINITY_DN392_c0_g1_i1 len=346 path=[324:0-345] [-1, 324, -2]
+CGAACAAGGCCACCCTTGGTAGCAATTATAAGTCCTTTGTAAGGGTATAAAGCTTCTCGT
+AAAAGATTCTCGCTGACCTCAGGGCCGTAAGAATCGGCGGTATCAATAAAGTTAATATTG
+AGTTCAGGCAAACGTTTTAAAGTTGCGATGCAAGCCTCTTTGTCTTTGGGTTCATCCCAT
+ATACCATCACCGGTAACTCTCATTGCTCCGAATCCCATTCTATTGACAACCATGTCGCCA
+ACCTTGACAGTCCCAGCTTGTGAAGCATCTACGGCGGAAGAAGCTGCAGTTTTACTCATT
+TTTGTGTCTTTTGTCGCTTTTCTTAGAAATCAAGATCAAGTACTAT
+>TRINITY_DN393_c0_g1_i1 len=543 path=[521:0-542] [-1, 521, -2]
+AAATGACCAAGCGTGCTCCTTCTGATCCTCGTGGCTTTGGTAACCGTGCTGCTGCCTATC
+TGAAGGTGATGGCTCCCGCAGAGTGCATTCGTGATTGCAACAAGGCAATCGAGTTAGATC
+CCAACTTTGCAAAAGCGTATGTTCGCAAAGCTCAAGCTCTTTTTATGTTGAAAGATTACA
+ATAAATGTATTGATGCATGCAATGAAGCTTCTGAAGTTGACCGTCGTGAGCCCAATACCG
+GTAAGAACCTTCGTGAAATCGAGTCTCAATTGTCCAAGTGTATGAGCGCAATGGCTAGTC
+AGAGACAAAATGAAACTGAGGAGGAGACGATGGCTCGAATTCAAAAAGATCCTGAAGTTC
+TAGGAATCTTACAAGACCCTGCTATGCAAGCTATCCTTGGACAAGCTCGTGAGAATCCTG
+CTGCTTTGATGGAACACATGAAGAACCCAACCGTTAAAAGCAAAATTGAGAAGCTGATTG
+CCAGCGGTGTTATTCGCCTGGGCTAAATTTGCGCTTTTGTGAGAAGTGAGATTTAAAAAA
+AAG
+>TRINITY_DN394_c0_g1_i1 len=213 path=[279:0-179 280:180-212] [-1, 279, 280, -2]
+AATGGTTCGAGGTCCTAAAAAGCATTTGAAGCGTGTTGCTGCCCCTCACCACTGGCTTTT
+GGACAAGCTCTCCGGAACTTACGCTCCAAAGCCTTCTCCAGGTCCTCATAAGGCCCGTGA
+GTGCCTTCCTTTGATTGTTTTCTTGCGTAACCGTCTTAAATATGCTTTGAACGGACGTGA
+GGTTAAGGCCATCCTTATGCAACGCCTCATCAA
+>TRINITY_DN394_c1_g1_i1 len=209 path=[251:0-100 252:101-208] [-1, 251, 252, -2]
+GTTGACGGAAAGGTTCGTACTGACTCTACCTTTCCTACCGGCTTTATGGATGTAATCTCC
+GTTGACAAGACTGGCGAGCACTTCCGCCTTGTCTACGACATCAAGGGCCGCTTCACTGTT
+CACCGTATTACTGCTGAAGAAGCTAAGTATAAGCTCTGCAAGGTCAAGCGTGTTCAATTG
+GGAGCTAAGGGGGTTCCCTTCCTTGTCAC
+>TRINITY_DN394_c2_g1_i1 len=286 path=[264:0-285] [-1, 264, -2]
+TTTGAACGGACGTGAGGTTAAGGCTATCCTTATGCAACGTCTCATTAAGGTAGATGGAAA
+GGTTCGTACCGACTCTACTTTCCCTACCGGCTTTATGGATGTGATCTCCGTTGAAAAGAC
+TGGTGAGCACTTCCGCCTTGTCTATGACATTAAGGGCCGTTTCACTGTCCACCGTATTAC
+TGCTGAAGAGGCTAAATACAAGCTTTGCAAAGTTAAGCGTGTTCAATTAGGAGCTAAGGG
+CGTCCCTTTCCTTGTCACTCATGATGGACGTACTATCCGTTATCCG
+>TRINITY_DN395_c0_g1_i1 len=237 path=[239:0-193 240:194-236] [-1, 239, 240, -2]
+CCTGATTTGGTTCGCTCCGTTCATACCGCTGTTGCCAAGAACAAGCGTCAACCTTACGCT
+GTTTCTGAAAAGGCCGGTCATCAAACTTCCGCCGAGTCTTGGGGTACTGGTCGTGCCCTT
+GCTCGTATTCCTCGTGTTGGTGGTGGTGGTACCCATCGTTCCGGTCAAGCTGCTTTTGGT
+AATATGTGTCGTAGCGGTCGTATGTTCGCTCCAACCAAGACCTGGCGCAAGTGGCAC
+>TRINITY_DN395_c1_g1_i1 len=211 path=[189:0-210] [-1, 189, -2]
+CCCAAGACTCGGCGGAAGTTTGATGACCGGCCTTTTCAGAAACAGCGTAAGGTTGACGCT
+TGTTCTTGGCAACAGCGGTATGAACGGAGCGAACCAAATCAGGTCTGATAGGGGCTTTGA
+AAACAAAAGGCAAAGCAATAGTCTCAGAAGAGACACTGCCGTCTTTGCTGTAAATACTAA
+CTGTGGGACGAGCTGCTGCCATTGAAGCTGT
+>TRINITY_DN395_c2_g1_i1 len=264 path=[242:0-263] [-1, 242, -2]
+AAGTGGCACGTTAAGGTCAATCAGAACGAAAAGCGTTATGCTATTTCTTCTGCCGTTGCT
+GCCTCTGGTGTCCCTTCTCTCCTTTTGGCTCGTGGTCACCGTATTGAGGAGATTCCTGAG
+GTCCCTTTGGTTGTCGACGATGCTGTCCAATCTTTCCAAAAGACCAAGGAGGCTGTTGCC
+CTTTTGAAGGAGATTAAGGCTTACCGCGATGTTGTCAAGGTTGCCAACTCTCGCAAGCTT
+CGTGCTGGAAAGGGTAAGCTTCGT
+>TRINITY_DN395_c3_g1_i1 len=281 path=[259:0-280] [-1, 259, -2]
+CTGCTTTCGGTCTCCTTGACAGTGTCTTTGGAAGCACTACTGAGGCTGCTCAACTCAAGA
+AAAACTATTTCCTCCCTGAGAACATCATCTCTAATGCCGATGTTACTCGTCTCATCAACT
+CTGATGAAATTCAAAGCATTGTCAAGGCCGCTGGTCCTTCTCGAGTCAAGCGTGCTCATG
+TCCAAAAGAAGAACCCTCTTAAGAACAAGGCTGTTTTGGCTCGTCTTAACCCTTATGCTA
+AGGCTTACAAGGCCAATGTCAAATTAAACACTGGAAAGACC
+>TRINITY_DN396_c0_g1_i1 len=205 path=[183:0-204] [-1, 183, -2]
+CGGTACTACTGCCGAAGAGAAGGCTAAAGTCCTCCAATACTGTTCTTTTACCAACAGTGA
+GCTCCCTGGCGCCTTTCGCCCTATAATTGCTCCCCGTGTCTTTGGCGCTCCCTATGATGA
+GCAAGCTGCTAAGGAAGCTGAAACTGCCATTGCTTTGATTTTCGCCCGTTTTGATGAGGA
+ATTGGCTTCTAAGACCTACTTGGGT
+>TRINITY_DN398_c0_g1_i1 len=211 path=[308:0-143 309:144-147 310:148-210] [-1, 308, 309, 310, -2]
+CTTAGATTCTCGTGGCTATCTTAAAACCCGCTACAACTGGGGATGGTTCTACTATACCTT
+GACCAACGAGGGTGTTGAGTATTTGCGTGAGTACTTACACCTCCCTGCTGAAGTTGTGCC
+TGCTACTCACAAGCGTCAAGTTCGTCCTACTGCTCCTCGTGCTGGCCGCCCTGAGCCTCG
+TGAGCGTGTTTCTGCTGATGCTGGTTACCGC
+>TRINITY_DN398_c1_g1_i1 len=218 path=[196:0-217] [-1, 196, -2]
+CACAAAATGCTTATTCCCAAGGAGAACCGCAAGGCCATTCATCAAGCTTTGTTCCAACAA
+GGTGTCCTCGTTGCTAAGAAGGATTTCAACCTCCCCAAGCACCCCGAAGTTGGTGTCCCC
+AACTTGCAAGTCATTAAGGCTTGTCAATCCTTGGATTCTCGCGGCTATCTTAAGACCCGC
+TACAATTGGGGATGGTTTTACTACACCTTGACCAACGA
+>TRINITY_DN399_c0_g1_i1 len=558 path=[536:0-557] [-1, 536, -2]
+AGAGGGAATAGGGGAAATACGCTTGCATCCAGGTTCATTGTGAATACCCATTCCAAGTTC
+CATTTCATCATGTTTCATTTCATCTTCTTTTGCAATTGGCTCATGACCAGGGACGTGAAC
+GTGAGCGAGTGAAGCACCGATACTAACCAAATTGTCAATAGCAGCCTTAGCAATGGTCGT
+AACGGCTTCCAAAGGTAACCCTCTGGCGGCAGCTGCACCAGCGATTTTGTGAACAAGAAC
+AGTACCAGACAAACCACGACGTCCGACCTTACCGCTCTTCTTACGACCTACTGATACGTC
+ATCTGCAACGGCAATAAGTTCAGCCTTCTTACCAGCCGTTCTTTGCTTCTCCAAGGCCAT
+ACCAAAGTGAAGGATGTCACCGGTGTAGTTTTTGCAAATTACCAAGGTGCCAGCCTCAGA
+TTCGACTTGCTTAATACCGGTATAAATTTGCTTTGACGAAGGAGAAGCAAAAATGGAGCC
+TGAGACGGCGGCAGTAAGCATACCCTTGCCCACGAACGAAGAATGAGTGGGTTCATGACC
+AGCACCACCGCCGGAAAT
+>TRINITY_DN399_c1_g1_i1 len=590 path=[568:0-589] [-1, 568, -2]
+TTCAGCACCACGCTTCAAAGTAGTACCACAGTCACCATCACCAGCCATCGTATCGAACTT
+TGTAATTTTAGGCTCTGCTTTGATGAGATTCTCCATCGAATTGACAATCGCCTGACGAAC
+CTTCTCCTTATCGACAGTAACGGGAGACTTGACATCCTTCTGACCCTCCTCGATGCTGAC
+ATTGCCAATCTTGTTTTTGGACTTCAAGTCAGAGGGTTGACACAAAGGCCATCCGATAGC
+TTCAACAGGTTGGTCAATCAAATCAACCAAAGAGTATTCTTCGCCCTCGACTTTGACGCG
+GTCAGTGGTACGGAGCAAAGTGATACCGAAACCCAAGCCATTCAAACTGGTGGTAAATGG
+ACCGGCAAAGATGCGAACGGGGTTGATTTTGTATTCTTTAGCCAATGCTTCCTTCACCTT
+GTGGCTAATGGCACTGAATTCAAGCATGGAAAGACCACCAAGGTTATTCATAAGTAAGAC
+TACTTCATCGTCACCCTCAATCTTTACATAGGCACGGTCCTTGTCGGATTGATCCAACAT
+TTGCTTAAGCATCTGAGCGATTAGGTCATCAATAGAGGGAATAGGGGAAA
+>TRINITY_DN400_c0_g1_i1 len=206 path=[184:0-205] [-1, 184, -2]
+TGTGGCCCACTGTTGGGAAAATTTACCAACACGAGAACTGCCGTATCGCCTACGTTGCCC
+AAGCCGCTTTCACTCACTTGGGTCATCACCCTGATAAGACTCCCTCAGAATATATCCAAT
+GGCGTTTCCAATCTGGTGAAGATTTGGAGGCTATGGATAAGGCTTCTCGTGTCATCAGCG
+AGGCTGATGAGGAGGCTATGAAGAAC
+>TRINITY_DN400_c1_g1_i1 len=220 path=[198:0-219] [-1, 198, -2]
+TAAGAAGGTTCCTTCCGCCAAGTCCTACTATGAGTTGGGTGCCTCCGAAATGGAATTCAA
+ATTCCCTGAACCCGGTTTCTTGGAAGGTGTTAAGACCAAGCAACGTGCTATCATCAAGGT
+CCAACACATGTCTTTCCAATACCCTGGTACCTCAAAGCCTCAATTGAACGACATTTCTTT
+CCAAGTTTCTCTCTCTTCTCGTATTGCCGTTATTGGTCCC
+>TRINITY_DN401_c0_g1_i1 len=656 path=[634:0-655] [-1, 634, -2]
+GATAGCAACACCACTTTGTATGCTGAGACTGGTGACTCCTGGTTCAACGGTCTTCAAATG
+AAGTTACCCGCTGGTGCCAAGTTTGAGGTTGAGATGCAATGGGGTCACATTGGTTGGTCT
+GTTCCTTCTGCTATGGGTTATGCTGTCGCTGCCCCTGAGAGAAGAACCATTGTCATGGTT
+GGTGACGGTTCTTTCCAACTTACTGGTCAAGAGATCTCTCAAATGATCCGCCACAAGCTC
+CCCGTTCTCATTTTCTTGCTTAACAACCGTGGTTACACCATTGAGATTCAAATCCACGAT
+GGTCCTTACAACCGTATCCAAAACTGGGACTTCGCTGCTTTCTGCGAGTCTTTGAACGGT
+GAAACCGGTAAGGCTAAGGGTCTTCATGCTAAGACTGGTGAAGAGCTTACCAGCGCCATC
+AAGGTTGCTCTTCAAAACAAGGAGGGTCCTACTTTGATTGAGTGTGCCATCGACACCGAT
+GACTGCACCCAAGAGTTGGTTGACTGGGGTAAGGCTGTTGCCTCCGCCAACGCCCGTCCT
+CCTACCGCTGATAACTAGATTAAAACGGACGTTGTTTGGTAAGAATATGTTACATTTAGA
+TTACAAGAATTATTTGGATATTAGAAATACATGAATGCTTATCCTAGATAATATAA
+>TRINITY_DN401_c1_g1_i1 len=719 path=[697:0-718] [-1, 697, -2]
+CTAAGGAACTCTACTTTGAATACAGACATTAGCAACAATGACTAAGGACGCTGAATCTAC
+TATGACCGTTGGTACCTATCTCGCCCAGAGATTGGTCGAAATCGGTATCAAGAACCACTT
+TGTTGTTCCTGGTGACTACAACCTTCGTCTTTTGGACTTCTTGGAGTACTATCCCGGTTT
+GTCTGAGATTGGTTGCTGTAACGAGTTGAACTGTGCCTTCGCTGCTGAGGGTTACGCTCG
+TTCTAACGGTATTGCTTGCGCCGTCGTCACCTACTCCGTCGGTGCCTTGACCGCTTTCGA
+TGGTATTGGAGGTGCCTACGCTGAGAACCTTCCCGTCATTTTGGTCTCTGGTTCCCCCAA
+CACCAATGACCTTAGCTCTGGTCATTTGTTGCACCACACTCTTGGTACTCATGACTTTGA
+ATACCAAATGGAGATTGCCAAGAAGCTCACTTGTGCCGCTGTTGCCATCAAGAGAGCTGA
+GGATGCTCCCGTTATGATTGACCATGCCATCCGTCAAGCTATCCTCCAACACAAGCCTGT
+CTACATTGAAATCCCCACCAACATGGCTAACCAACCTTGCCCTGTCCCCGGTCCCATTAG
+CGCTGTCATCTCCCCTGAGATCAGTGATAAGGAGTCCCTTGAGAAGGCCACTGACATTGC
+TGCTGAATTAATCAGCAAGAAGGAGAAACCCATTCTTTTAGCTGGTCCCACGCTCCGTG
+>TRINITY_DN401_c2_g1_i1 len=325 path=[303:0-324] [-1, 303, -2]
+ATGCCCGCTGCTAAGGGTTTCTACTCTGAGGAGCACAAGAACTATGCTGGTGTCTACTGG
+GGTGAAGTTAGCAGCTCCGAGACCACCAAGGCTGTTTATGAGAGCTCCGACCTTGTCATC
+GGTGCTGGTGTCCTTTTCAACGATTACAGCACTGTCGGTTGGAGAGCTGCTCCCAACCCC
+AACATCTTGTTGAACTCTGACTACACTAGCGTTTCCATCCCTGGTTACGTTTTCTCCCGT
+GTCTACATGGCCGAATTCTTGGAGCTTCTTGCCAAGAAGGTTTCCAAGAAGCCCGCTACT
+CTTGAGGCTTACAACAAGGCTCGCC
+>TRINITY_DN402_c0_g1_i1 len=1582 path=[2075:0-384 2082:385-897 2074:898-1581] [-1, 2075, 2082, 2074, -2]
+ACTCCCAACGTCAGGCCACGAAGGATGCCGGTTTGATTGCTGGACTAAACGTCCTTCGTA
+TCATTAACGAGCCCACAGCTGCCGCCATTGCTTATGGTTTAGACAGAAGCAACCAGCATG
+AAACCAATGTCCTTATTTTCGACCTTGGTGGTGGTACTTTTGATGTCTCCCTTCTTACTA
+TTGAAGAGGGTATTTTCGAAGTTAAAGCCACCGCTGGTGATACCCACTTGGGTGGTGAAG
+ATTTTGACTCTCGCTTAGTGAACCACTTTGCCCAAGAATTCAAGCGTAAGAACAAGAAGG
+ACATCACTGGCAACGCTCGTGCTGTTCGTCGACTACGTACTGCTTGCGAGCGTGCCAAGC
+GTACTCTTTCTTCTTCTGCTCAAGCCAGCATTGAAATTGATTCTTTGTATGAAGGTATTG
+ATTTCTACACCTCCATTACTCGTGCTCGATTTGAAGAGCTTTGTGCCGATCTCTTCCGTA
+ACACCATGGAGCCTGTGGAGAAGGTCCTCCGCGACTCCAAGATCGACAAGTCCTCTGTTA
+ACGAAATCGTCTTGGTAGGTGGTTCTACTCGTATTCCTCGTATTCAAAAGCTTGTTTCCG
+ACTTCTTCAATGGAAAGGAGCCCTGCAAGTCTATTAACCCTGATGAGGCTGTCGCGTATG
+GTGCTGCTGTCCAAGCCGCTATTTTGGTGGGTGATACTTCTGAAAAGACCCAGGATTTGT
+TGCTTCTTGACGTTGCCCCTCTTTCTTTAGGTATTGAGACCGCTGGTGGAGTCATGACTC
+CTCTTATTAAGCGTAACACGACTATTCCTACCAAGAAATCCGAAGTCTTTTCCACCTACG
+CCGATAATCAACCCGGTGTGTTGATTCAAGTATTCGAAGGTGAGCGTGCTCGTACCAAGG
+ACTGTAACTTGCTTGGTAAGTTTGAGCTTTCCGGTATCCCCCCTGCACCTCGTGGCGTTC
+CTCAAATTGAAGTCACTTTTGATGTTGATGCTAACGGTATTTTGAATGTCTCTGCTCTCG
+AGAAGGGTACTGGTAAGACTCAGAAGATTACCATCACCAATGACAAGGGTCGTCTTTCCA
+AGGAGGAAATTGACCGTATGGTTGCCGAAGCTGAGAAGTACAAGGCTGAGGATGAGGCCG
+AGTCCGGTCGTATCCAAGCCAAGAACCACTTGGAGTCTTATGCTTACTCTCTTCGTAACT
+CTTTGGATGATCCTAACCTTAAGGACAAGGTTGATGCTTCCGACAAGGAGACCGTTGACA
+AGGCTGTCAAAGAGACCATTGAATGGCTCGACAGTAACACTACTGCTGCCAAGGATGAGT
+TCGAGGCCAAGCAAAAGGAGCTTGAAAGTGTTGCTAACCCCATCATGGCTAAGATCTACC
+AAGCTGGTGGTGCTCCCGGTGGCATGCCTGGCGCCGCTCCTGGTGCTGCTCCTGGTGCTG
+CCCCTGGTGGTGACAATGGTCCTGAGGTTGAGGAGGTTGATTAAAATACTGTGCATGAAG
+AAAAATCTTTTAATGGGCGGTTTTAATTGTGAAAATTATGTTGTGAACAATGTTTTTTTG
+TAATAGACATGACTAACGAGGG
+>TRINITY_DN402_c0_g2_i1 len=1582 path=[2079:0-384 2081:385-897 2078:898-1581] [-1, 2079, 2081, 2078, -2]
+ACTCCCAACGTCAGGCCACGAAGGATGCCGGTTTGATTGCTGGACTAAACGTCCTTCGTA
+TCATTAACGAGCCCACAGCTGCCGCCATTGCTTATGGTTTAGACAGAAGCAACCAGCATG
+AAACCAATGTCCTTATTTTCGACCTTGGTGGTGGTACTTTTGATGTCTCCCTTCTTACTA
+TTGAAGAGGGTATTTTCGAAGTTAAAGCCACCGCTGGTGATACCCACTTGGGTGGTGAAG
+ATTTTGACTCTCGCTTAGTGAACCACTTTGCCCAAGAATTCAAGCGTAAGAACAAGAAGG
+ACATCACTGGCAACGCTCGTGCTGTTCGTCGACTACGTACTGCTTGCGAGCGTGCCAAGC
+GTACTCTTTCTTCTTCTGCTCAAGCTAGCATTGAGATTGACTCTTTGTTCGAGGGTATTG
+ACTTCTACACCTCCATTACTCGTGCCCGTTTTGAGGAGCTTTGCGCCGATCTCTTCCGTA
+AAACCATGGAGCCCGTCGAGCGTGTTCTCCGTGACTCCAAGGTCGACAAGGCCTCCGTCA
+ACGAGATTGTTTTAGTCGGTGGTTCCACCCGTATTCCCCGTGTTCAAAAGCTTGTCTCTG
+ACTTCTTCAACGGTAAGGAGCCTTGCAAGTCCATCAACCCTGATGAAGCTGTTGCCTATG
+GTGCTGCCGTCCAAGCTGCTGTCTTGACTGGTGACACTTCTGAGAAGACTCAAGATCTTT
+TGTTGCTTGATGTTGCTCCCCTTTCCATGGGTATCGAGACTGCTGGTGGTGTCATGACTC
+CCCTTATCAAGCGTAACACTACCATCCCTACCAAGAAGTCCGAGATCTTTTCCACTTACT
+CTGATAACCAACCCGGTGTGTTGATTCAAGTGTTTGAAGGTGAGCGTGCTCGTACCAAGG
+ACTGTAACTTGCTTGGTAAGTTTGAGCTTTCCGGTATCCCCCCTGCACCTCGTGGCGTTC
+CTCAAATTGAAGTCACTTTTGATGTTGATGCTAACGGTATTTTGAATGTCTCTGCTCTCG
+AGAAGGGTACTGGTAAGACTCAGAAGATTACCATCACCAATGACAAGGGTCGTCTTTCCA
+AGGAGGAAATTGACCGTATGGTTGCCGAAGCTGAGAAGTACAAGGCTGAGGATGAGGCCG
+AGTCCGGTCGTATCCAAGCCAAGAACCACTTGGAGTCTTATGCTTACTCTCTTCGTAACT
+CTTTGGATGATCCTAACCTTAAGGACAAGGTTGATGCTTCCGACAAGGAGACCGTTGACA
+AGGCTGTCAAAGAGACCATTGAATGGCTCGACAGTAACACTACTGCTGCCAAGGATGAGT
+TCGAGGCCAAGCAAAAGGAGCTTGAAAGTGTTGCTAACCCCATCATGGCTAAGATCTACC
+AAGCTGGTGGTGCTCCCGGTGGCATGCCTGGCGCCGCTCCTGGTGCTGCTCCTGGTGCTG
+CCCCTGGTGGTGACAATGGTCCTGAGGTTGAGGAGGTTGATTAAAATACTGTGCATGAAG
+AAAAATCTTTTAATGGGCGGTTTTAATTGTGAAAATTATGTTGTGAACAATGTTTTTTTG
+TAATAGACATGACTAACGAGGG
+>TRINITY_DN402_c1_g1_i1 len=255 path=[233:0-254] [-1, 233, -2]
+ACGTTTTTGGGCTTGTCGGACTTGGCATCAAGACCGTAAGCAATAGCAGCAGCGGTGGGC
+TCGTTGATGATACGAAGAACGTTAAGGCCAGCGATGGCACCAGCATCCTTAGTAGCAGCA
+CGTTGAGAGTCAGAGAAGTAGGCGGGGACGGTAATGACAGCCTTCTCGACACGCTTGTTC
+AACTTAGCTTCGGAAATCTCCTTCATCTTAGTCAAAACCATAGCGGAAATTTCTTGAGCA
+GTAAATTGCTTTTTC
+>TRINITY_DN402_c2_g1_i1 len=776 path=[754:0-775] [-1, 754, -2]
+CTTGCATTAATATCAATTAAGGAGTAATAAATCATTTTCCTTATAGGAAGTTAACGAAGA
+AAGTTATCTATTGCATCTTAAATAAGGAGTGCTATATTAAATTATTTATATCCCACGTTC
+CTTTTTATAATCCCCAAATAAACTTTAGTCTTTTTTATTTGTTTTTTGTCTTTTCACATC
+AATATGAGCAAATCAATCGGAATTGATTTGGGTACTACCTACTCTTGTGTTGGACACTTT
+TCCAACAACCGTGTCGAAATTATCGCCAACGATCAAGGTAACCGCACTACCCCTTCTTAT
+GTTGCCTTTACCGATACCGAGCGTCTCATTGGTGACGCTGCTAAGAACCAAGTCGCCATG
+AACCCCCACAACACCATCTTTGATGCCAAGCGTTTGATCGGCCGTAAATTTGATGATCCT
+GAGGTTCAGTCTGACATGAAGCACTGGCCCTTCAAGGTCATCTCCAAGGATGGCAAGCCT
+GTTTTGCAGGTTGAGTACAAGGGTGAGACCAAGACCTTTACCCCCGAGGAAATCTCATCC
+ATGGTTTTGATGAAGATGCGTGAGACTGCTGAGGCCTACCTTGGTGGTAAGGTCACTGAC
+GCCGTCGTCACTGTCCCCGCCTATTTCAACGACTCTCAACGTCAAGCCACCAAGGATGCT
+GGTCTTATTGCCGGTTTGAACGTTCTCCGTATTATCAACGAACCCACTGCCGCCGCTATT
+GCCTATGGTTTAGACCGTAGCAACCAAGGCGAATCCAATGTCCTCATTTTCGATCT
+>TRINITY_DN402_c3_g1_i1 len=397 path=[380:0-396] [-1, 380, -2]
+ACCGTCCCCGCCTACTTCTCTGACTCTCAACGTGCTGCTACTAAGGATGCTGGTGCCATC
+GCTGGCCTTAACGTTCTTCGTATCATCAACGAGCCCACCGCTGCTGCTATTGCTTACGGT
+CTTGATGCCAAGTCCGACAAGCCCAAAAACGTCTTGATTTTCGATCTTGGTGGTGGTACT
+TTTGATGTTTCTCTTCTTACCATCGAAGAGGGTATCTTTGAAGTTAAGGCCACTGCTGGT
+GACACTCACTTGGGTGGTGAGGACTTTGACTCCCGTCTTGTAAACCACTTTATCCAAGAA
+TTCAAGCGCAAGAACAAGAAGGATATCACCGGTAACGCTCGTGCTGTCCGTCGTCTTCGT
+ACCGCTTGTGAGCGTGCTAAGCGTACTCTTTCTTCTT
+>TRINITY_DN402_c4_g1_i1 len=662 path=[640:0-661] [-1, 640, -2]
+CAGCAATTGTCGTTTCGATTGTTTATTTCGTCTTAAATTAAAAAAAGCATTTTCTAAAGC
+GCATTTGTGCGAATCTATCGTACCTGTGTTATAATACTTATTAATTCACGTTTATTTTGT
+TTACGAATTTAATTTCATTCCCCCGTTTTTCATTGATACGAATTTTCTTTACGAACTATT
+AATACATTTCAAATATGAGCAAGTCTATCGGTATTGATTTGGGTACTACTTACTCGTGCG
+TCGGTCATTTCTCGAATAATCGAGTGGAAATTATTGCCAATGACCAGGGAAATCGCACGA
+CTCCCTCCTATGTTGCATTCACTGACACAGAACGATTGATCGGTGATGCTGCAAAAAATC
+AAGTTGCTATGAATCCTCACAACACTATTTTCGATGCCAAACGATTGATTGGCCGCAGAT
+TTAACGATCCCGAAGTCCAATCTGATATGAAACATTGGCCTTTTAAGGTCATCGAGAAGG
+ATGGTAAGCCTTTGATTCAGGTAGAGTTCAAGGGTGAGACCAAGACCTTTACACCAGAGG
+AAATCTCCTCTATGGTTTTATTGAAGATGCGTGAAAGCGCAGAAGCCTTTTTGGGTGGCA
+AAGTCACCGATGCCGTTGTTACTGTTCCCGCTTATTTCAATGACTCCCAACGTCAGGCCA
+CG
+>TRINITY_DN402_c5_g1_i1 len=303 path=[281:0-302] [-1, 281, -2]
+TAACAGAAGACAAGGCACGCTTAGCACGCTCACAAGCAGAGCGAAGACGACGAAGAGCAC
+GAGGATCGTCAGAGATGTCAATCTTTTGCTTGCGCTTGAATTCTTGAATAAAGTGCTCGA
+CCAAAGCGTTATCAAAATCTTCACCACCCAAGTGAGTGTCACCAGCGGTAGCCAAAACTT
+CAAAGACACCACCTTGAATCTTCAAAAGAGAAACATCAAAAGTACCACCACCAAGATCGA
+AAATGAGGACATTGGATTCGCCTTGGTTGCTACGGTCTAAACCATAGGCAATAGCGGCGG
+CAG
+>TRINITY_DN402_c6_g1_i1 len=229 path=[207:0-228] [-1, 207, -2]
+CTGAGCGTTTAGTCGGTGATGCCGCCAAGAACCAGGCTGCTATGAACCCTCGTAACACCG
+TTTTTGACGCCAAGCGTCTTATTGGTCGTCGTTACGAAGACCCTGAGACTCAAAAGGATA
+TTAAGCACTGGCCCTTTAAGGTTATTGACAACAATGGTATCCCTACCATTGAGGTTAACT
+ATTTGGGCGAGAAAAAGCAATTTACTGCTCAAGAAATTTCCGCTATGGT
+>TRINITY_DN403_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2]
+GGTAAGGTTGTCACGCAACAATTGCATGATTAAAGTAGAATCTTTGTAGGATTCCTCGGA
+AAGGCTGTCCAACTCGGAGATAGCTTCATCAAAGGCTTGCTTGGCTAAGTAGCAAGCACG
+GTCGGGGGAGTTCAAGATCTCATAGTAGAAAACGGAGAAATTAAGAGCAAGACCTAAGCG
+GATAGGATGAGTAGGTGCAAGTTCGGCGGTAGCAATTTCAGAAGCGGCCTTGTAACCTTC
+AAGAGATTGATCAGCGGAGTGTTGGCGCTTCTCACCAAC
+>TRINITY_DN404_c0_g1_i1 len=504 path=[708:0-112 735:113-256 732:257-313 734:314-361 727:362-412 711:413-415 712:416-418 726:419-463 717:464-503] [-1, 708, 735, 732, 734, 727, 711, 712, 726, 717, -2]
+TTCCGTAATCCTTATCACTACAGAACTGATGTTGAAACCTTTGTTGCAACTGAGGGTATG
+TACACTGGCCAATTCGTTTACTGCGGTAAAAACGCTGCTTTGACCGTTGGTAATGTCTTG
+CCTGTTGGTGAGATGCCTGAGGGTACTATCATCTCCAACGTTGAGGAGAAGGCTGGTGAC
+CGTGGTGCATTAGGTCGTTCTTCTGGTAACTACGTTATCATTGTCGGACATGATGTTGAC
+ACTGGCAAGACCCGTGTTAAGTTGCCCTCTGGCGCCAAAAAGGTTGTCCCCTCTTCTGCT
+CGTGGTGTTGTCGGTATTGTCGCTGGTGGTGGACGTATTGACAAGCCTTTGCTCAAGGCT
+GGTCGTGCTTTCCACAAATACCGTGTTAAGCGCAACTGCTGGCCTCGTACTCGTGGTGTT
+GCTATGAACCCCGTCGATCATCCTCACGGTGGTGGTAACCATCAACACGTTGGTCACTCT
+ACCACTGTTCCTCGCCAATCCGCC
+>TRINITY_DN404_c0_g1_i2 len=504 path=[708:0-112 735:113-256 733:257-313 734:314-361 706:362-382 731:383-415 729:416-418 725:419-463 693:464-503] [-1, 708, 735, 733, 734, 706, 731, 729, 725, 693, -2]
+TTCCGTAATCCTTATCACTACAGAACTGATGTTGAAACCTTTGTTGCAACTGAGGGTATG
+TACACTGGCCAATTCGTTTACTGCGGTAAAAACGCTGCTTTGACCGTTGGTAATGTCTTG
+CCTGTTGGTGAGATGCCTGAGGGTACTATCATCTCCAACGTTGAGGAGAAGGCTGGTGAC
+CGTGGTGCATTAGGTCGTTCTTCTGGTAACTACGTTATCATTGTCGGACATGATGTTGAC
+ACTGGCAAGACCCGTGTCAAGTTGCCCTCTGGTGCTAAGAAGGTTGTCCCTTCTTCTGCT
+CGTGGTGTTGTCGGTATTGTCGCTGGTGGTGGACGTATTGACAAGCCTTTGCTCAAGGCT
+GGACGTGCATTCCACAAGTACCGCGTCAAGCGTAACTGCTGGCCTCGTACTCGTGGTGTC
+GCTATGAACCCCGTCGATCACCCTCACGGTGGTGGTAACCATCAACACGTTGGTCACTCT
+ACCACTGTTCCTCGCCAATCCGCC
+>TRINITY_DN405_c0_g1_i1 len=548 path=[654:0-111 659:112-270 657:271-547] [-1, 654, 659, 657, -2]
+GTGTGGCTCTTACCCTTTCCAAGATTCGTCGTGCCGCCCGTGAGCTTTTGACACTTGATG
+AGAAGGATCCCAAGCGTCTTTTTGAAGGTAATGCCATCATTCGTCGTCTTGTTCGTTTGG
+GCATTTTGGATGAGTCCCGTATGAAGCTTGATTATGTGTTGGCTCTCCGTATCGAGGACT
+TTTTGGAGCGTCGTTTGCAAACTCAAGTCTTTAAGCTTGGTTTGGCTAAGTCCATCCATC
+ATGCACGTGTGTTGATCTTCCAACGTCACATTCGTGTTGGTAAGCAAATTGTCAATGTTC
+CTTCTTTTGTTGTCCGTTTGGATACTCAAAAGCACATTGACTTTGCCCTCTCCTCTCCTT
+ATGGTGGTGGTCGTCCTGGTCGCTGCAAGAGAAAACGTCTCCGCTCTCAAGAGGGCGGTG
+AAGGAGAAGAAGCCGAAGAAGAGTAAATTAAGCAGGTGTGACATTCTCTTCTATACATTT
+CTAAATGGGATTTCTTCATAGCCGCTTCTATCTGCCTAATAAAGAAGTTTGTTTGATTGC
+ATAAAAAA
+>TRINITY_DN405_c0_g1_i2 len=306 path=[652:0-123 659:124-282 651:283-305] [-1, 652, 659, 651, -2]
+ATGAAATTTGGCGTGTAGCACTTACCCTTTCTAAAATCCGTCGTGCTGCTCGTGAGCTTT
+TGACCCTTGACGAGAAGGATCCTAAGCGTCTTTTCGAGGGAAATGCCATCATTCGTCGTC
+TTGTTCGTTTGGGCATTTTGGATGAGTCCCGTATGAAGCTTGATTATGTGTTGGCTCTCC
+GTATCGAGGACTTTTTGGAGCGTCGTTTGCAAACTCAAGTCTTTAAGCTTGGTTTGGCTA
+AGTCCATCCATCATGCACGTGTGTTGATCTTCCAACGTCACATCCGTGTTGGTAAGCAAA
+TTGTCA
+>TRINITY_DN406_c0_g1_i1 len=408 path=[540:0-240 554:241-252 552:253-285 551:286-407] [-1, 540, 554, 552, 551, -2]
+CAGCAATGCCTCATTCTTACGGTATCAGAGCTCGCACCCGTTACACCTTTCAACGTGGTT
+TCAGAGAGCATGGTCAAATTCGTTTGTCCACTTATTTGAAGACCTATAAGGTTGGTGACA
+TTGTCGACATTAAGGTTAATGGTGCTGTCCAAAAGGGTATGCCTCACAAGTACTACCATG
+GCAAGACTGGTGTTGTTTACAACGTTACTCAATCTTCTGTTGGTGTCTTGATCTACAAGG
+TTGTTGGTAACCGCTACATGGAGAAGCGTGTCAATGTTCGTATTGAGCACGTTAAGCACT
+CTAAGTGCCGTCAAGACTTCTTGGACCGTGTTAAGGCCAATGAGGCTAAGCGTAAGGAGG
+CCAAGGCTCAGGGTAAGACTGTTCAACTTCGTCGTCAACCCGCTCCCC
+>TRINITY_DN406_c0_g2_i1 len=311 path=[546:0-143 555:144-155 553:156-188 545:189-310] [-1, 546, 555, 553, 545, -2]
+GAAAACTTACAAAGTTGGTGATATTGTCGACATTAAGGTCAATGGTGCTGTCCAGAAGGG
+TATGCCTCACAAGTATTACCATGGTAAGACTGGTGTCGTTTACAACGTTACTCAATCATC
+CGTTGGTGTCTTGATCTACAAGGTTGTTGGTAACCGTTACATGGAAAAGCGTGTCAATGT
+TCGTATTGAGCACGTTAAGCACTCTAAGTGCCGTCAAGACTTCTTGGACCGTGTTAAGGC
+CAATGAGGCTAAGCGTAAGGAGGCCAAGGCTCAGGGTAAGACTGTTCAACTTCGTCGTCA
+ACCCGCTCCCC
+>TRINITY_DN407_c0_g1_i1 len=275 path=[303:0-165 304:166-189 311:190-195 310:196-219 309:220-274] [-1, 303, 304, 311, 310, 309, -2]
+CCTTCATCAAAGCAGTCAAGAGCAGCCCATACTTCTCACGTTACCAGACGAAATATCGTC
+GTCGTCGTGAGGGTAAAACCGATTATTACGCTCGTAAGCGTTTGATTGCCCAGGCCAAGA
+ACAAGTACAATGCTCCCAAGTACCGTTTGGTCGTTCGTTTCTCCAACCGTTTCGTCACAT
+GCCAAATAGTTTCTTCCAGAGTAAACGGTGACTATGTTCTTGCTCATGCTCACTCTTCTG
+AGCTCCCTCGCTACGGTATCAAATGGGGTTTGGCC
+>TRINITY_DN407_c1_g1_i1 len=540 path=[731:0-95 746:96-209 745:210-323 742:324-392 730:393-539] [-1, 731, 746, 745, 742, 730, -2]
+CTCTTCTGAGCTTCCTCGTTACGGTATCAAATGGGGTTTGGCCAACTGGACTGCCGCCTA
+CGCTACCGGTCTTTTGGTCGCTCGTCGTGCTCTTGCTAAGGTTGGCCTTGCTGATAAGTA
+TGAGGGTGTTACTGAACCTGAGGGTGAGTTCGAGCTCACTGAGGCTATTGAGGATGGTCC
+TCGCCCCTTCAAGGTTTTCTTGGATGTTGGTTTGAAGCGTACTTCTACCGGTTCCCGTGT
+CTTTGGTGCAATGAAGGGTGCTTCTGATGGTGGTTTGTTTATTCCCCACTCTCCCAACCG
+TTTCCCTGGTTTCGATATTGAAACTGAGGAATTGGATGATGAGACTCTCCGTAAGTATAT
+CTATGGTGGTCATGTTGCTGAATACATGGAGATGCTTATTGATGATGATGAAGAGCGTTA
+TCAAAAGCAATTCTCTGGTTTGATCGCTGATGGTATTGAGAGTGATCAACTTGAGGACAT
+CTATGCTGAGGCCTATGCCAAGATCCGTGAGGATCCCTCTTTCCAAAAGTCTGGTAAGGA
+>TRINITY_DN407_c1_g2_i1 len=540 path=[723:0-95 743:96-167 747:168-209 745:210-323 741:324-392 722:393-539] [-1, 723, 743, 747, 745, 741, 722, -2]
+CTCTTCTGAGCTTCCTCGTTACGGTATCAAATGGGGTTTGGCCAACTGGACTGCCGCCTA
+CGCTACCGGTCTTTTGGTCGCTCGTCGTGCTCTTGCCAAGGTTGGCCTCGCTGACAAATA
+TGAGGGTGTCACTGAACCCGAAGGAGAATTTGAGCTTACCGAGGCCATCGAGGATGGTCC
+TCGTCCTTTCAAGGTTTTCTTGGATGTTGGTTTGAAGCGTACTTCTACCGGTTCCCGTGT
+CTTTGGTGCAATGAAGGGTGCTTCTGATGGTGGTTTGTTTATTCCCCACTCTCCCAACCG
+TTTCCCTGGTTTCGATATTGAAACCGAGGAGTTGGATGATGAGACTCTCCGCAAATATAT
+CTATGGTGGCCATGTTGCTGAATACATGGAGATGCTTATTGATGATGATGAAGAGCGTTA
+TCAAAAGCAATTCTCTGGTTTGATCGCTGATGGTATTGAGAGTGATCAACTTGAGGACAT
+CTATGCTGAGGCCTATGCCAAGATCCGTGAGGATCCCTCTTTCCAAAAGTCTGGTAAGGA
+>TRINITY_DN408_c0_g1_i1 len=526 path=[688:0-132 702:133-198 691:199-213 703:214-276 705:277-277 698:278-462 694:463-486 695:487-525] [-1, 688, 702, 691, 703, 705, 698, 694, 695, -2]
+CCAACATGGGAATTACCAGAGACTCACGACACAAGCGCTCTGCTACCGGTGCTAAGCGTG
+CTCAGTACCGCAAGAAGAGAAAATTCGAGTTGGGTCGTCAACCTTCCAACACTCGTATTG
+GACCTAAGCGTATTCACGAGGTCCGTGTTCGTGGTGGAAATAAGAAGTTCCGTGCCCTTC
+GTCTTGACTCTGGTAACTTCTCTTGGGGCTCTGAGGGTGTTTCCAAGAAGACTCGTATTA
+TTCAAGTTGCCTATCACCCTTCTAACAACGAGTTGGTTCGTACCAACACTTTAACCAAGT
+CAGCTATTGTCCAAATTGATGCTGCTCCTTTCCGTGTCTGGTATGAAACCCATTACGGTA
+TCTTGATGGGAAGCAAGGGAAAGAAGGCCACTTCAACCCCTAATCCCAAATCCAAGCATG
+TTCAACGTAAGCATAGCGCTCGTCTTGGCGATTCTAAGGTTGACTCCGCTTTGGAAACTC
+AGTTTGCTGCTGGCCGTTTGTATGCTGTAGTTTCCTCTCGCCCTGG
+>TRINITY_DN409_c0_g1_i1 len=1479 path=[1668:0-164 1678:165-278 1664:279-302 1682:303-464 1676:465-509 1680:510-656 1648:657-680 1675:681-713 1658:714-737 1679:738-932 1661:933-956 1674:957-1085 1653:1086-1109 1654:1110-1478] [-1, 1668, 1678, 1664, 1682, 1676, 1680, 1648, 1675, 1658, 1679, 1661, 1674, 1653, 1654, -2]
+CCTGTATCACATGTATTAAAAATTAAAACCTAAACAATTATTTTTTCCGTAAGCAAACAT
+TGCCTAAGCTTATTTCTTAGCACCAGCCTTAACAGCGGCCTTGGTAACCTTAGCGGCACC
+AGGAGCAACCTTCTCGACAGCTTTGATGACACCGACAGCGACGGTTTGACGCATGTCACG
+GACAGCGAAACGACCAAGAGGAGCGTAGTCAGTGAAAGCTTCAACACACATAGGCTTGGA
+AGGAACCATCTTAGCAATGCAAGCATCACCAGACTTGACGAACTTGGGGGACTCCTCAAT
+CTTCTTACCGGAACGACGGTCAATCTTCTCAATGAGCTCAGCGAACTTGCAAGCAATGTG
+AGCAGTGTGGCAATCCAAAACAGGAGAGTAACCAGCAGAGATTTGACCGGGGTGGTTAAG
+AATGATGACTTGAGCGGTGAAGCTAGCACAACCCATGGGAGGATCATTCTTGGAGTCACC
+ACAGACATTACCACGGCGAATATCCTTGACGGAAACGTTCTTAACGTTGAAACCAACGTT
+GTCACCGGGAAGACCAGCGTCGAGAGACTCGTGGTGCATCTCAACAGACTTGACTTCGGT
+AGTGACACCAGCGGGAGCGAAGGTGACAATCATACCGGGCTTGATAACACCAGTCTCGAC
+ACGACCGACGGGAACTGTACCAATACCACCGATCTTGTAAACATCTTGAAGGGGAAGACG
+AAGAGGCTTGTCAGTGGGACGTGCAGGGGGCTCAATGGAGTCAATAGCCTCCAAAAGAGT
+CTTACCCTTGACGACACCAGCCTTGGTCTCCTTTTGCCAGCCTTGGTACCAGGGCATGTT
+GGTGGTGGGCTCAATCATGTTATCACCTTGGAAACCGGAGACAGGGACGAAAGGAACGGT
+CTTGGGGTTGAAACCGACCTTCTTGATGAAGTTAGAGGTCTCCTTAACGATTTCCTCGAA
+ACGAGCTTGGGACCAGCCAGTGGTGTCCATCTTGTTGACGGCAACAATAAGTTGCTTGAC
+ACCCAAGGTGTAAGCAAGCAAAGCGTGCTCACGGGTTTGACCATCCTTGGAGATACCAGC
+CTCGAACTCACCAGTACCACCACCAATAATAAGGATAGCACAGTCAGCTTGAGAAGTACC
+GGTAATCATGTTCTTGATGAAATCACGGTGACCGGGGGCATCAATGACAGTAACATTGTA
+CTTGGGAGTCTCGAACTTCCAAAGGGCAATGTCGATGGTGATACCACGTTCACGCTCGGC
+CTTGAGCTTGTCCAAAACCCAGGCGTACTTGAAGGAACCCTTACCCAACTCGGTGGCTTC
+CTTCTCGAATTTTTCAATGGTACGCTTGTCAATACCACCGCACTTGTAAATCAAGTGACC
+AGTGGTGGTAGACTTACCAGAATCGACGTGACCGATAACAACGACGTTAATATGTCCCTT
+TTCCTTTCCCATTTTTGTTTAATGTGAGTTCGATGAAAC
+>TRINITY_DN410_c0_g1_i1 len=1342 path=[1955:0-340 2013:341-420 2001:421-467 1947:468-477 2012:478-525 2007:526-705 2015:706-729 2016:730-730 2014:731-747 2010:748-795 2005:796-831 1998:832-924 1967:925-966 2004:967-1055 1975:1056-1064 1996:1065-1137 1978:1138-1146 1979:1147-1341] [-1, 1955, 2013, 2001, 1947, 2012, 2007, 2015, 2016, 2014, 2010, 2005, 1998, 1967, 2004, 1975, 1996, 1978, 1979, -2]
+GTAGAAAGGTCGTCAGCTATAGAGATCGCCCTAGGAGCGCAATCAAAATGATAACGTGGA
+ATAAAAGAGGAAAATCTCATACATGTCTATCATTATCGTAGCAAACCCCAGAAAAGGAAA
+AGGGGGAAAACAAGCATAAGAATAAAAAACCAAAAGTTCGCACATATGTAAGACCCCCCA
+AAACCGAACGCATGTTCAGTTGAATAGCTTGGAGTTTAACAACGGCTGATTAGAGAGATA
+TAGATTGACGACGGAATAAATCGAAAGAAGCAATCTAATCCTTGGAAGCAGTGTAGGCAA
+CCAAGTCAACAACACGGTGGGAGTAACCCCATTCGTTATCGTACCAAGAGACGAGCTTGA
+CGAATTGAGGAGAAAGTTGGATACCGGCAGAGGCATCGAAGATGGAGGAGTGGTTGTCAC
+CACAGAAGTCGGTGGAGACAACAGAGTCCTCGGTGTAACCCAACACACCCTTCATGGGAC
+CCTCAGAGGCAGCCTTGATAGCAGCCTTGATGTCCTCGTAGTTGGTAGGCTTGGCCAACT
+TGACGGTCAAGTCAACAACGGAAACATCGGGGGTAGGGACACGGAAAGCCATACCGGTAA
+GCTTACCGTTAAGAGCGGGAATAACCTTACCGACGGCCTTGGCGGCACCAGTGGAGGAGG
+GGATGATGTTGGCGCTGGCGCCACGACCACCACGCCAGTCCTTCTTAGAGGGACCGTCAA
+CGGTCTTTTGGGTGGCAGTGGTAGCGTGAACAGTGGTCATGAGACCCTCTTCAATACCGA
+AGGTGTCGTTGATGACCTTGGCAAGGGGAGCCAAACAGTTGGTGGTGCAAGAGGCGTTGG
+AGATAACCTTCTCGGAGGGGTTGAACTTCTCCAAGTTAACACCGACGACGAACATGGGAG
+CATCCTTGGAAGGAGCAGAGATGATGACACGCTTGGCACCACCCTTCAAGTGAGCAGAGG
+CAGTCTCCTTGGTAGTGAAGACACCAGTGGACTCAATAACGTACTCAGCACCAGAGGCAG
+ACCACTTGATGTTGGCGGGGTCACGCTCGTTGTGGACATCGATGGAGTGACCGTCGATGA
+CAAGCTTGCCACCCTTGGTCTCAACGGAGCCCTCAAAGCGACCGTGGGTAGAGTCGTACT
+TGAACATATATGCCATGTAGTCAAGATCGATGAAAGGATCGTTGACAGCGACAACTTGGA
+TCTTGCCAGTGAGGATGGCGTTACGGAGGACGATACGGCCAATACGACCGAAACCGTTGA
+TACCAACTTTAGGAATTGCCATTGTTATCTAATTAATTCGATTGCTATTTCTCAAAACCA
+AACAAGTACTATTGCTGATTTC
+>TRINITY_DN410_c0_g1_i2 len=1304 path=[1955:0-340 2013:341-420 2001:421-467 1947:468-477 2012:478-525 2007:526-705 2015:706-729 2016:730-730 2014:731-747 1999:748-795 1972:796-831 2009:832-924 1997:925-966 2003:967-1055 1964:1056-1064 1995:1065-1137 1940:1138-1146 1941:1147-1303] [-1, 1955, 2013, 2001, 1947, 2012, 2007, 2015, 2016, 2014, 1999, 1972, 2009, 1997, 2003, 1964, 1995, 1940, 1941, -2]
+GTAGAAAGGTCGTCAGCTATAGAGATCGCCCTAGGAGCGCAATCAAAATGATAACGTGGA
+ATAAAAGAGGAAAATCTCATACATGTCTATCATTATCGTAGCAAACCCCAGAAAAGGAAA
+AGGGGGAAAACAAGCATAAGAATAAAAAACCAAAAGTTCGCACATATGTAAGACCCCCCA
+AAACCGAACGCATGTTCAGTTGAATAGCTTGGAGTTTAACAACGGCTGATTAGAGAGATA
+TAGATTGACGACGGAATAAATCGAAAGAAGCAATCTAATCCTTGGAAGCAGTGTAGGCAA
+CCAAGTCAACAACACGGTGGGAGTAACCCCATTCGTTATCGTACCAAGAGACGAGCTTGA
+CGAATTGAGGAGAAAGTTGGATACCGGCAGAGGCATCGAAGATGGAGGAGTGGTTGTCAC
+CACAGAAGTCGGTGGAGACAACAGAGTCCTCGGTGTAACCCAACACACCCTTCATGGGAC
+CCTCAGAGGCAGCCTTGATAGCAGCCTTGATGTCCTCGTAGTTGGTAGGCTTGGCCAACT
+TGACGGTCAAGTCAACAACGGAAACATCGGGGGTAGGGACACGGAAAGCCATACCGGTAA
+GCTTACCGTTAAGAGCGGGAATAACCTTACCGACGGCCTTGGCGGCACCAGTGGAGGAGG
+GGATGATGTTGGCGCTGGCGCCACGACCACCACGCCAGTCCTTCTTAGAGGGACCGTCAA
+CGGTCTTTTGGGTGGCAGTGGTAGCGTGGACAGTGGTCATGAGACCCTCCTCGATACCGA
+AGGTGTCGTTGATGACCTTGGCAAGGGGAGCCAAACAGTTGGTGGTGCAAGAAGCGTTGG
+AGATAACCTTCTCAGAGGGGTTGAACTTCTCCTCGTTGACACCGACAACGTACATGGGGG
+CGTCCTTGGAAGGAGCAGAGATGATGACACGCTTGGCACCACCCTTCAAGTGAGCAGAGG
+CAGTCTCTTGAGTGGTGAAGACACCGGTGGACTCGATAACGTAGTCAGCACCAGAGGTAG
+ACCACTTGATGTCGGCGGGGTCACGCTCGTTGTGGACATCGATGGCATTGCCATCAATGA
+CGAGCTTACCATCCTTGATCTCGACGGAGCCATCGAAGCGACCGTGGGTAGAGTCGTACT
+TGAACATGTAGGCCATGTATTCAAGATCGATAAAAGGATCGTTGATAGCAACGACTTGGA
+TGGTCTTAGCGACCAAAGCGTTACGGAGGACAATACGTCCAATACGACCGAAACCGTTAA
+TACCAACCTTAGGAATTGCCATTTTGAATCAAGTGTAAATCAAT
+>TRINITY_DN411_c0_g1_i1 len=1363 path=[1738:0-55 1788:56-58 1783:59-104 1759:105-128 1787:129-241 1770:242-265 1782:266-362 1749:363-386 1750:387-387 1786:388-544 1765:545-568 1781:569-763 1744:764-787 1790:788-820 1736:821-844 1785:845-955 1791:956-979 1792:980-991 1778:992-1036 1789:1037-1198 1775:1199-1222 1784:1223-1246 1773:1247-1362] [-1, 1738, 1788, 1783, 1759, 1787, 1770, 1782, 1749, 1750, 1786, 1765, 1781, 1744, 1790, 1736, 1785, 1791, 1792, 1778, 1789, 1775, 1784, 1773, -2]
+GTTTCATCGAACTCACATTAAACAAAAATGGGAAAGGAAAAGGGACATATTAACGTCGTT
+GTTATCGGTCACGTCGATTCTGGTAAGTCTACCACCACTGGTCACTTGATTTACAAGTGC
+GGTGGTATTGACAAGCGTACCATTGAAAAATTCGAGAAGGAAGCCACCGAGTTGGGTAAG
+GGTTCCTTCAAGTACGCCTGGGTTTTGGACAAGCTCAAGGCCGAGCGTGAACGTGGTATC
+ACCATCGACATTGCCCTTTGGAAGTTCGAGACTCCCAAGTACAATGTTACTGTCATTGAT
+GCCCCCGGTCACCGTGATTTCATCAAGAACATGATTACCGGTACTTCTCAAGCTGACTGT
+GCTATCCTTATTATTGGTGGTGGTACTGGTGAGTTCGAGGCTGGTATCTCCAAGGATGGT
+CAAACCCGTGAGCACGCTTTGCTTGCTTACACCTTGGGTGTCAAGCAACTTATTGTTGCC
+GTCAACAAGATGGACACCACTGGCTGGTCCCAAGCTCGTTTCGAGGAAATCGTTAAGGAG
+ACCTCTAACTTCATCAAGAAGGTCGGTTTCAACCCCAAGACCGTTCCTTTCGTCCCTGTC
+TCCGGTTTCCAAGGTGATAACATGATTGAGCCCACCACCAACATGCCCTGGTACCAAGGC
+TGGCAAAAGGAGACCAAGGCTGGTGTCGTCAAGGGTAAGACTCTTTTGGAGGCTATTGAC
+TCCATTGAGCCCCCTGCACGTCCCACTGACAAGCCTCTTCGTCTTCCCCTTCAAGATGTT
+TACAAGATCGGTGGTATTGGTACAGTTCCCGTCGGTCGTGTTGAGACTGGTGTTATCAAG
+CCCGGTATGATTGTCACCTTCGCTCCCGCTGGTGTCACTACCGAAGTCAAGTCTGTTGAG
+ATGCACCACGAGTCTCTCGACGCTGGTCTTCCCGGTGACAACGTTGGTTTCAACGTTAAG
+AACGTTTCCGTCAAGGATATTCGCCGTGGTAACGTCTGTGGTGACTCCAAGAACGATCCT
+CCCATGGGTTGTGCTAGCTTCACCGCTCAAGTCATCATTCTTAACCACCCCGGTCAAATC
+TCTGCTGGTTACTCTCCTGTTTTGGATTGCCACACTGCTCACATTGCTTGCAAGTTCGCT
+GAGCTCATTGAGAAGATTGACCGTCGTTCCGGTAAGAAGATTGAGGAGTCCCCCAAGTTC
+GTCAAGTCTGGTGATGCTTGCATTGCTAAGATGGTTCCTTCCAAGCCTATGTGTGTTGAA
+GCTTTCACTGACTACGCTCCTCTTGGTCGTTTCGCTGTCCGTGACATGCGTCAAACCGTC
+GCTGTCGGTGTCATCAAGGCCGTTGAGAAGGTTGCCCCTGGAA
+>TRINITY_DN412_c0_g1_i1 len=213 path=[191:0-212] [-1, 191, -2]
+AATAACGATTGACAACTAAAGAGAGGAACAACGCAGATCCGCAGAGATACAAATTTCTTT
+GAGCGTAGAATTGGCTAGCCTTATATCCCGAACGAGCACTTTCGGTGGTGCTAGGAGCGG
+CAATAGCAAGATCATATTCTTTGGTCACACGAACAACACGGCGAACAGAGTCAGCAAACA
+GAATCAAGATGCAAATAATAGTAATCTTTAAAA
+>TRINITY_DN413_c0_g1_i1 len=1381 path=[1359:0-1380] [-1, 1359, -2]
+ATTGATTTACACTTGATTCAAAATGGCAATTCCTAAGGTTGGTATTAACGGTTTCGGTCG
+TATTGGACGTATTGTCCTCCGTAACGCTTTGGTCGCTAAGACCATCCAAGTCGTTGCTAT
+CAACGATCCTTTTATCGATCTTGAATACATGGCCTACATGTTCAAGTACGACTCTACCCA
+CGGTCGCTTCGATGGCTCCGTCGAGATCAAGGATGGTAAGCTCGTCATTGATGGCAATGC
+CATCGATGTCCACAACGAGCGTGACCCCGCCGACATCAAGTGGTCTACCTCTGGTGCTGA
+CTACGTTATCGAGTCCACCGGTGTCTTCACCACTCAAGAGACTGCCTCTGCTCACTTGAA
+GGGTGGTGCCAAGCGTGTCATCATCTCTGCTCCTTCCAAGGACGCCCCCATGTACGTTGT
+CGGTGTCAACGAGGAGAAGTTCAACCCCTCTGAGAAGGTTATCTCCAACGCTTCTTGCAC
+CACCAACTGTTTGGCTCCCCTTGCCAAGGTCATCAACGACACCTTCGGTATCGAGGAGGG
+TCTCATGACCACTGTCCACGCTACCACTGCCACCCAAAAGACCGTTGACGGTCCCTCCAA
+GAAGGACTGGCGTGGTGGTCGTGGCGCCAGCGCCAACATCATCCCCTCCTCCACTGGTGC
+CGCCAAGGCCGTCGGTAAGGTTATTCCCGCTCTTAACGGTAAGCTTACCGGTATGGCTTT
+CCGTGTCCCTACCCCCGATGTTTCCGTTGTTGACTTGACCGTCAAGTTGGCCAAGCCTAC
+CAACTACGAGGACATCAAGGCCGCCATCAAGGCTGCCTCTGAGGGCCCCATGAAGGGTGT
+GTTGGGTTACACCGAGGACGCTGTTGTCTCCACTGACTTCTGCGGTGACAACCACTCCTC
+CATCTTCGATGCCTCTGCCGGTATCCAACTTTCTCCTCAATTCGTCAAGCTCGTCTCTTG
+GTACGATAACGAATGGGGTTACTCCCGCCGTGTCGTTGACTTGGTTGCCTACACTGCCGC
+CAAGGACAACTAACTAGCTAATCATCCCGATGCTAAGAAACGTCGGGTGGGTGCTTAAAG
+GCAATGCAGGAAAGTCTTTTGGAGTTGTTTTCCCCGTTTTTTCTTTATGTTAGACAAAGG
+AGTCGTTGTCGTTTGCAGTGCGGGAGTTTTCTTTTTTAGATTTTCGCATTTTTTTTGTGG
+ACGCGCACTCTATGTGAATAAATAGATGGATGACTTTTTTACAAATTTCCTCTGTTCTTT
+GATACCCTCCTTCTCATTCATTGTTGCATATATTTTTTTTAATTTTGTTGCAGTGATGAG
+ATGGCTGAGCGTTTGTTTTTGAACTTATAAATACTTATAAATAAATTTTATGATTTTGAT
+T
+>TRINITY_DN414_c0_g1_i1 len=205 path=[183:0-204] [-1, 183, -2]
+ATTGGTGGTAAGCGTCATGGTAATCTCGGTTACTTTGTCGAACCTACTATTCTCTCCAAC
+GTTACCGAGGACATGGCTGTCGGTAAGGAGGAAATTTTTGGACCCGTTCTTGCCGTCATT
+AAATTCAAGACCATCGAGGAGGCCATCCGTCGCGGTAACAACAGTACATATGGTTTAGCT
+GCTGGTGTACACACTAACAATATTA
+>TRINITY_DN415_c0_g1_i1 len=333 path=[311:0-332] [-1, 311, -2]
+CCGCCGTCGTGTTGTTGCGAGAAAGGCAAACTAGCCACAGCGTCTCTTTGGTAAAGGGCA
+GGTGCTAGGGGCACCTGGAAACAAGATTACTTGCTCAACGCCGGCAAGTAGGAAAAACGC
+CTAGTTTTGAAAAGGGTTAGGCAATTTAGAGAGACATGACAGAGCAAGCGACAGCAATCA
+TGGCAATGACAAAGGCACCAGAGCTGAAGTTGGTGATAGAGGCAGCGCTAGATTGAGTGG
+CAGTAGAGCTGGTGGTGGTGTTGGTGCCGTTAGTACCGTTGGTGGTACCAGTGGAGTTGG
+TGGTGTTACCGTAAGGGGCGGTAGAGGTGGCGG
+>TRINITY_DN416_c0_g1_i1 len=625 path=[603:0-624] [-1, 603, -2]
+CAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCACAAGCCAGTTATCCCTGTGGTAACT
+TTTCTGGCACCTCTGTCCTCAAATTTCGAGGGAACAAAGGATCGATAGGCCACACTTTCA
+TGGTTTGTATTCACACTGAAAATCAAAATCAAGGGGACTTTTACCCTTTTATTCTACTCG
+AGATTTCTGTTCTCGATGAGTCCCCCTTAGGACACCTGCGTTATCTTTTTACAGATGTGC
+CGCCCCAGCCAAACTCCCCACCTGACAATGTCATCAACGCGGATCAGTTCGCGAAGAAAC
+TTTAACGCTAGAATATGGGAAATAAATCCCAATTCCGCTTCATTGATTAAGTAAAGAAAC
+GATAAAGGTAGTGGTATTTCACCGGCGTATGCCGAAACATACTCCCACTTATCCTACACC
+CTCTATGTCTCTTCACAATGTCAAACTAGAGTCAAGCTCAACAGGGTCTTCTTTCCCCGC
+TGATTTTGCCTGGCCCGTTCCCCAGGCTGTGGTTTCGCTAGATAGTAGATAGGGACAGTG
+GGAATCTCGTTAATCCATTCATGCGCGTCACTAGTTAGATGACGAGGCATTTGGCTACCT
+TAAGAGAGTCATAGTTACTCCCGCC
+>TRINITY_DN417_c0_g1_i1 len=1441 path=[1419:0-1440] [-1, 1419, -2]
+TAGTATTCTACAGTAAACATCGTTAATCATGGCCATTCAGAAAGTCTTTGCTCGTCAAAT
+CTACGACTCTCGTGGTAACCCCACTGTCGAGGTCGACCTCACCACCGAGACCGGTATCCA
+CCGTGCTATCGTCCCCTCTGGTGCCTCCACTGGTATATGGGAGGCTCTTGAGATGCGTGA
+TGGTGACAAGACCAAGTGGGGTGGTAAGGGTGTTTTGAAGGCTGTTGGCAATGTCAACAA
+CATCATTGCCCCTGCCGTCGTTAAGGCCAACCTTGACGTTACCGACCAAAAGGCCGCCGA
+CGAGTTCTTGCTTAAGCTCGACGGTACTGAGAACAAGTCCAAGTTGGGTGCTAACGCCAT
+CTTGGGTGTCTCCATGGCTATCTGCCGTGCCGGTGCTGCCCAAAAGAAGCTCCCTCTCTG
+GAAGTACATTGCCGAGAACTTTGGCACCAAGGGTCCCTATGTCCTCCCCGTTCCCTCTTT
+CAACGTCTTGAACGGTGGTTCCCACGCTGGTGGTGACTTGGCTTTCCAAGAATTCATGAT
+CCTCCCCACCGGTGCTCCCTCTTTCTCCGAGGCTATGCGTTGGGGTGCTGAGACCTACCA
+CACTCTCAAGTCCATTGCCAAGAAGCGTTATGGTTCTTCTGCCGGCAATGTCGGTGATGA
+GGGTGGTATTGCTCCCGATTTGCAAACCCCTCAAGAGGCTCTTGACCTTATTGTTGAGGC
+CATCAACAAGGCTGGTTACGAGGGTAAGATCAAGATTGGTCTTGATGTTGCCTCCTCCGA
+GTTCTACGTTGACGGCAAGTACGACCTTGACATCAAGGCCGCCAAGCCCAAGCCCGAGAA
+CAAGCTTACCTACCAACAACTTACCGACCTTTACGTCGAGCTCTCCAAGAAGTACCCCAT
+TGTCTCCATTGAGGACCCCTTCGACCAAGATGACTGGTCTGCCTGGACTCACATGAAGGC
+TGAGACCGACTTCCAAATTGTCGGTGACGATTTGACTGTTACCAACGTCAAGCGTCTTCG
+TACCGCCATCGACAAGAAGTGCGCTAACGCTCTTCTTTTGAAGGTCAACCAAATCGGTTC
+CGTCACCGAGTCTTTGAACGCCGTCCGCATGTCCTACGAGGCTGGTTGGGGTGTTATGGT
+TTCTCACCGTTCCGGTGAGACCGCTGACACCTTCATCTCCCACTTGACTGTTGGTATTGG
+TGCCGGTCAACTTAAGTCTGGTGCTCCTTGCCGTTCCGAGCGTTTGGCCAAGTACAACGA
+GCTTCTCCGTATCGAGGAGGAACTCGGTTCCGAGGGTGTTTACGCTGGTGCCCATGCTGG
+CAAGTACATCAAGGCTGCTAAGTTTTAAACTCTGAGCATACATTAAATTTTACTAATGTT
+TACAATACATGTTTATTTTTATAGAATGCAATGAAATTTTTATCCTTTTTGCGTTTTGGA
+G
+>TRINITY_DN418_c0_g1_i1 len=835 path=[813:0-834] [-1, 813, -2]
+TTTTTAGGAATAAAAAAATATTTATTTATTTATTTATTTTGAAAAATTGCTAGAGATCAC
+TTGCTCATCATTGGAGAATCGTAACAAGTGGTAGTCAAGATCATTAAAACACTGTCTGAC
+AGCTGGCCATAAATTGCTTGATGTGGAATTTAAATGCTCTTTTACTGTTTAGAAGACCGT
+GTTCAATTCATTATCAAAATTCATCAATCCAATGGCAAGCGGATCATTAATTGCATATGT
+TATGATTGATTGTTAAATCAAACAATAATATATGCTCACAATCCAACAAGATTGGTCTCA
+TAACCATTTCGAAACTATCATATTAAAATCGGAAGAGACGATTTTACTTAATAGCAATTT
+GTTTCTTAGTTTGGGACTTCTCGACCTTGGGCAAGGTGACAGTCAATAGGCCATTACTGA
+AGTTGGCCTCAATGCGATCTGCATCAATCTTGGCTGGAATAGTAATGGTACGAGAGAATG
+AGCCAAAGCGACGCTCTGACCAGCGTTGGTTACCCTCGGTGCTTTCATTCTTTCTCTCAT
+TGACGACTTCGCCAGAAATAGTAAGTTTTCCGCTATCATAATGGACTTGAACGTCCTCTT
+TCTTAACACCAGGGAGTTCTACATCAACGCTAACAGTGTCTTTACCCTCATGCACATCAA
+TCGAAGGAGACAACTCCCCAGGAATTTGGTTGTTCAAACGAGGGGAGTAACTAACAAAGT
+CAGAGAACAAGTCGTTGACAGTAGGGGGAAAGCCGAAAAAAGGTTGCAAAGACATTTTTT
+AAAATTTAAACAATTGCGAGTAACTTGAAATTATATGAATTCAATTCAAATCTGT
+>TRINITY_DN419_c0_g1_i1 len=286 path=[264:0-285] [-1, 264, -2]
+TTTTCATGATTGATCGTTGCGGTTTGCTTTTGGAGAGACATGCTAAGATTGCTACTGATG
+GACAAAAGCCATTTTTGAAGAAGGACTCTGACTTTAAGGAAGTCCCTTCTGGAGACATTA
+ATTTAGAGAGTGCTATTGCACTCGTCAAGCCCACCATTCTTTTGGGATGTTCCGGTCAAC
+CGGGTAAATTTACAGAGAAAGCCATTCGTGAAATGAGCAAGCACGTCGAGCGCCCCATCA
+TTTTCCCAATCTCTAATCCCACTACTCTTATGGAAGCGAAGCCCGG
+>TRINITY_DN420_c0_g1_i1 len=418 path=[396:0-417] [-1, 396, -2]
+AAAAACTCCAAGCATAAAAAGATGTCTACAGTCAAGGTCAACGGAGCTAAGAACGGCGGA
+GAACGTATGGTGTTGCCTGCCGGCGAGGCCGCCGCTAAATACTATCCTGCCTACCGTGAA
+AACGTCCCCAAGAAGGCTCGTAAGGCTGTACGCCCTACCAAGCTCCGTGCTTCTTTAGCA
+CCCGGAACTGTTTGCATTTTGTTGGCTGGACGCTTCCGTGGTAAGCGTGTTGTTGTCCTC
+AGTCAATTGGAGGACACTCTTGTCGTTACTGGCCCTTACAAGGTCAACGGTGTCCCTATC
+CGTCGTGTCAACCACCGTTATGTGATTGCTACCTCTGCCCCCAAGATCGATGTCTCCGGT
+GTCTCTGTTGAGAAGTTCACCAAGGCTTACTTTGCCAAGCAAAAGCGTAGCGGACCCG
+>TRINITY_DN421_c0_g1_i1 len=368 path=[346:0-367] [-1, 346, -2]
+ACTCTGGTGATGGTGTTACCCACACTGTTCCCATTTATGAGGGTTATGCTCTTCCTCATG
+CTATCATGCGTCTTGATCTCGCCGGTCGTGACTTGACTGACTACCTTATGAAGATTCTCA
+TGGAGCGTGGTTATACTTTCTCTACTACCGCCGAACGTGAAATTGTTCGTGACATCAAGG
+AGAAACTTTGCTACGTCGCTTTGGACTTTGAGCAAGAACTTCAAACTGCTGCTCAATCTT
+CCTCCCTTGAGAAATCTTATGAGCTTCCTGATGGTCAAGTTATCACTATCGGAAACGAGC
+GTTTCCGTGCCCCTGAAGCTCTTTTCCAACCCTCAGCTTTGGGTCTTGAAAACGCCGGTA
+TTCATGAG
+>TRINITY_DN422_c0_g1_i1 len=281 path=[259:0-280] [-1, 259, -2]
+GTCTGCACTGCATTTTTGAGTGGTTAGTGTTTGTTGCCCTACCTCTTTTCACATACTCCT
+TTTCTCCATTTTATATAATATATATATATATACATTTTTTTAATTCTTTAAATTCTCTAC
+ACAATGTCTGGATATGGTCAACAAGGTGTTTCTGCTGCCAACATCGACAGCATCCGCCCC
+AAGAAACGTTTGTCAATTGGTGTAGTTGGCTCCGGTAACTGGGGTACTGCCATTGCCAAG
+ATTTGCGGTGAAAATGCCCGTGCCCACGGTCACCATTTCAG
+>TRINITY_DN423_c0_g1_i1 len=1016 path=[994:0-1015] [-1, 994, -2]
+CTCAACCTATTCTCAAACTTTAAATATGTAAGACGCCCTTGTCGCTTAATTGGACGTGGG
+CCATCGAATGAGAGTTTCTAGTGGGCCATTTTTGGTAAGCAGAACTGGCGATGCGGGATG
+AACCGAACGTGAGGTTAAGGTGCCGGAATGTACGCTCATCAGACACCAGAAAAGGTGTTA
+GTTCATCTAGACAGCAGGACGGTGGCCATGGAAGTCGGAATCCGCTAAGGAGTGTGTAAC
+AACTCACCTGCCGAATGAACTAGCCCTGAAAATGGATGGCGCTTAAGCGTACTACCCATA
+CCTCACCGTCTGGGTTAGCTTTGAGAAGCTCAGACGAGTAGGCAGGCGTGGAGGTTTGTG
+ACGAAGCCTTGGGCGTGAGCCTGGGTCGAACAGCCTCTAGTGCAGATCTTGGTGGAAGTA
+GCAAATATTCAAATGAGAACTTTGAAGACTGAAGTGGGGAAAGGTTCCATGTGAACAGCA
+GTTGGACATGGGTTAGTCGATCCTAAGAGATAGGGAAGCTCCGTATGAAAGTTGCACGAT
+TTTTCGTGCCTCCTATCGAAAGGGAATCCGGTTAATATTCCGGAACCAGAAGGTGGAATC
+AACACGGCAACGTAAATGAAGTTGGAGACGTCGGCGGGAGCCCTGGGAAGAGTTCTCTTT
+TCTTTTTAACAAACCATTGAACTACCCTGAAATCGGTTTATCCGGAGCTAGGGTATGGTG
+TTTGGAAGAGTTCAGCGCCTCATGCTGAATCCGGTGCGCTCTCGACGGCCCTTGAAAATC
+CAACGGAAGAATGGACCTTCGGGTCCTTGTTTTCACATCTGGTCGTACTCATAACCGCAG
+CAGGTCTCCAAGGTGAACAGCCTCTAGTTGATAGAACAATGTAGATAAGGGAAGTCGGCA
+AAATGGATCCGTAACTTCGGGATAAGGATTGGCTCTAAGGGTTGGGTACGTTGGGCCTTG
+GAACCTGAACGGTTGCTGGACTGAGCGTGGACCGATGTCTTTTCTCGCCTTTCGGG
+>TRINITY_DN424_c0_g1_i1 len=207 path=[185:0-206] [-1, 185, -2]
+AACAAGACCAGAGGCGCTGTTTCCTCTGCTGGTTACAGCGGTGAGGGATATGGCAAAGGT
+ACCTATGCTACTGATACCACTGCTGAAGCTAATCGCCGTGCCGCAACTGGTACCCGTAAT
+GCTCGTACAACTGCACAAAGAAATGCACAGTTGGCCGAGGATGAGCATGTCAGTATGGGT
+GACAAAATGAAGGGTAATATGGAGAAA
+>TRINITY_DN425_c0_g1_i1 len=233 path=[211:0-232] [-1, 211, -2]
+CTGGTACTCACAAAGAGTTAGCTCCTTACGACCCCGATTGGTATTATGTCCGCGCTGCTG
+CCATTGCCCGCCACATCTATCTCCGCAAGCAAGTTGGTGTTGGCCGTCTTTGCAAGGTCT
+ATGGTGGTTCCGTTAACCGTGGCATGCGCCCTTCTCATCACCGTGATGGTTCTGGCAGTG
+TACAACGCAAAGTTGTTCAAAGCTTGGAGAAAATCGGTGTTCTTGAAAAGTCC
+>TRINITY_DN426_c0_g1_i1 len=233 path=[211:0-232] [-1, 211, -2]
+TTCAGTAATGAAATGGAAAATATGAGGTGTTAACGATTGTATAAAATAATTTTATATCAA
+CCAAAGTAAACAACGTCGTCAAAAAGTTATGGGCGAAACCAAACTATAAGTAAAAGAGCA
+CCTAATACGAAAAGATTAGATGGTCAGAAAAGGACCGGGGTAAATAAACAATGGCCTCTT
+ATTATTCTTAAGAAGAGGGGGATGCAGTTTTTATAAAATGTGATAAAAACCGA
+>TRINITY_DN427_c0_g1_i1 len=689 path=[667:0-688] [-1, 667, -2]
+ATTCCATTGTCTTGACTATCACAAACTTTTAAGTCTTTTCTTTTTTCTAACCACATAATG
+ACTATTCCTGACAAGCAGTTGGCTGCCGTTTTCCATACCCACGGTGGTCCCGAGAACGTC
+AAGTTCGAGGAAGTCCCCGTCGCCGAGCCCGGTCAAGACGAGGTCTTGGTTAACATCAAG
+TACACCGGTGTCTGCCACACCGATTTACACGCTCTTCAAGGTGACTGGCCTCTTCCCGCC
+AAGATGCCTTTGATCGGTGGTCACGAAGGTGCTGGTGTCGTCGTCAAGGTCGGTGCCGGT
+GTCACTCGTCTTAAGATTGGTGACCGTGTTGGTGTCAAGTGGATGAACTCTTCTTGCGGT
+AACTGCGAGTACTGTATGAAGGCTGAGGAGACCATCTGCCCTCACATTCAACTTTCCGGT
+TACACCGTTGACGGTACTTTCCAACACTACTGCATTGCCAATGCCACCCATGCTACCATC
+ATCCCCGAGTCCGTTCCCCTCGAGGTTGCTGCTCCCATCATGTGCGCTGGTATCACTTGC
+TATCGTGCCTTGAAGGAATCCAAGGTCGGCCCTGGTGAGTGGATCTGCATTCCCGGTGCC
+GGTGGTGGTCTTGGCCATCTTGCCGTCCAATACGCCAAGGCTATGGCTATGCGTGTTGTT
+GCCATTGATACTGGTGATGACAAGGCTGG
+>TRINITY_DN428_c0_g1_i1 len=356 path=[334:0-355] [-1, 334, -2]
+CATTGGCACCAGTGGTGTCAGGACCGAAACACCAAATCTTACGAGCATCAGTGACATCCC
+ATCCAAACTCGTCAGCCATGATACGAGCACGAACCTTGAAATCATCACGAGGATTGACGT
+GACCAGTCTCAATGGCGACAGAGAGTTCTTCACTCATGGGCTCAGCAGTCATGAAGATAC
+GGTTGTGCTTGTTGGGAGACTTAGAGAGAGCAGTCATGCTAGAGGGCTCGCTAACGGACT
+CACGGTAAGAAACGACGGGAGGAGAAATCTTAAGAGGGATACCAGCATGGTCTTCTTGCA
+AATCCTTCAAGCAAATCTCCAAGTGGAGCTCACCAGCACCAGCAACAATGTGTTCA
+>TRINITY_DN429_c0_g1_i1 len=286 path=[264:0-285] [-1, 264, -2]
+CTTGAAGGGTAAAGTGGTCCTTGTTGTCAATACAGCGAGCAAATGTGGATTCACTCCTCA
+ATACAAAGGTCTTGAGGCGTTGTATCAGAAATACAAGGATAGAGGATTTATCATCCTTGG
+ATTCCCTTGCAATCAATTTGGAAACCAAGAACCCGGTTCTGACGAAGAAATCGCTCAATT
+TTGCCAAAAGAACTATGGCGTAACCTTCCCTGTACTGGCCAAGATCAATGTTAATGGCGA
+CAACGTCGACCCTGTTTATCAATTCTTGAAGAGCCAAAAGAAGCAA
+>TRINITY_DN430_c0_g1_i1 len=268 path=[246:0-267] [-1, 246, -2]
+AAAACGCCGGTATTCATGAGGCTACTTACAACTCTATCATGAAATGTGATGTTGATATTC
+GTAAAGATTTGTACGGTAACGTTGTTATGTCTGGTGGTACCACTATGTATCCCGGTATTG
+CCGATCGTATGCAAAAGGAGATTCAAGCCCTTGCTCCTAGCTCCATGAAGGTCAAGATTG
+TTGCTCCTCCTGAGCGTAAATACTCTGTCTGGATTGGTGGATCCATTCTTGCTTCTCTTT
+CTACTTTCCAACAGATGTGGATCTCCAA
+>TRINITY_DN431_c0_g1_i1 len=239 path=[217:0-238] [-1, 217, -2]
+AGCGTTCTCGGCGAAGAAAGCTTCATCCTTCTTGACGGGTCCGCTACGCTTTTGCTTGGC
+AAAGTAAGCCTTGGTGAACTTCTCAACAGAGACACCGGAGACATCGATCTTGGGGGCAGA
+GGTAGCAATCACATAACGGTGGTTGACACGACGGATAGGGACACCGTTGACCTTGTAAGG
+GCCAGTAACGACAAGAGTGTCCTCCAATTGACTGAGGACAACAACACGCTTACCACGGA
+>TRINITY_DN432_c0_g1_i1 len=1179 path=[1157:0-1178] [-1, 1157, -2]
+ACAAAAAAATATAATTTTAATGAAGCCCACCGTCTATTCAATCATTTCCATCTTTCAAAA
+ACCACAAATTTAGAGAGTGTTGACAGTGTAGAAGTCCTCAAGAGCGGTAAGAACACGCTT
+GGTCATGGTCTTCTCACCCTCATGGATCCAGACACGAGGGTCGAACTTCTTCTTGTTGGG
+CTTGTCAGCTCCCTCGGGGTTACCGACGGGGGTCATAAGGTAGTCCTTGTACTTCAAGAC
+ATAGTCACGGACACCCTCGACGTAGGCGAATTGGGTATCAGTGTCAATGTTGACCTTGAC
+GACACCGCACTTGATACCAGTACGGAACTCGTTGACAGAGGAACCGGAACCACCGTGGAA
+GACGAAGAAAACGGGCTTGTCGTTGGTGGTCTTGAGTTGCTCCTTAACATAGGCTTGGTG
+TTGACCCAAAAGAGCGGGTTGGAGCTTGACGTTACCGGGCTTGTAGACACCGTGGACGTT
+ACCGAAAGCGGCGGCAATGGAGAAGTAAGGGGTAACGGAGGAGAGCTCACGGTAGACATC
+CCAGATGTCCTCGGGTTGAGTGTAGAGCTCGGTGTGGGAGACGTGAGAGTTGTCGACACC
+GTCTTCCTCACCACCAGTGATACCGATCTCCATCTCGATCCAGATCTTCATGGGAACGGC
+ACGCTTGCAGTACTCCTTAACTTGAGCAATGTTCTCCTTCTTGGGCTCCTCGGACAAGTC
+AAGCATGTGAGAAGAGAAAAGAGGCTCACCGTGAATCTTGAAGTAGGCCTCATCGGCTTC
+GAACATACCGTCCATCCAGGGGAGAAGCTTCTTGGCGCAGTGGTCAGAGTGCATGACGAC
+GGGGACACCGAAGAAAGGAGCGATGGAACGGATGTAGTGGGCAGCGGCGATGGAACCGGC
+AATGGAGGCCTTTTGGCCCTCGTTGGAGGATTCCTTACCAGCAAAGAAGTGAGCACCACC
+GTTGGAGGTTTGCAAGATGATGGGGGAACGAGCCTCACGAGCAGCCTCAAGAGCAGCAAT
+AGCAGTGGAGGAGGAGGTGACGTTAATGGCAGGGATGGCGAATCCGTGCTCACGAGCGTA
+GGTGAACAACTTTAAAACGTTGTCACCTGTAATAACACCAGTAGGTACAATATCGAGAAT
+TCCCATTTTGCTAATTTGTGTGTGTGTTCTATACGACCT
+>TRINITY_DN433_c0_g1_i1 len=256 path=[234:0-255] [-1, 234, -2]
+GGCCGGCGCTCTCTTGGCGCGCGGTATCATCGGTGCTAAGGCCGATCCAGTTAACTTTGC
+TGGTATTGGCGGTGCCGCTTACGAATACAACTACACTGCTACTGGTTCCTTTAATCAATC
+TATCATGCCTGCTAACTTTACTCCTGCTGGCGGCATCGATACTAATGATAGCAGCCCTAC
+TTATCACCCTTTCAGTGACTTTGACTACCAGTCCTTGTCTCTCGCTCTATACCACGAGTA
+CATCGAGTACGACCTC
+>TRINITY_DN434_c0_g1_i1 len=203 path=[181:0-202] [-1, 181, -2]
+CTATGATGCTGAGCACGTTGCCGCCGTTCGCAAAGATCTTGAGAAGGCCAACCTTCCTCC
+TCGTATCATGATCGATTGCTCTCATGGCAACTCAAGCAAGAATCATTTGAACCAACCAAA
+GGTCTCCAAGAGCATCGCCGAACAAATCAGAAATGGCGACTCTTCCATTGTTGGTGTTAT
+GATTGAATCTCATATCAATGAAG
+>TRINITY_DN435_c0_g1_i1 len=207 path=[185:0-206] [-1, 185, -2]
+GTGATTTTCAAGATCTTGGTGGGAAGACGAACAGGACCCTTAACACGCAATTGCTTGTCC
+TTGGCACGGTTGACCAAGTCAGAGCAAACCTTCTCCAAGTTACGAACGTTACGAGAAGTA
+AGGGTAATGCGAATGCGGTGAACAGTAGAGGGAATTTGTTGTTCCTTTTGATCTTTGGCG
+ACTTGACTCATTTTGTAGACAGCGGTG
+>TRINITY_DN436_c0_g1_i1 len=378 path=[356:0-377] [-1, 356, -2]
+TCGCTCCTCTTCGTCATTGCCAACAACGACATTGTAGTAACGCAACTCGTAGACACCCTT
+CTTGGTGGAAACGACACGAAGCCAGTCACGGAGAGAGTGCTTCTTCAAGAATTTCTTAGT
+CAAATACTTCAAGTAACGGCCAGAGAAATCAATGTGAGCAATAACAGCAATCTTGCTGGA
+ACCTTCACGGGAAACGACGACAGAAGAGCCCAAGTTACCAGTCTTGCCATCAACCTTGAT
+ACGGTCAATCAAGTACTTCTCAAAGGCAGCGACATCGAAAATTTTGTCGTTGACAGCGGC
+AGTAGCGTCAATAATGTATTTGTTGCTAACCTTAGTGTTCTTTTTAACCATGATGACTTT
+TGTCTCTCTACGAGTATG
+>TRINITY_DN437_c0_g1_i1 len=329 path=[307:0-328] [-1, 307, -2]
+TCCAACGACTCCTCCAAAGACCTTTACGACACTTTCTTTCTCCTACTCTTGCTCTTCGCT
+CCAACTTCTCCAGTGTCCATGCGGTCGTCTATTGTGTTTAGAACGTGATGTTAACCGTTC
+CGATTTCGAATATTCATCAAATCCTCTTTCCATCATTTCCACTACTTTCGATAAAAAAAG
+ATAATGTTCAATAAAAAACAGAAAAAGCTACTCGACTATATCAAAAACACGAAACAATTA
+AAAACACTTTCTAAACACGCACACAAACACAGATACAAACGAAAAATAATTTGAAAGAGG
+AGAAAGGGGAAAAACAAAAATAAAAAATA
+>TRINITY_DN438_c0_g1_i1 len=393 path=[371:0-392] [-1, 371, -2]
+GCAAGTGATACCAGCGCACATGATGGGAGCAGCAACCTCGAGGGGAACGGACTCGGGGAT
+GATGGTAGCATGGGTGGCATTGGCAATGCAGTAGTGTTGGAAAGTACCGTCAACGGTGTA
+ACCGGAAAGTTGAATGTGAGGGCAGATGGTCTCCTCAGCCTTCATACAGTACTCGCAGTT
+ACCGCAAGAAGAGTTCATCCACTTGACACCAACACGGTCACCAATCTTAAGACGAGTGAC
+ACCGGCACCGACCTTGACGACGACACCAGCACCTTCGTGACCACCGATCAAAGGCATCTT
+GGCGGGAAGAGGCCAGTCACCTTGAAGAGCGTGTAAATCGGTGTGGCAGACACCGGTGTA
+CTTGATGTTAACCAAGACCTCGTCTTGACCGGG
+>TRINITY_DN439_c0_g1_i1 len=223 path=[201:0-222] [-1, 201, -2]
+GGGTGCCGGGTTCGGTATTGCTGGATTAACCGCCTGGGAGGTATTGGTCCGACAAATGAA
+GGTAAAGCCAGGTACCAAATTGGTTATCGAGGGAGCTAGTGGAGGTGTTGGTACGTTTGC
+AGTTGCGTTAGCTAAAGCTTTGGAATGTGAAGTCACTACGATTTCCTCAACCGAGAACTT
+GGATCTCTGTAAATCTTTGGGTGCCACTCATACACTCGACTAT
+>TRINITY_DN440_c0_g1_i1 len=366 path=[344:0-365] [-1, 344, -2]
+AATTGGTGCTCTTCAAGAAGCTGTCGAGGCTTATCTTGTCTCTCTCTTCGAAGATACCAA
+TCTTTGCGCTATCCATGGCAAGCGTGTTACCATTCAACCCAAGGATATGCAATTGGCTCG
+TCGTCTTCGCGGTGAACGCTCATAAGCAACTTTACCAAATTGTGGTTGCCATCTGATGGT
+GTGATTTGGAATCTTTTGGTCGTCTATCCCATTGTAATCCTTCCCTCATTTACTTTGCCT
+TTCGAAACAAAATTTAACCTTGAGTGTTGTGGAATGTAACAAACGATATGCAAGTCTAAT
+TTTTTGTTTCCGTGAGCTGCACTATCTATTTATATTTTTGTTTTCTTTTTTCGAGTTATA
+CCGCGG
+>TRINITY_DN441_c0_g1_i1 len=660 path=[638:0-659] [-1, 638, -2]
+CAAAAATAAGAATTGTTTGTTTGTATTTGGATAATTCTATAGTTTGTTCTCTCTTTTCAC
+AAGACTATTAAATTTTATTTTTTTGCATTGTCCAACCGTCTATTAATATATTTATCAATA
+CTTCCAAAATGTCTAGCTCTAAGGCCAACCAAACCCGTGTTTGTTACCAACCTGAGGATA
+CTACCTTTATTATCATCGCCTCAAACGGTCCCGATGTCATGAGATGGCGCAAGGACAAGA
+CTGTTCCCTTAACTGAGATCGTCGACTCTTTTCAAGTTTTTACAACTAGCAACAACAAAG
+GTAACGAAGGTCAATTAATTACTGCTTCCAAACAAGAACTTGAGAATACCTTTGGTACTA
+GCAAGGACGTTGATGTTGTCACTAAAATTTTGACTGACGGAAAAATCATTCCCCATCGTG
+AACATGGCAAGCACAAAGAAGTCAACTAAATGACTAATTCTACTAGTTGAGGCTAGTTAT
+ACCACCGACTTTAATGAGTTAAAACATATGGCCCACGTATATCTATTATAGGTATTCCCA
+TTTGTGTTATATAATGATGCAATCTGACGAAGTACACAATGTCCGCATTCCAACATTACC
+TGAACTTCATGGCAATTTTTGGAATCCTTTCCCGTTCCTTTGGTAATTATTCGACTTTAA
+>TRINITY_DN442_c0_g1_i1 len=341 path=[319:0-340] [-1, 319, -2]
+AAAAATTCCTATAATAATATAACTCGATATGGCTGATTATCCTTTTACTGACAAAGCCGC
+AAAGACATTGTCTGATGCGTACTCAATTGCACAATCTTATGGTCATTCACAATTAACCCC
+TATTCACATTGCTGCTGCTCTTTTGTCCGACAGTGACAGTAACGGTACTACCTTACTGCG
+CACCATCGTCGACAAAGCTGGTGGTGATGGTCAAAAGTTTGAGCGAAGTGTTACTAGTCG
+GTTAGTTCGCTTGCCTGCTCAGGATCCACCTCCAGAACAAGTGACTCTGTCACCTGAAAG
+TGCGAAACTGCTGCGAAATGCTCATGAACTTCAAAAAACAC
+>TRINITY_DN443_c0_g1_i1 len=354 path=[332:0-353] [-1, 332, -2]
+CAGGGTTAATAGACTTGCAGGGCTCCTTTCCATTGAAGAAGTCGGAAACAAGCTTTTGAA
+TACGAGGAATACGAGTAGAACCACCTACCAAGACGATTTCGTTAACAGAGGACTTGTCGA
+TCTTGGAGTCGCGGAGGACCTTCTCCACAGGCTCCATGGTGTTACGGAAGAGATCGGCAC
+AAAGCTCTTCAAATCGAGCACGAGTAATGGAGGTGTAGAAATCAATACCTTCATACAAAG
+AATCAATTTCAATGCTGGCTTGAGCAGAAGAAGAAAGAGTACGCTTGGCACGCTCGCAAG
+CAGTACGTAGTCGACGAACAGCACGAGCGTTGCCAGTGGTGTCCTACTTGTACT
+>TRINITY_DN444_c0_g1_i1 len=266 path=[244:0-265] [-1, 244, -2]
+GAATTGCGCACCTGGCTGCATGATGTAGGTGTTCCCATTTCTTCCCATGAAAGTACTCGT
+TCTCACTTGCTTAGAAAGCTGAAGAACTATATTTCTACTAAAGCTGACGAAGCCCAACCT
+TCTGTTGAAGCTGTAAAGGGCAAGGCTTCCGAGAAGGCAAAGCAAGCTGGAGAATTTGTT
+TCTGACAAAGCTGGCGATGCTAAAGAATTGGTTAACGAGAAATCTAGTGAAGCTGGTCAA
+TATGCAGGACAAAAGATGGAAGAAGG
+>TRINITY_DN445_c0_g1_i1 len=549 path=[527:0-548] [-1, 527, -2]
+TTTATCTCTACCCTTCCCACCGGCGCTGAAACTGGTGACTTCTTGGCCCTTGACTTTGGT
+GGTACCAACTTGCGTGTTTGTTGGATCCAACTTCTCGGTGACGGCAAGTATGAGATGAAG
+CACAGCAAGTCCGTCTTGCCCCGTGAATGCGTTCGTAACGAGTCTGTTAAGCCCATCATT
+GACTTTATGAGTGACCATGTTGAGCTTTTCATCAAGGAGCACTTCCCTTCCAAGTTTGGC
+TGCCCTGAGGAGGAATACCTTCCTATGGGTTTCACCTTTTCTTATCCCGCCAACCAAGTT
+TCCATCACCGAGAGCTACTTGCTTCGTTGGACCAAGGGTCTTAACATTCCTGAGGCCATC
+AACAAGGACTTTGCCCAATTTTTGACTGAAGGTTTCAAGGCTCGTAACCTTCCTATTAGA
+ATCGAGGCTGTCATCAACGATACCGTCGGTACTCTCGTTACCCGTGCTTATACTTCAAAG
+GAGAGCGACACCTTTATGGGTATCATTTTCGGAACCGGTACCAACGGTGCTTACGTCGAG
+CAAATGAAC
+>TRINITY_DN446_c0_g1_i1 len=473 path=[451:0-472] [-1, 451, -2]
+TTTCCCGTAAGGAATGGTACGACATTAAAGCTCCCGCCTTCTTCGAAGTTAAGAACGTTG
+GAAAGACTCTTGTCAACCGCACAGCCGGTCTAAAGAATGCCAATGACTCCCTCAAGGGAC
+GTATCTTGGAGGTTTCCCTTGCTGACTTGCAAAAGGATGAGGAGCACGCATTCCGCAAGG
+TTAAGCTTCGTGTCGAAGATATCCAAGGCAAGTCTTGCCTTACCAGCTTCAATGGTTTAA
+GCATCACTTCTGACAAGTTGCGCTCTCTTGTCCGCAAATGGCAAACAACCATCGAGGCTG
+ATCAAACTATCAAGACTACTGATGGTTATCTTTGCCGTGTCTTTGTCATTGGCTTCACAC
+GTCGTCGTGCTAACCAAGTTAAGAAGACTACTTATGCTCAATCTTCTCAAATCCGTGCCA
+TCCGCCAGAAGATGTTCCAAGTTATCCAAAACCAAACTTCTTCTTGCTCCATG
+>TRINITY_DN447_c0_g1_i1 len=239 path=[217:0-238] [-1, 217, -2]
+AAAATAAATTATGACCAAACAAGGACCTGGGGAAAAGAGTAGTAAAAAAGAGTCGACAAA
+CGAAGGAAGAATATCATAAACCCATTATCGTTTGTCAGTAACGATTGTTTCTGGGATCAT
+CAATCCATCCAAAAAGGAAAAAGTCACGAAAAAGCCCAAATGGGATTACGATAAGCTTTC
+AAGAAATTTCTTTTTTATTTTCGCTTGACACTGCAATTTCCCTCTCCACGACGACAAAT
+>TRINITY_DN448_c0_g1_i1 len=252 path=[230:0-251] [-1, 230, -2]
+CGCTTACCGTCAAATGTCTCTTCTATTACGTCGTCCTCCTGGTCGTGAGGCTTACCCTGG
+TGATGTTTTCTACCTTCATTCCCGTCTTTTGGAACGTGCTGCCAAGATGTCTCCTAAACA
+CGGTGGTGGTTCTTTAACCGCCTTACCCGTTATCGAAACTCAAGGTGGTGATGTCTCAGC
+TTATATTCCCACTAACGTTATTTCTATTACTGATGGCCAAATTTTCTTGGAATCTGAACT
+TTTCTTTAAGGG
+>TRINITY_DN449_c0_g1_i1 len=209 path=[187:0-208] [-1, 187, -2]
+CCTCAGGCTTTGTCCATTCAGATTTTGGCAAAATTTTATTCTCAATGCTAAGTTGCATGG
+CACGGCGAATACGATAGACTCGATCGTAGGATTCCATCTTAGGCAAACGAGATAACGCCT
+TTTGAGTATCGTCATTCTCCTCCAACATCAAATCGTCGTATCGAAGACCATATTTACGGT
+ATCCTGACAAATACACATAGGCATTGGAG
+>TRINITY_DN450_c0_g1_i1 len=529 path=[507:0-528] [-1, 507, -2]
+GGCCGGGAAGTCCTTGGTCGGGCTTTTCTCCTTCTCGGGGATTATGCTCTTACTGGCGTA
+CGTTTAACAACCAACTTAGAACTGGTACGGACAAGGGGAATCTGACTGTCTAATTAAAAC
+ATAGCATTGCGATGGCCAGAAAGTGGTGTTGACGCAATGTGATTTCTGCCCAGTGCTCTG
+AATGTCAAAGTGAAGAAATTCAACCAAGCGCGGGTAAACGGCGGGAGTAACTATGACTCT
+CTTAAGGTAGCCAAATGCCTCGTCATCTAACTAGTGACGCGCATGAATGGATTAACGAGA
+TTCCCACTGTCCCTATCTACTATCTAGCGAAACCACAGCCTGGGGAACGGGCCAGGCAAA
+ATCAGCGGGGAAAGAAGACCCTGTTGAGCTTGACTCTAGTTTGACATTGTGAAGAGACAT
+AGAGGGTGTAGGATAAGTGGGAGTATGTTTCGGCATACGCCGGTGAAATACCACTACCTT
+TATCGTTTCTTTACTTAATCAATGAAGCGGAATTGGGATTTATTTCCCA
+>TRINITY_DN451_c0_g1_i1 len=238 path=[216:0-237] [-1, 216, -2]
+GCGGACGGAAACAGCCTTCTTAATAAGATTGTAGAGATCCTCGGGGAGCTCGGGAGCAAG
+ACCATTAGCCTTCAAGATACGCATGATCTTTTGACCAGTGATGAAACGAACTTGAGGAAT
+TCCATGAGAGTCACGGAGAGTCACACCAATTTGAGAAGGGGACATACCCTTCTTGGAGAA
+CTTAAGAATTTGCTCGACAACGGAGTCGGCATCAGCCTTGCACCAAGCAGGGGGAGAG
+>TRINITY_DN452_c0_g1_i1 len=318 path=[296:0-317] [-1, 296, -2]
+GTCATAATATTCAGTGTAGTCGGGAACATTTTCCTTAAGACCCTTACGCTTACGAGCTTC
+GCAAACAATTTGACCAGGTTTAGAAGTAGGATCCAATGGATCACCAGACATGGGAGACCA
+ATGGTCAAATACCAATTGAGGGAAAGCTTGACCAGCAGTAGCTTGACGAAGTTCACCAGT
+GAAACCGAAAGACTCGTTGACGGGAAGGTAAGCCTTGATGTTGTACAAGGGAGTACCAAC
+ACGTTGCTCCTCAGAAAAGACATGACCACGCTTCTTGTTAAGGACAGAGTAAATACCACC
+CATAGCGTTTTCGGAAAC
+>TRINITY_DN453_c0_g1_i1 len=253 path=[231:0-252] [-1, 231, -2]
+GCGGTCCTTGTGGTTGGCCATGAAGGTGGACGCACCACAGTTGGGACACTCACGACGAAG
+ACGCTTAACGCTTCCATCATCCTCAACCTTGTAGTATTTGAGGACGGCGAGCTCAACCTT
+CTTGTGCTTGTGCTTGATCTTCTTGGGAGTAGTGTAAGTCTTCTTTTTACGCTTCTTACC
+ACCACCACGAAGACGCAAAACGAGGTGAAGAGTGGACTCCTTTTGGATGTTATAATCAGA
+CAAAGTACGTCCG
+>TRINITY_DN454_c0_g1_i1 len=356 path=[334:0-355] [-1, 334, -2]
+CTGCCAACGTCCAATGGACTGTTGCTCGTGCTGGTAACGCTGGTTACATGCACCGTACTC
+AATTGAACTCCAAGATCTACCGCATTGGTGCTGGTGATGATGCCAAGAATGCTTCCACCG
+ATTTTGATGCCACTGAGAAGCGTATCACTCCTATGGGTGGTTTCGTTCGTTATGGTGTTG
+TTGAGAATGACTTTGTCATGTTGAATGGTGCCACTCCTGGCCCCGTTAAGCGTGTCTTGA
+CCCTCCGCAAGTCTCTTCTTACTCACACCTCTCGTAAGGCTTTGGAGCCTGTCTCCCTCA
+AATGGATCGACACTGCTTCCAAGTTTGGTCATGGTCGTTTCCAAACTCCTGCCGAA
+>TRINITY_DN455_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2]
+GCACCAGACTTAAGTTGACCGGCACCAATACCAACAGTCAAGTGGGAGATGAAGGTGTCA
+GCGGTCTCACCGGAACGGTGAGAAACCATAACACCCCAACCAGCCTCGTAGGACATGCGG
+ACGGCGTTCAAAGACTCGGTGACGGAACCGATTTGGTTGACCTTCAAAAGAAGAGCGTTA
+GCGCACTTCTTGTCGATGGCGGTACGAAGACGCTTG
+>TRINITY_DN456_c0_g1_i1 len=319 path=[297:0-318] [-1, 297, -2]
+CAAAATGTCTGCCTCCGAACTTGCTACAAGTTACTCTGCTCTCATCTTGGCCGACGAGGG
+TATTGAGATCACCTCAGATAAACTCTTGTCTTTGACTAAGGCTGCCAACGTCGATGTTGA
+GCCTATCTGGGCAACCATCTTTGCTAAGGCTTTGGAGGGCAAGGACTTGAAGGAACTCCT
+TTTGAACATTGGCTCTGCTGCTGCCGCTCCTGCTGCTGGTGGCGCCGGTGCTCCTGCCGC
+TGCTGCTGGTGGTGAAGCCGCTGCTGAAGAACAGAAGGAAGAGGCTAAAGAAGAAGAGGA
+GTCTGATGAAGATATGGGG
+>TRINITY_DN457_c0_g1_i1 len=252 path=[230:0-251] [-1, 230, -2]
+TTGATTGTTTTAATTCATTGATTTTGTCGTCTTTCGGTTTTTATCACATTTTATAAAAAC
+TGCATCCCCCTCTTCTTAAGAATAATAAGAGGCCATTGTTTATTTACCCCGGTCCTTTTC
+TGACCATCTAATCTTTTCGTATTAGGTGCTCTTTTACTTATAGTTTGGTTTCGCCCATAA
+CTTTTTGACGACGTTGTTTACTTTGGTTGATATAAAATTATTTTATACAATCGTTAACAC
+CTCATATTTTCC
+>TRINITY_DN458_c0_g1_i1 len=210 path=[188:0-209] [-1, 188, -2]
+TCAACCTTCTTGACAACATCCATACCCTCAGTGACCTCACCGAAAACGACATGCTTGCCA
+TCTAACCAGGGAGTGACAACGGTGGTAATGAAAAATTGAGAACCGTTGGTGTTAGGACCA
+GCGTTGGCCATAGACAACAAACCAGGCTTGTTATGCTTCAAGGCAAAGTTTTCATCAGGA
+AATTTCTCGCCATAAATGGACTTTCCACCG
+>TRINITY_DN459_c0_g1_i1 len=220 path=[198:0-219] [-1, 198, -2]
+GGACGGCGGTTTGCTGAGGAACGGCATCGCTAGACTCAGAAGCAATGCGAGACATACGCT
+CAGCATGGACATGAGGGTGCATGCCAGGCTCGTTCTCAATGATCTCGCTAGTGTCGGATT
+GAACGTCGTCTTGTAAGTGGGTGACTTGCTCAACGGGGACGGGCTCACCTTGAGCCTCAT
+ACTCGTTCCAGGAACGAGCGTCACTTTGGGCATCATCCTC
+>TRINITY_DN460_c0_g1_i1 len=211 path=[189:0-210] [-1, 189, -2]
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTGGTATTGCTATAGCTGGTTTGGCTC
+CTGACGCCAGAGTTTTGAGTAACTATATGAAGCAAGAAGCTTTATCGTCTAAGACTTTGT
+TTACTCGACCTATTCCTGTCCGTCGTCTAATGAGCAAGGTTGCTGAAAAGGCTCAAATTA
+ATACTCAGGAGTACGGAAGGAGACCTTATGG
+>TRINITY_DN461_c0_g1_i1 len=213 path=[191:0-212] [-1, 191, -2]
+GCCAAGCGCATTGCTAGGCGTTCTAGAGTCAAGCCTTTTATCAAGGTTGTCAACTACAAC
+CACTTGATGCCTACTCGTTATGCTCTTGAACTCGACAACCTTAAGGGCCTTATCACTGCT
+GACACCTTCAAGGAGCCCACTCAACGCTCAGCTGCTAGAAAGACTGTCAAAAAGACTTTC
+GAAGAGAAGTACCAATCCGGAAAGTCTGCCTGG
+>TRINITY_DN462_c0_g1_i1 len=228 path=[206:0-227] [-1, 206, -2]
+CTCTTAGGAGCAGCAACAGGAGCAGACGCAGCCTTTTCGGCTTGCTTTTTTGCTTTAGCT
+AATTCACGAGCACGTTGTTTTTCGCGCTTCTTTAACTCAGTCTTTGAGACTTGTTCACCA
+GTGACGGGATCAAGGACTAAAGCCTTTACAGCCTGTGTAACTCCATTCACCTGTTCCTCA
+CTCATTTTAGCTTACAATTGCCGTTTTCAGGTTTCAGAGAAATTTTCG
+>TRINITY_DN463_c0_g1_i1 len=245 path=[223:0-244] [-1, 223, -2]
+TCTTGGATCAAATCTATGCTCTTAAGCATAAGGATCCTGAATCCCCTCGCTTGGTCACCA
+TGGAGCAAGAGCTTGTTCGTGAGGAGGCTGCCTGTTTGGTTGCCGAGGCTCAACTTTCCA
+ACACCACCCGTGAAAAGTTCAAGCAAGCCATGACCTTCAACTTGGATGCCCTCCACGAGC
+ATGCCGAGAAGCTCAACCTCATTGCCACCTATGGCAGACATTTGTTGAACTTGATTGACG
+ACACC
+>TRINITY_DN464_c0_g1_i1 len=241 path=[219:0-240] [-1, 219, -2]
+TTTAGTACGTGCTCCTTTTGGAATTCGTGGTTATGCCCAAGCTGTTCAGAAAAATGAAAA
+ATTAGTACTTTCCATGGCATTGCCATACCAAACCATCTATGAGAAGGTTCCTGTAACTCA
+GGTCGACATCCCTGCGGAAGATGGCGAGATGGGTATCCTTAAAGATCATGTTCCCATGAT
+TCAGTGTCTTAAGCCAGGAGTTATTTCTGTTACTGATGAATCCAGCAACAAATCAAAATA
+T
+>TRINITY_DN465_c0_g1_i1 len=1079 path=[1057:0-1078] [-1, 1057, -2]
+TTTTACGATACCTACAATGTTGTTCAAAATTTCCTTTTTGGCTTTGATTGCTTCTGCTCT
+CGCTATGTCGATTAACTCTCCCACCAATGGTGACACTTGGCAAACCAACGGCGAGGAGCA
+AATCACCTGGAATGTCGTTTCCACTGATGAACCCAGTGCTGCTCTTTACTTGACCAACTT
+TGCTGTTTATCCCACCGTTACCCAATACTTGGACACTGTTGACACCAGCACTGGTTCTTA
+CACCACCAACACCACCAACTGGCCCACTGGTCAAGGTTTCCAAATCAACATGGCTTACCC
+TGGTCGTCCTGAGCAAATTTATGCTCAATCTCAACAATTTAACATTGTTGAGGGTGCTGC
+TTCTTCTTCTTCCTCTTCCTCTTCTTCCTCCAGCTCTTTGGTTTCCTCCACAACCTCTTC
+TTCCAGCTCTGCCACTCCTTCGACCACTTCTTCCTCCTCCTCCTCTTCTTCTTCCTCTTC
+CTCATCCTCATCTAAATCTTCATCCTCTTCTTCCAAGTCTTCCTCTCGTAGCTCTTCTCG
+TACTACTTCTCACCGCACTACTTCCCATAAGTCCTCCTCTTATCGCCCTACTGTATTCCC
+TTACACCACCATCTCTCACTACAACATTACCAATGCTACCAATGGTACATATTGCAATGG
+TACTAACGGTACTAACTTCACTTGCATCGTCAATGCTTCTAATGCCACCAACTCTACTTT
+CTGGTTGAATGGTACCAACTCTACCAACGGTACCAACTCTACCAACTCCACCAGTACCAC
+TTCTCACAGTTTGACCAAGCTCCCTACTAGCAGCAAGAGTTTGACTACTTCTAAGACCAC
+TGCTAGCGGACATATCACAAAAGGTGTAATGGAGGCCCTTAGCACCAATGACACTACCAA
+CACCACTGATGACGCTACCAACACCACCTCTGACTCCAGCTCTTCTAGCTCAGCCAGTGC
+CTCTAGCTCTTCCAGCTCATCATCTGCTGCCTCTTTAGTCAGCCAACCTGTTGGTATTTC
+TGCTGTGATTGCATTCTTTGCTGTCGCTCTCTCTCTCACTCTTTAAGGAGATTCTTGCC
+>TRINITY_DN466_c0_g1_i1 len=533 path=[511:0-532] [-1, 511, -2]
+TCCATTTTCAGGGCTAGTTCATTCGGCAGGTGAGTTGTTACACACTCCTTAGCGGATTCC
+GACTTCCATGGCCACCGTCCTGCTGTCTAGATGAACTAACACCTTTTCTGGTGTCTGATG
+AGCGTACATTCCGGCACCTTAACCTCACGTTCGGTTCATCCCGCATCGCCAGTTCTGCTT
+ACCAAAAATGGCCCACTAGAAACTCTCATTCGATGGCCCACGTCCAATTAAGCGACAAGG
+GCGTCTTACATATTTAAAGTTTGAGAATAGGTTGAGGAAATTCCTTCCCCAAGACCTCTA
+ATCATTCGCTTTACCTCATAAAACTGATCTGAGTTTCTGCTATCCTGAGGGAAACTTCGG
+CAGGAACCAGCTACTAGATGGTTCGATTAGTCTTTCGCCCCTATACCCAAATTTGAAGAT
+CGATTTGCACGTCAGAATCTCTACGAGCCTCCACCAGAGTTTCCTCTGGCTTCACCCTAT
+TCAGGCATAGTTCACCATCTTTCGGGTCCCAACAGCTATGCTCTTACTCACAC
+>TRINITY_DN467_c0_g1_i1 len=351 path=[329:0-350] [-1, 329, -2]
+GGTGAACGTACCCGTGAGGGTAACGATTTATACCGGGAAATGCAAGAAACCGGTGTCATT
+AAATTAGAAGGCGAGTCTAAGGCTGCTCTTGTCTTTGGTCAAATGAATGAGCCTCCAGGT
+GCTCGTGCACGTGTTGCTCTCACTGGTTTGACTGTTGCTGAATATTTCCGCGATATTGAA
+GGACAAGACGTTTTGCTTTTCATTGATAACATTTTCCGTTTTACTCAAGCAGGTTCTGAA
+GTATCAGCTTTGCTTGGTCGTATTCCCTCTGCCGTCGGTTACCAACCCACGTTAGCCACT
+GATATGGGTGCTATGCAAGAACGTATTACCACTACTAAGAAAGGTTCTATT
+>TRINITY_DN468_c0_g1_i1 len=408 path=[386:0-407] [-1, 386, -2]
+CGATGCCACTCTCCTTATAACCAACAAAGGGAATTTGGTGATGAAGTAAGTTATAACAAT
+TCACCCAAACAGTACCGGCTTCAAGAGCATTGCTGACCTTGATGGCATTGGTAATATTGT
+TAGTGTGTACACCAGCAGCTAAACCATATGTACTGTTGTTACCGCGACGGATGGCCTCCT
+CGATGGTCTTGAATTTAATGACGGCAAGAACGGGTCCAAAAATTTCCTCCTTACCGACAG
+CCATGTCCTCGGTAACGTTGGAGAGAATAGTAGGTTCGACAAAGTAACCGAGATTACCAT
+GACGCTTACCACCAATCTCTAATTTGGCACCATGAGCAATGCCACTCTCAATATAACTAA
+CAATACGTTCATACTGTTGCTTACTAACTTGAGCACCTTGGAAGGTAT
+>TRINITY_DN469_c0_g1_i1 len=550 path=[528:0-549] [-1, 528, -2]
+CTTCACAGGTCTTGACACAAGCATCAAGCATAGACTTGGTACCCTTGGCAAAGTTGTCAA
+ACTCAAAGACACCAGCGGGACCATTCCAGACAATGGTCTTGGAGGTGGTGATAACCTCGG
+CAAACTTAGCAGAGGACTTGGGTCCACAGTCCAAACCCATCCATCCGTCGGGGATACCCT
+CCTCGGCGGTGGCAGAGCCAACCTTGGCGTCCTTGTCGAACTTGTCGGCAGTGACGAAGT
+CAACGGGGAGGAAGACCTCGACGTTGTTCTTCTTGGCCTTGGCCATCATGGATTCGACGT
+TCTTGGAACCAGCCTCATCGAAAAGAGAGTCACCAATCTTCATACCGTTAAGGACCTTCA
+AGAAGGTGAAAGCCATACCACCGCAGATGATAAGGCGGTTGACCTTGTCAAGAAGGTTGT
+CAATAAGTTGGATCTTGTCAGCAACCTTGGCACCACCCAAGATGGCAAGGAAGGGACGAG
+CGGGGTTCTCCAAAGCCTTGGAGAAGTAGTCGAGCTCCTTCTTCATAAGGAAACCGGAGA
+CACGGGGGAG
+>TRINITY_DN470_c0_g1_i1 len=387 path=[365:0-386] [-1, 365, -2]
+CCTTGGGTTGAATAGTTACACGCTTTCCGTGAATAGCACACAAGTTAGTGTCTTCAAATA
+GAGAGACAAGATAGGCCTCAACAGCTTCTTGGAGAGCACCAATGGCAGAAGACTGGAAAC
+GCAAGTCAGTCTTGAAATCTTGGGCGATTTCACGGACCAAGCGTTGGAAAGGTAGCTTAC
+GAATCAAAAGTTCAGTAGACTTTTGATAACGACGAATTTCACGAAGAGCGACTGTACCGG
+GACGATAACGATGAGGCTTCTTAACACCACCAGTAGCGGGAGCAGCCTTACGGGCAGCCT
+TAGAGGCAAGTTGCTTACGAGGAGCCTTACCACCAGTTGATTTACGTGCAGTTTGCTTAG
+TACGAGCCATTATTTTCTAGTGTTCTG
+>TRINITY_DN472_c0_g1_i1 len=496 path=[474:0-495] [-1, 474, -2]
+TTCCAATCAATTTAATTGTCTTAAATATTCAAAATGTCTGATCCCGCAAGAAAGTCTTTT
+ACTGAACAAGGCAAGGAGAAAATGACTCCTGACTCCTCCAAGTCTACCCTCGACAAGGCC
+AAGGAATCCATTACTGGTGCCTACGACAAGGTCGCCTCTGCTTTTACCTCTGACGAGGAC
+AAGAGCACCTCTCAAGAGGCTCATGACAAGGCTCAACGCTTTGTTGATGACAAGTTGTAA
+AGAGGTTCTTATGACTTAAAATTCATGCTTTTGGCTGGTGAAACTCAATCCACCAAAGCA
+TCGGGATGATTTCTTTACCGATGAACGGACGAAAATGGTTTGAGGTCTCCTCAATTTAGT
+AGGTAGTGGTTGGATTGTTTTTATGAACGATCCATCTCATCACTTTCTAATGCGAGGTTG
+CATCCTTGACCAATTACCATCTAATTTTATGATATATAACGAGGTTACGTGATACCATCA
+TATATATATATTTGCT
+>TRINITY_DN473_c0_g1_i1 len=397 path=[375:0-396] [-1, 375, -2]
+TGTTACCGTACAAATCTTTACGAATATCAACATCACATTTCATGATAGAGTTGTAAGTAG
+CCTCATGAATACCGGCGTTTTCAAGACCCAAAGCTGAGGGTTGGAAAAGAGCTTCAGGGG
+CACGGAAACGCTCGTTTCCGATAGTGATAACTTGACCATCAGGAAGCTCATAAGATTTCT
+CAAGGGAGGAAGATTGAGCAGCAGTTTGAAGTTCTTGCTCAAAGTCCAAAGCGACGTAGC
+AAAGTTTCTCCTTGATGTCACGAACAATTTCACGTTCGGCGGTAGTAGAGAAAGTATAAC
+CACGCTCCATGAGAATCTTCATAAGGTAGTCAGTCAAGTCACGACCGGCGAGATCAAGAC
+GCATGATAGCATGAGGAAGAGCATAACCCTCATAAAT
+>TRINITY_DN474_c0_g1_i1 len=259 path=[237:0-258] [-1, 237, -2]
+TTCCAGTTGTCATACTCGTTTCTCTAAATAAACTATCAATATGTCTGCTCCTTACAAAAA
+CTTGGATCGCGATACTAAGCACACTCATCCCAAATTGAATGAGACCGAACGAAACTTGAA
+TCGTGGTTGGGGCGATGTGAAGAAGGAGGAGTTGTATGAGGATTTGGCTCAGAGTGATGC
+TGACAAGCAACTTGCTGAGGATAAGATGGAAACAAAATACGAGAAAAGCAAGCCTGCCCC
+CTCCGACTAGAAGAAGTGC
+>TRINITY_DN475_c0_g1_i1 len=498 path=[476:0-497] [-1, 476, -2]
+CGGGAGCAGCAACAAGACCAGCACCACGGGGAGCAGGGACGAGACGAACAGTAACGGAAC
+CGCACTTGCCAGAAACCTTGACGGGGACAGTGTGAGGATCACCCAAAGCAGTACCCCAGT
+AACCACGACGAATAGGCATGATGGAAAGCTTGCCCATGATGATAGCACCACGAATAGCAG
+TAGCAACTTCCTTAGCGCACTTGATACCTAAACCAACGTGACCATCGCTGTCACCAATAA
+CAACGAAAGCCTTGAAACGGGTACGTTGACCGGCACGAGTTTGCTTTTGGACGGGAACGA
+CCTTCATAACTTCGTCGTTCAAACGAGGCAAGAAGTAGTCGACAATTTGGTACTCCTTGA
+TGGGGAGAGAGTACAAGTAGATCTCTTCAATAGACTTGATCTTACCAGCCTTCACCAGAC
+GGCCCAACTTGGTGACGGGAACCCATTCCTTCTCCTCATCACGCTTGGCTCCACGACGGC
+CACGTCCGCGACCACGAC
+>TRINITY_DN476_c0_g1_i1 len=334 path=[312:0-333] [-1, 312, -2]
+CCCGTTCCACATTAAAGTCGTATGCAATGGATTCGATTCCGCACAAGATTTCAATGGAAT
+TTCATGGACAAGTCAATAAAACACTTCCGTTTCATCAACCATCGCCCATCTTCTACGATA
+CAGGAGAGTAGGAACAAGTCCTACCTCTATTTTTATACATATAAATCATGCGGACCAAAA
+AATCGTCGCTTTCTGGCACGGATTCTGGCTTAGAGGCGTTCAGCCGTTATCCGGCAGATG
+ATAGCTCCGCGGCATTGCCTTGTCAGGCAGCCGCAAATACCAATGATCTGAATCAACGGT
+TCCTCTCGTACTAAGTTGAATTACCATTGCGACG
+>TRINITY_DN477_c0_g1_i1 len=391 path=[369:0-390] [-1, 369, -2]
+TAGTTTGTTAATTGAATGCACTTCTTCTAGTCGGAGGGGGCAGGCTTGCTTTTCTCGTAT
+TTTGTTTCCATCTTATCCTCAGCAAGTTGCTTGTCAGCATCACTCTGAGCCAAATCCTCA
+TACAACTCCTCCTTCTTCACATCGCCCCAACCACGATTCAAGTTTCGTTCGGTCTCATTC
+AATTTGGGATGAGTGTGCTTAGTATCGCGATCCAAGTTTTTGTAAGGAGCAGACATATTG
+ATAGTTTATTTAGAGAAACGAGTATGACAACTGGAAAAAAATGTGGTCAAAAAAAGATTT
+ATTCCAAATTAATATAGGAAATGCTGAATCTTGTAAAAATGCGAATATTTAATTGTCTTT
+TTACAATTACAATTCGTATTTGAGAATGAAT
+>TRINITY_DN478_c0_g1_i1 len=760 path=[738:0-759] [-1, 738, -2]
+AGCGACAGCAAAGAATGCAATCACAGCAGAAATACCAACAGGTTGGCTGACTAAAGAGGC
+AGCAGATGATGAGCTGGAAGAGCTAGAGGCACTGGCTGAGCTAGAAGAGCTGGAGTCAGA
+GGTGGTGTTGGTAGCGTCATCAGTGGTGTTGGTAGTGTCATTGGTGCTAAGGGCCTCCAT
+TACACCTTTTGTGATATGTCCGCTAGCAGTGGTCTTAGAAGTAGTCAAACTCTTGCTGCT
+AGTAGGGAGCTTGGTCAAACTGTGAGAAGTGGTACTGGTGGAGTTGGTAGAGTTGGTACC
+GTTGGTAGAGTTGGTACCATTCAACCAGAAAGTAGAGTTGGTGGCATTAGAAGCATTGAC
+GATGCAAGTGAAGTTAGTACCGTTAGTACCATTGCAATATGTACCATTGGTAGCATTGGT
+AATGTTGTAGTGAGAGATGGTGGTGTAAGGGAATACAGTAGGGCGATAAGAGGAGGACTT
+ATGGGAAGTAGTGCGGTGAGAAGTAGTACGAGAAGAGCTACGAGAGGAAGACTTGGAAGA
+AGAGGATGAAGATTTAGATGAGGATGAGGAAGAGGAAGAAGAAGAGGAGGAGGAGGAAGA
+AGTGGTCGAAGGAGTGGCAGAGCTGGAAGAAGAGGTTGTGGAGGAAACCAAAGAGCTGGA
+GGAAGAAGAGGAAGAGGAAGAAGAAGAAGCAGCACCCTCAACAATGTTAAATTGTTGAGA
+TTGAGCATAAATTTGCTCAGGACGACCAGGGTAAGCCATG
+>TRINITY_DN479_c0_g1_i1 len=619 path=[597:0-618] [-1, 597, -2]
+AGTCACTTTACTTACACCACACTATACAACGTTAACGATGACTACCGAAGCTGCACCTAA
+CTTGCTCGTCCTTACCCGTCACGGTGAATCCGAATGGAACAAGTTGAACTTGTTCACTGG
+TTGGAAGGACCCTGCCTTGTCCGAGACTGGTATTAAGGAGGCCAAGCTCGGTGGTGAGCG
+CTTGAAGTCTCGTGGCTACAAGTTTGACATTGCCTTCACCTCTGCTCTTCAACGTGCCCA
+AAAGACCTGCCAAATCATCTTGGAGGAGGTTGGTGAGCCCAACTTGGAGACCATCAAGAG
+CGAGAAGCTCAACGAGCGTTACTACGGTGACTTGCAAGGTTTGAACAAGGATGATGCTCG
+TAAGAAATGGGGTGCTGAGCAAGTCCAAATCTGGCGCCGTTCTTATGACATTGCTCCTCC
+CAACGGTGAGTCCTTGAAGGACACCGCCGAGCGTGTCTTGCCCTACTACAAGTCCACCAT
+TGTCCCTCACATCCTTAAGGGTGAGAAGGTTCTCATTGCCGCTCACGGTAACTCTCTCCG
+TGCCTTGATCATGGACTTGGAGGGTCTTACTGGTGACCAAATTGTCAAGCGTGAGCTTGC
+CACTGGTGTCCCCATTGTC
+>TRINITY_DN480_c0_g1_i1 len=254 path=[232:0-253] [-1, 232, -2]
+TATGAAACGTGGCCTTGGTATGTCTTGTGATGAGATTGCCGATGTTTTTGAGAAGTGGAA
+CACTGGTAAACTTGACTCTTTCTTAATTGAAATCACTCGCGATGTTTTGCGTTACAAGGC
+TGATGACGGCAAGCCCTTGGTTGAGAAGATTCTCGACGCTGCTGGACAGAAGGGTACTGG
+TAAGTGGACTGCTCAAAACGCTTTGGAAATGGGTACCCCTGTCAGTTTGATCACCGAAGC
+CGTTTTTGCTCGTT
+>TRINITY_DN481_c0_g1_i1 len=258 path=[236:0-257] [-1, 236, -2]
+GTGGATATCAACTGTTTGCTTGAAAAGCCTTAAGAGGGGAGATTTTTAAAAGATGAAGAA
+ATGGGTCTTTATTTTAACAACAAAGAAAATATATCAGGGGTAAAATAATATTCGGTCAGT
+TGAAGAAATGGATAGGATCAACAGAGGCCGCAAAGACTGAATAATTAAGTTGAGTTGGGA
+GGGGGTGGTTAAAGTGACTCCGAAGAGAAGCAAACTACAAAGAAAAAGAAAAAAAAATAT
+AATAAACCAAGTACAACA
+>TRINITY_DN482_c0_g1_i1 len=205 path=[183:0-204] [-1, 183, -2]
+CTGGCAGGGTCCATAGAAGAGATACTCAGACGTTTTGGAGTAGATGTTGCCGATGAAGTA
+GAGCCATGTGACGCCGACCTCTGATGACCCTGTTCCTCATTGCTGGGAAAGGATAACATA
+ATATTTCGGGTAGTCATTAGAAAATCAGCGTCTGGAACCTCCGCACGAGACTTTTCAAGC
+CATAATTCCATCAATTGTGTAAACT
+>TRINITY_DN483_c0_g1_i1 len=337 path=[315:0-336] [-1, 315, -2]
+CTAACTGGTTGCAGCTAAAATATTTAGGCCTCAAGCTTAGCCTTCAAGATGGTACGAAGA
+GTATCAGCATCCTTGGCAAAGGCAGCGATACCAGTGGACAACTTGACTACAGCCATTTCG
+TCGTTGTTAAAGTCGAAACGGAACTTGGGCTCATCAGTAAGGTAGGAAACCTTCTCCAAA
+TTGAGGCTGGAAGCCTTGGAGGCATCAAGCTTCTTGGGGACAGCGTCGGTGCTGTTGTTG
+AGCTGCTCAAGAAGGGCGGGGGAGATGGTCAAAAAGTCAACACCAGCGAGTTCCTTGATC
+TCACCGACGTTACGGAAAGAAGCACCCATGACAATGG
+>TRINITY_DN484_c0_g1_i1 len=1114 path=[1092:0-1113] [-1, 1092, -2]
+CGTGCCCACGGTCACCATTTCAGAAGTAAGGTCCGCATGTGGGTCTTTGAGGAGGAGATT
+GAGTACAAGGGTGAGAAGAGAAAGCTCACCGAAGTATTCAACGAAGCTCACGAGAATGTC
+AAATACTTACCCGGCATCGAATGCCCTCCCAACGTTATTGCCGTCCCCGATGTTCGTGAG
+GTCGCTAGACGTGCCGACATCCTTGTCTTTGTCGTTCCTCATCAATTTATTGAACGCGTT
+TGCGACCAAATGGTCGGTCTCATTCGCCCTGGTGCCGTTGGTATTTCCTGTATCAAGGGT
+GTTGCTGTCAGCAAGGAAGGCGTCCGCCTTTACTCTGAGGTTATCAGCGAGAAACTCGGT
+ATTTACTGTGGTGTTCTTTCTGGTGCTAACGTTGCAAACGAAGTTGCCCGTGAGCAATTC
+TGTGAGACTACTATTGGTTTCAACCCTCCTAATGAAGTTGATATCCCTCGCGAGCAAATC
+GCCGCCGTCTTTGATCGCCCTTACTTCTCAGTTGTCTCCGTTGACGACGTTGCCGGTGTC
+GCCTTGGGTGGTGCTTTGAAGAACGTAGTTGCCATGGCCGTTGGTTTCGCTGATGGTTTG
+GAATGGGGCGGTAATACCAAGGCCGCTATTATGCGTCGTGGTTTGTTGGAGATGCAAAAG
+TTTGCTACTACCTTCTTCGACTCTGATCCTCGTACCATGGTTGAGCAATCTTGCGGTATC
+GCTGACTTGGTCACTTCTTGTTTGGGTGGCCGTAACAATCGTTGTGCTGAAGCATTTGTC
+AAGACTGGTAAATCTTTAGAGACGCTTGAAAAAGAGCTCTTAGGTGGTCAACTTCTTCAA
+GGAGCTGCCACTTCCAAGGATGTTCATGAATTCCTTCTCACCAAGGATATGGTCAAGGAT
+TTCCCCTTGTTCACTGCCGTTTATAACATTTCCTATGAAGACATGGATCCCAAGGATTTG
+ATCATCGTCCTTCAACCCCTTAAGGAGGACTCTGAGAACGAGGGCGGTACTGAAACCGAG
+TAAACTTCTTTTTAAATATTCAATTCCGTATACCTCTTTAAGGGATCGAGAGCTCTTATA
+TGTTCGTTCGATTACCTACACTACACTCTTCTTG
+>TRINITY_DN485_c0_g1_i1 len=632 path=[610:0-631] [-1, 610, -2]
+CCACACCAACTCACCTGAACCACCATGGCAATTCACGTTAAAGGACAGTTGCCCAACGCT
+CACTTCCACAAGGACTGGCAGCGTTATGTGAAGACATGGTTTAACCAACCTGGCCGTAAG
+TTGCGTCGTCGTCAAGCTCGTCAAACCAAGGCTGCCAAGATCGCTCCTCGTCCCGTTGAG
+GCTATTCGTCCCGCCGTTAAGCCTCCCACCATCCGCTACAACATGAAGGTTCGTGCTGGT
+CGTGGTTTTACTCTTGAGGAGCTCAAGGCTGCTGGTGTTTCTCGTCGTGTTGCCTCTACC
+ATCGGTATCCCCGTTGACCACCGCCGTCGCAACCGCTCTGAGGAGTCCTTACAACGTAAC
+GTTGAGCGCATCAAAGTTTACCTTGCTCACTTGATTGTTTTCCCCCGTAAGGCTGGTCAA
+CCCAAGAAGGGAGATGCTACTGATGTCTCTGGTGCTGAGCAAACTGATGTTGCCGCTGTT
+CTTCCCATCACTCAAGAAGCTGTTGAGGAGGCCAAGCCCATTACTGAAGAAGCCAAGAAC
+TTCAACGCTTTCTCTACCCTTAGCAACGAGCGTGCTTATGCTCGTTATGCCGGTGCTCGC
+GCTGCTTTCCAAAAGAAGCGTGCTGAAGAGGC
+>TRINITY_DN486_c0_g1_i1 len=481 path=[459:0-480] [-1, 459, -2]
+ACCGATAAGATCCTCCTCAGAGACGTCAAGAATCTCAGGACTAAAGACGTTTCCTTGGTC
+ATAGATCGTGAGAACATCCATACCATAGGTGAAGGGAGAGATGTTTAACATGTTAAGCAA
+AGTAGCCTCGGAAGGACCAACTTTAGCATCCTTGGAGACCAAATGGACATCGGAAGTAAT
+TTCAATGGTACCACGAGTAATCTTGGTGGGGATACCAAGAGCTTGGAAGAAAGAGGTCTT
+ACCGGGTTCCATACCAGTGTTACCGGCAGGGACAAAGACATCCAAGGGAGCAATGGCGTT
+AGGACGAGCAGGAGCAGCAATAACATTAGCAATAATGGTCTCACGGACTTCCTTCAAATC
+AGCGTTGGTGAAGACGAAACCAACGTTACCACGAACAACAGGCAAAAGACGCTCAAGCTC
+AGGCATATCGTTGATGATACCACGCATAGCACGACGAATCATGGTGTTCTTACCCATGAT
+A
+>TRINITY_DN487_c0_g1_i1 len=213 path=[191:0-212] [-1, 191, -2]
+TGGTTTTGGCCCTTCTGTTGTCGGTATTGTTGTTTACCGTGGTTTGTACTTCGGTATGTA
+TGATACCTTGAAACCCGTCGTTTTGGTTGGTCCTTTGGAGGGCAACTTCTTGGCCTCCTT
+CCTTCTCGGTTGGGCCGTTACCACTGGTTCTGGTGTTGCTTCTTATCCTCTTGATACCAT
+CCGTCGTCGTATGATGATGACATCTGGTGAAGC
+>TRINITY_DN488_c0_g1_i1 len=422 path=[400:0-421] [-1, 400, -2]
+CTTAATTTGACTCAACACGGGGAAACTCACCAGGTCCAGACATAGTAAGGATTGACAGAT
+TGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTG
+ATTTGTCTGCTTAATTGCGATAACGAACGAGACCTTAACCTGCTAAATAGCTGGATCAGC
+CATTTTGGCTGATCATTAGCTTCTTAGAGGGACTATTGGCATAAAGCCAATGGAAGTTTG
+AGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAC
+GGAGCCAACGAGTTGAAAAAAAATCTTTTGATTTTTTATCCTTGGCCGGAAGGTCTGGGT
+AATCTTGTTAAACTCCGTCGTGCTGGGGATAGAGCATTGCAATTATTGCTCTTCAACGAG
+GG
+>TRINITY_DN489_c0_g1_i1 len=300 path=[278:0-299] [-1, 278, -2]
+GGCTCCCAAGAAGAAATGGTCTAAAGGAAAAGTGAAGGACAAGGCTCAACACGCCACTGT
+CTTTGACAAGAGCATCATCGACCGTATCAACAAGGAGGTTCCTGCCTTCAAGTTCATCTC
+GGTTTCAGTCCTTGTTGACCGCATGAAGATCAACGGATCTCTTGCTCGTATTGCCATTCG
+CGACTTGGCTGAACGCGGTGTCATCCAAAAAGTGGACCAACACTCTAAGCAAGCTATCTA
+CACACGTGTACCTGCTGCTACTGCTTAAGTTATGGTGTTGCCATTAATCAATAAATCCAA
+>TRINITY_DN490_c0_g1_i1 len=357 path=[335:0-356] [-1, 335, -2]
+TCGTATTGGTAAGCACAGGAAGCATCCCGGTGGTCGTGGTAAGGCCGGTGGTTTGCAACA
+CCTCCGTAGTCACTTTGATAAGTATCACCCTGGTTACTTTGGTAAGGTTGGTATGCGTCG
+ATTCCACCTCATGAAGAATCCTTTGTGGCGTCCTACTGTCAATTTGGATCGTCTTTGGAC
+CTTGGTTCCCAACGAAACTCGTGAAAAGTATCTTGGTAAAAACACGGAGGTTGCCCCCGT
+TATTAATGTCTTACAATCTGGTTACGGTAAGGTTTTGGGTAAGGGTCGTCTGCCTGATAC
+TCCCGTCATCATTCAAACACGTTATGTCTCTCGTCGTGCTGAAGAGAAGATCAAGCA
+>TRINITY_DN491_c0_g1_i1 len=277 path=[255:0-276] [-1, 255, -2]
+CACGAAATTTCGTATCGCCCTTTGGTAAAGTGTTAAACATTTTTCGTCCTACTCTTTTTT
+TTTTACTTATAACTCGTCCTCTCTCTACTAAATTATTCTCACTATAATTGTTCTTATTAG
+TATCATCACATACTAATATACTACTACTACTACCACTTATTTTTATTATTACTACCATCT
+CTTCTTATTTACCCACATCTATTTCTATTTCTGCAAGATGATGAACCGTGCGTACTCTTT
+AAGAAACAGCCGTGCCCCTACGGCCTCACAATTGTTA
+>TRINITY_DN492_c0_g1_i1 len=502 path=[480:0-501] [-1, 480, -2]
+CGCTGTTGAAAATAAATCAATTTATGATTTCATTATTATTCATAACAATCATATCTTAAG
+AGTTGAGTTGTAAGTAAGAATGCTCTGTAAAAAAGTAGCAATGTAGTAGGATCAAGACAT
+CAGGGCGATTCGTTGGTCCATAATAGTATTGTTTTCTCGACTGATGCTTCGAAAAACAAT
+AAGACGAGGCGGACATTGCTTTATGGATGAAATATTTCGTCAAGGCCAGAACTACAGTCC
+GTAAATCTCATATAGATTACTTCGAAGCACATTTGCAAGAAGAGCACTTGCAGTTATCAA
+CAGCGCTGCTCTTGCAACCACAAGACTCTTTGCAATCTTGGCAACCGCACTTGGATTGGC
+AGTCGCAAGGCTTGCCTTGTTTGCTCTTACATTGGGTAGTGTGTTCCATCGTTGAAAGTT
+TGTTAGGGTGATATGAGTTGTTGAAAGTCGATTGTCTCAAGCACGCTTAAAGTGGTAAAA
+AAAGGTGAGAGTAGGGTGCCTT
+>TRINITY_DN493_c0_g1_i1 len=202 path=[180:0-201] [-1, 180, -2]
+CCCTGCTCTTGGTGTTGCATGTGTGTTATCCCGTTGCAAGTTATTGAGTGATGGTATGCT
+GAAAGCAGCTTCCGATGCTTTGGCCACTGTTCCCAGATCTTTATTTGCTGCTGATGAAGC
+CCTCTTGCCAGATTTGAACAATGCTCGCGAAATTTCTCGTCACATTGTTTTTGCAGTCTT
+GAAGCAAGCTGTTTCTGAGGGA
+>TRINITY_DN494_c0_g1_i1 len=220 path=[198:0-219] [-1, 198, -2]
+GGAATTTGCTTGATGAGGACTTCAGAAGCAATGAAAGCATCATACTTCTTGGCCAACTTC
+TTGACAAGCTTCTTGTTCTTGTTAAGCTTTTTCAAGTCATCGACGGACATAGCATCGACA
+CCACCGTGCTTGGCACGATCCAAATCATGGGCATCACCGAGAATGCAAATGGCCATGTTG
+GGACGAGGAACATTGGGCAACTTGATAGTACCGGAGAAAC
+>TRINITY_DN495_c0_g1_i1 len=234 path=[212:0-233] [-1, 212, -2]
+AAAGAAAAGCCTTGAAGATGGAAAAAAGGAAATAAAAGAACAAGACTTTCTTTCCACTCT
+AACCCCGAGATGGTTTGATGAAGATTCTATGAGAGAATGGTATAAACGTGTGGTGAAATG
+GTAAAAGATTCATGAGATGAACAGATTTGAAACCAAGCTGCAACCAAGCACACAAACTGA
+GATTGACAACGGCCGTACCATCGAAAAACGACATAAAGAACAAAAGAAAAGAAC
+>TRINITY_DN496_c0_g1_i1 len=447 path=[425:0-446] [-1, 425, -2]
+CGGGCTATAGCAAAAAGTATACGGTAAAATCATTCGCCCAATTATGGATAAAAAAAGATA
+TCATGGTTAAGCACAGTCGATTTTGGGAAAGGAAAAAAAAATGAGTGCAAACAACCGTGA
+TACTATTTTGAACTTTTTTCTTAGTAAAGAAAATCCGTTTTTTTGTTTACTAATACAAAA
+GCCATGATATCCTCACAACATTTGGTATTAAATGAAGCGAATAATAAATTCCTAGAACAG
+ACAAGAGAAGAAGCAAAGAATACACATGTCTATTTCACTTTCCTTTATAAACATGATAAG
+TAGCGAAAAGAACAAATATTAGAGGATTGAAATAGAGGGATGCTTAGTATTTTAAGATGA
+TATAGAGAGCGTGAATAATACCGGGAACGTAACCAAGACAACAAAGAAGAATGTTGATAA
+TAACGTCAGCACCACAGCCACGTTCCA
+>TRINITY_DN497_c0_g1_i1 len=237 path=[215:0-236] [-1, 215, -2]
+CTTTCGTCGGTCGTATTCTCGATTTCTACAAGGCTAAGAATAACCGTGACTATACCGCTC
+AAGAAGACCCCGGTGTCGTCAGTGTCTCTAACATCTTCAACTACTACAAAAAATTCGGTT
+ACAAGACCATTGTCATGGGTGCTTCTTTCCGTAACGTCGGTGAGATCAAGGAACTCGCTG
+GTGTTGACTTTTTGACCATCTCCCCCGCCCTTCTTGAGCAGCTCAACAACAGCACCG
+>TRINITY_DN498_c0_g1_i1 len=272 path=[250:0-271] [-1, 250, -2]
+GCAGATACGTAACCAGTATGGCCATAGTGAGAAGTGCGAAGGGAGAAGGTTTCCAAATCC
+CAAACCTTAACGGCCTTGTCCCAACCAGCAGAGACGAAGGTAAGGTTATCGGGGTTAGGA
+GAGAAGCGCACACAAGAAACCCAGTCAGAGTGACCACCATCGGTGATAGTGTACTTGCAG
+TTACCAATAATGTTCCAAATCTTAATGGTCTTGTCACGGGAACCAGAAACAACCTGGCGG
+TTGTCAGGAGAAATGGAGACAGATAAGACATC
+>TRINITY_DN499_c0_g1_i1 len=211 path=[189:0-210] [-1, 189, -2]
+TTTTTTCTTTCTTTTTCTCTCTCTCCAATCAGGAAAATTCGAAAAAAAATTTCATTGGTC
+GTCGATTTTTTTTTTAAACAAAAATTTACTACTCTTGGGCAGCCAAGCCAGTCTAGTTTA
+GTCTAGTCAGCCAACCAACCAGCATTTTTTTCATATTCTCTTTTTTTTTCTCTTTTCTAA
+TCACCACCGCTCTCCACTCTGAAAAACGTGC
+>TRINITY_DN500_c0_g1_i1 len=297 path=[275:0-296] [-1, 275, -2]
+GCCGCTGTCAACGACAAAATTTTCGATGTCGCTGCCTTTGAGAAGTACTTGATTGACCGT
+ATCAAGGTTGATGGCAAGACTGGTAACTTGGGCTCTTCTGTCGTCGTTTCCCGTGAAGGT
+TCCAGCAAGATTGCTGTTATTGCTCACATTGATTTCTCTGGCCGTTACTTGAAGTATTTG
+ACTAAGAAATTCTTGAAGAAGCACTCTCTCCGTGACTGGCTTCGTGTCGTTTCCACCAAG
+AAGGGTGTCTACGAGTTGCGTTACTACAATGTCGTTGTTGGCAATGACGAAGAGGAG
+>TRINITY_DN501_c0_g1_i1 len=250 path=[228:0-249] [-1, 228, -2]
+TCAAAAGGATATCAACGATGGCAAGTCATTCCAATTACTTGCCAACAATGTTGACAGTAA
+GCTTCGTGAGGATCTTGAGCGCCTTAAGAAGATCCAAACCCACCGTGGTCTTCGTCACGC
+TCTCGACCTTCGTGTTCGTGGTCAACACACTAAGACTACTGGACGTCGCGGTAAGACCGT
+TGGTGTCTCTAAGAAGAAGTAAAATAAGTAAAATGATTAGCCTAATATTACTTGGATAAT
+AAATTTCCAT
+>TRINITY_DN502_c0_g1_i1 len=201 path=[179:0-200] [-1, 179, -2]
+ATTTTGAAATATACTGCTGATGAGGCACGCACCTTGAAAAATCAAGGCGAATTGCCCGAA
+ACAGCCAAGATCAACGAAACGGATACATTTGGCGCTGAAGGAGAGGATGATCTTGACTTT
+GAGTTTGATGTCGATGCTATTTAAAATTTTTCGGAAGGATAAGGTTTATTTTATTAAGTG
+GGTTTTTCTACCATGTTTCCT
+>TRINITY_DN503_c0_g1_i1 len=256 path=[234:0-255] [-1, 234, -2]
+GCGGTACGAAGACGCTTGACGTTGGTAACAGTCAAATCGTCACCGACAATTTGGAAGTCG
+GTCTCAGCCTTCATGTGAGTCCAGGCAGACCAGTCATCTTGGTCGAAGGGGTCCTCAATG
+GAGACAATGGGGTACTTCTTGGAGAGCTCGACGTAAAGGTCGGTAAGTTGTTGGTAGGTA
+AGCTTGTTCTCGGGCTTGGGCTTGGCGGCCTTGATGTCAAGGTCGTACTTGCCGTCAACG
+TAGAACTCGGAGGAGG
+>TRINITY_DN504_c0_g1_i1 len=215 path=[193:0-214] [-1, 193, -2]
+CCATTGGACGTTGGCAGGGTGCCAAGCACCGATACAAGCAACCTTACGAAGACCACGATG
+AGTCTTACGGGGAAGACGCTTGGTACCCCAACGGGCAGTAGTACCCTCGTTACCCTTACC
+TCTGGTGACACCAATAACATCGATCATTTCGTTTTGCTCAAAGGTAGACTTAATGTCAAC
+AGTCTTCTCAAAGTGCTCACGGGCCCATTCAACCT
+>TRINITY_DN505_c0_g1_i1 len=218 path=[196:0-217] [-1, 196, -2]
+TGAAGCTCCTCCTCAGCTTCACGGGCCTCACGAAGAGCGACCTGTCTTTGTTCGAGCAAG
+TCTTGGAGGGTCTTTTCGTCGGGTTGGATGCGGGCATTGGTGGTGGTGACGATACGGATG
+GGAGCACCGGTCAAGGCATCCACGTTGTTTTGGGTAGCGGTGATCTTGACGTTGGTATAG
+TTGGAGGAACGGCTAGATTGGGAGGAGAGGGGTTGAGC
+>TRINITY_DN506_c0_g1_i1 len=331 path=[309:0-330] [-1, 309, -2]
+CTCAAAGACCCACATGCGGACCTTACTTCTGAAATGGTGACCGTGGGCACGGGCATTTTC
+ACCGCAAATCTTGGCAATGGCAGTACCCCAGTTACCGGAGCCAACTACACCAATTGACAA
+ACGTTTCTTGGGGCGGATGCTGTCGATGTTGGCAGCAGAAACACCTTGTTGACCATATCC
+AGACATTGTGTAGAGAATTTAAAGAATTAAAAAAATGTATATATATATATATTATATAAA
+ATGGAGAAAAGGAGTATGTGAAAAGAGGTAGGGCAACAAACACTAACCACTCAAAAATGC
+AGTGCAGACTTCGTTAAAAAATGATAAATAG
+>TRINITY_DN507_c0_g1_i1 len=203 path=[181:0-202] [-1, 181, -2]
+AATTTTTTTTAAATTTAATCGTTGTCGTTCTGCAATATTCGTTAATATCTTATAATTTCG
+AAGAGGACATCGGTTAAACAGTTGTCTGCTTTTTTTATAATTTTATAACATTAATCACAA
+ATTTTAATCATGAAGTTTTTCTGGGTCTCATCGTTATTAGGATTGCTTGGTCTTTCAACT
+GCTATTCCACTTAGTACCGAAGC
+>TRINITY_DN508_c0_g1_i1 len=248 path=[226:0-247] [-1, 226, -2]
+GTGTGTGTGTACGTGTGTGTGTGTGTGTATATGGGTGTGATTTAATTTATTTTTGTCAAG
+GCGGTTGGTTTGTCGTCGGCGGCTCTTGTAATTCTTTTCTTATGTCGATTGCAGTATGTT
+CTCAATTGACGATATATTTTTCTTATTTTTTTAAAAAAGTTTCCCCTTCCTCTTTTACTG
+GTTTCTTTTTCTTTTACTTGAAAACGTAGCATTAGGGGGGAATTTTTTTTAAAACGTTGG
+GTTTGGTG
+>TRINITY_DN509_c0_g1_i1 len=299 path=[277:0-298] [-1, 277, -2]
+CTCCCTTTCAGCAATTTCACGTACTATTTAACTCTCTTTTCAAAGTTCTTTTCATCTTTC
+GATCACTCTACTTGTTCGCTATCGGTCTCTCGCCAATATTTAGCTTTAGATGAAATTTAC
+CACCCATTTAGAGCTGCATTCCCAAACAACTCGACTCTTCGAAAGCGCTTTATATGGCAT
+ATCCAATCGACCAAAGACGGGGTTCTCACCCTCTCTGACGTCCTGTTCCAAGGAACTTAG
+ACCGATCGTCTACACTCAAAGCAGCTTCTTGAAATTACAACTCGGACAACAAAAGAAAT
+>TRINITY_DN510_c0_g1_i1 len=460 path=[438:0-459] [-1, 438, -2]
+CTCTCACTCAAAGTTGCACCTTAACCAAACAAATTAAATCAAAATGGGTCGTATGCATAG
+CAAAGGAAAGGGTATCGCTTCTTCCGCTTTACCCTACGTTCGCTCTCCCCCTGCTTGGTG
+CAAGGCTGATGCCGACTCCGTTGTCGAGCAAATTCTTAAGTTCTCCAAGAAGGGTATGTC
+CCCTTCTCAAATTGGTGTGACTCTCCGTGACTCTCATGGAATTCCTCAAGTTCGTTTCAT
+CACTGGTCAAAAGATCATGCGTATCTTGAAGGCTAATGGTCTTGCTCCCGAGCTCCCCGA
+GGATCTCTACAATCTTATTAAGAAGGCTGTTTCCGTCCGCAAGCATTTGGAACGTAACCG
+TAAGGATAAGGACTCCAAGTTCCGTTTGATTCTTATTGAGTCTCGTATCCACCGTCTTGC
+TCGTTACTACAGAAAGGTCGGTGCTCTTCCCCCTACCTGG
+>TRINITY_DN511_c0_g1_i1 len=219 path=[197:0-218] [-1, 197, -2]
+AACCAGCAAAAAGATGGCAATTTCCAAGGAAAGCAAGGCTCAATACTTCGAGAAGCTCCG
+CTCTCTCTTCGAAAAATACAACTCTCTCTTTGTTGTTAACATCGACAATGTGTCTTCTCA
+ACAAATGCATACTGTCCGTAAGCAGTTGCGTGGAACTGCTGAACTTATCATGGGTAAGAA
+CACCATGATTCGTCGTGCTATGCGTGGTATCATCAACGA
+>TRINITY_DN512_c0_g1_i1 len=371 path=[349:0-370] [-1, 349, -2]
+CGGCATAACGAGCATAAGCACGCTCGTTGCTAAGGGTAGAGAAAGCGTTGAAGTTCTTGG
+CTTCTTCAGTAATGGGCTTGGCCTCCTCAACAGCTTCTTGAGTGATGGGAAGAACAGCGG
+CAACATCAGTTTGCTCAGCACCAGAGACATCAGTAGCATCTCCCTTCTTGGGTTGACCAG
+CCTTACGGGGGAAAACAATCAAGTGAGCAAGGTAAACTTTGATGCGCTCAACGTTACGTT
+GTAAGGACTCCTCAGAGCGGTTGCGACGGCGGTGGTCAACGGGGATACCGATGGTAGAGG
+CAACACGACGAGAAACACCAGCAGCCTTGAGCTCCTCAAGAGTAAAACCACGACCAGCAC
+GAACCTTCATG
+>TRINITY_DN513_c0_g1_i1 len=586 path=[564:0-585] [-1, 564, -2]
+GCGGACATTGTGTACTTCGTCAGATTGCATCATTATATAACACAAATGGGAATACCTATA
+ATAGATATACGTGGGCCATATGTTTTAACTCATTAAAGTCGGTGGTATAACTAGCCTCAA
+CTAGTAGAATTAGTCATTTAGTTGACTTCTTTGTGCTTGCCATGTTCACGATGGGGAATG
+ATTTTTCCGTCAGTCAAAATTTTAGTGACAACATCAACGTCCTTGCTAGTACCAAAGGTA
+TTCTCAAGTTCTTGTTTGGAAGCAGTAATTAATTGACCTTCGTTACCTTTGTTGTTGCTA
+GTTGTAAAAACTTGAAAAGAGTCGACGATCTCAGTTAAGGGAACAGTCTTGTCCTTGCGC
+CATCTCATGACATCGGGACCGTTTGAGGCGATGATAATAAAGGTAGTATCCTCAGGTTGG
+TAACAAACACGGGTTTGGTTGGCCTTAGAGCTAGACATTTTGGAAGTATTGATAAATATA
+TTAATAGACGGTTGGACAATGCAAAAAAATAAAATTTAATAGTCTTGTGAAAAGAGAGAA
+CAAACTATAGAATTATCCAAATACAAACAAACAATTCTTATTTTTG
+>TRINITY_DN514_c0_g1_i1 len=254 path=[232:0-253] [-1, 232, -2]
+CGTTTACCGTAAGTGCTTCTAAGCTCCTCTTACTTTTTGTAACGTTTTTTACATACTTTT
+GAATAACATCGATTCTTCTGATATATATAAATTTCAATCTTTTTTTACCTATTTAACCAC
+CTTTTTCCGCTCTTAACATCTCATGAGGAACTTTGGGTATCAATTATTGGAGTGTTTTAT
+ATACTTTCTGATTACTATCGTTTTCTTGCTCTGTTTTCTTTTTTTCATTATAGACGAATG
+CAGAGCTAGCCTTT
+>TRINITY_DN515_c0_g1_i1 len=633 path=[611:0-632] [-1, 611, -2]
+CATTCATTAACCACACTACGAAAAGAAGAATCATGTCACAAAAAGAAGTTGCCGATTTTG
+GTCTCATCGGTTTGGCCGTCATGGGTCAAAACTTGATTCTCAACGGTGCCGACAAGGGCT
+TTACCGTCTGTTGCTACAACCGTACAACTTCCAGAGTTGACGAGTTTTTGGCAAACGAAG
+CCAAAGGTAAATCTATTGTTGGTGCTCACTCCCTTGAGGAATTTGTTTCCAAGCTTAAGA
+AGCCTCGTGTTTGTATTTTGCTTGTTAAGGCTGGTAAGCCTGTTGATTACCTTATTGAGG
+GATTGGCTCCTCTCCTCGAGAAGGGCGATATCATTGTTGACGGTGGTAACTCCCATTACC
+CTGATACTACCCGCCGTTGCGAGGAGTTGGCCAAGAAGGGCATTCTTTTTGTTGGTTCCG
+GTGTTTCTGGTGGTGAAGAGGGTGCTCGTTACGGTCCCTCTTTGATGCCTGGTGGTAATC
+CCGCTGCCTGGCCTCGTATCAAGCCCATCTTCCAAACTTTGGCCGCCAAAGCCGGAAACA
+ACGAGCCTTGCTGTGACTGGGTTGGTGAACAAGGTGCTGGTCATTATGTTAAGATGGTTC
+ACAATGGTATCGAATATGGTGACATGCAATTGA
+>TRINITY_DN516_c0_g1_i1 len=832 path=[810:0-831] [-1, 810, -2]
+ATAATAGAGGAACAAATAAGCTGGATTCGGGCCAGCAAATATTGATACTTGAATAGATTC
+TAACCAAGAAGAGTGTAGTGTAGGTAATCGAACGAACATATAAGAGCTCTCGATCCCTTA
+AAGAGGTATACGGAATTGAATATTTAAAAAGAAGTTTACTCGGTTTCAGTACCGCCCTCG
+TTCTCAGAGTCCTCCTTAAGGGGTTGAAGGACGATGATCAAATCCTTGGGATCCATGTCT
+TCATAGGAAATGTTATAAACGGCAGTGAACAAGGGGAAATCCTTGACCATATCCTTGGTG
+AGAAGGAATTCATGAACATCCTTGGAAGTGGCAGCTCCTTGAAGAAGTTGACCACCTAAG
+AGCTCTTTTTCAAGCGTCTCTAAAGATTTACCAGTCTTGACAAATGCTTCAGCACAACGA
+TTGTTACGGCCACCCAAACAAGAAGTGACCAAGTCAGCGATACCGCAAGATTGCTCAACC
+ATGGTACGAGGATCAGAGTCGAAGAAGGTAGTAGCAAACTTTTGCATCTCCAACAAACCA
+CGACGCATAATAGCGGCCTTGGTATTACCGCCCCATTCCAAACCATCAGCGAAACCAACG
+GCCATGGCAACTACGTTCTTCAAAGCACCACCCAAGGCGACACCGGCAACGTCGTCAACG
+GAGACAACTGAGAAGTAAGGGCGATCAAAGACGGCGGCGATTTGCTCGCGAGGGATATCA
+ACTTCATTAGGAGGGTTGAAACCAATAGTAGTCTCACAGAATTGCTCACGGGCAACTTCG
+TTTGCAACGTTAGCACCAGAAAGAACACCACAGTAAATACCGAGTTTCTCGC
+>TRINITY_DN517_c0_g1_i1 len=934 path=[912:0-933] [-1, 912, -2]
+ACTCAACGGTCGTATATTACTACCTCTAAAGTCACTAAGCATTCTTAATAAGCTCCAACC
+GTTTAATCTTTAATTTATTACCAACTCTAATCAAAATGTACTCTCGTGTTCTTTCCGTCG
+CTGCTATTGTCACCATGGCCTTGGCCGTCCAAGCCGCCAACTCTACCGCCCCTTACGGTA
+ACACCACCAACTCCACTGGTACCACCAACGGTACTAACGGCACCAACACCACCACCAGCT
+CTACTGCCACTCAATCTAGCGCTGCCTCTATCACCAACTTCAGCTCTGGTGCCTTTGTCA
+TTGCCATGATTGCTGTCGCTTGCTCTGTCATGTCTCTCTAAATTGCCTAACCCTTTTCAA
+AACTAGGCGTTTTTCCTACTTGCCGGCGTTGAGCAAGTAATCTTGTTTCCAGGTGCCCCT
+AGCACCTGCCCTTTACCAAAGAGACGCTGTGGCTAGTTTGCCTTTCTCGCAACAACACGA
+CGGCGTTCTTTCCTTTCATTTCTAGGGAGGTTTCTATAATAATATACCTTCACGCAATTT
+TTTTAGATGGGTCTTAAATTATATTTTTTTCCTCTGACAAAGAATTGTTATTTTTTTCCA
+TTCAACTATATTATTCTGTGTGGTGTCGAGAGCACGCCGGTTTGGTAATTAACAACATAG
+CGAGATAGGGATAAATGGTGTACATATTGATTCTAGGTATTCTTACATACGTTCTTTTTT
+TTCGAAACTTATAATTTTCTTGTGATTAGTTATGGCGAGAGTCTAAGTGATTTGCGGGTG
+ATTGTTTTTGTTTTGCGCATTTTTATTATTTTTTATTTTTGTTTTTCCCCTTTCTCCTCT
+TTCAAATTATTTTTCGTTTGTATCTGTGTTTGTGTGCGTGTTTAGAAAGTGTTTTTAATT
+GTTTCGTGTTTTTGATATAGTCGAGTAGCTTTTT
+>TRINITY_DN518_c0_g1_i1 len=251 path=[229:0-250] [-1, 229, -2]
+TTGGAAAGTTGAGCCTCGGCAACCAAACAGGCAGCCTCCTCACGAACAAGCTCTTGCTCC
+ATGGTGACCAAGCGAGGGGATTCAGGATCCTTATGCTTAAGAGCATAGATTTGATCCAAG
+AGCTTTTGCTTCTTCTCACGAGAGGGTTGGACAGAGGACTCGATGTTACGGATGGACTTC
+AACGTCATACGGTATTGGTCATAACGATCGATCAAGTAGTTCTCCAACTCTGCCATCTCG
+TAAAACAAGAC
+>TRINITY_DN519_c0_g1_i1 len=230 path=[208:0-229] [-1, 208, -2]
+CTCAGCGTTTCATTTACACAATTGCGCAGGACGTAAAGAGAGAATTAAAAATTTCTATAC
+ATTTCGAAAATAAAAACGTCCGCGGTATAACTCGAAAAAAGAAAACAAAAATATAAATAG
+ATAGTGCAGCTCACGGAAACAAAAAATTAGACTTGCATATCGTTTGTTACATTCCACAAC
+ACTCAAGGTTAAATTTTGTTTCGAAAGGCAAAGTAAATGAGGGAAGGATT
+>TRINITY_DN520_c0_g1_i1 len=666 path=[644:0-665] [-1, 644, -2]
+CGCATCCGCACAACACCAGCATTGCACCATGTCTAAGGTCAGCGTTGCCTCGGTCCGCTC
+TAACGTCGAGCAAATTCTCAAGGGCTCTGAAGAGAAGAAGCGTAACTTCACTGAGACTGT
+CGAGCTTCAAATTGGTTTGAAGAACTATGACCCTCAACGTGATAAGCGTTTCTCCGGTAC
+TATCAAGTTGCCCAATGTTCCTCGTCCCAACATGGCCATTTGCATTCTCGGTGATGCCCA
+TGATTTGGATCGTGCCAAGCACGGTGGTGTCGATGCTATGTCCGTCGATGACTTGAAAAA
+GCTTAACAAGAACAAGAAGCTTGTCAAGAAGTTGGCCAAGAAGTATGATGCTTTCATTGC
+TTCTGAAGTCCTCATCAAGCAAATTCCTCGTCTGTTGGGTCCCGGTCTTTCCAAGGCTGG
+TAAGTTCCCTTCCCCTGTCTCCCATGCTGACGACCTTTACGGTAAAATCACCGAGGTTAA
+GTCCACTATCAAGTTCCAATTGAAGAAGGTCCTTTGCCTTGGTGTTGCTGTCGGCCATGT
+CGAGATGTCTGAGGAGCAATTGATTGCTAACATCATGCTTGCCGTCAACTTCTTGGTTTC
+TTTGTTGAAGAAGGGCTGGCAAAACATTGGCTCCTTGGTCGTCAAATCTACCATGGGTAA
+GCCTCA
+>TRINITY_DN521_c0_g1_i1 len=606 path=[584:0-605] [-1, 584, -2]
+GTAAAAAGTATATAGGGTATAAGGGAAAATATATTTCATTACTTCAAATCGATAAAGATT
+TTGAACCAAAGAATATATAAGCACCCACTTTTTGAAAAAAATTTGTAAAAAAAGTCGAGC
+AAATATATATATATGATGGTATCACGTAACCTCGTTATATATCATAAAATTAGATGGTAA
+TTGGTCAAGGATGCAACCTCGCATTAGAAAGTGATGAGATGGATCGTTCATAAAAACAAT
+CCAACCACTACCTACTAAATTGAGGAGACCTCAAACCATTTTCGTCCGTTCATCGGTAAA
+GAAATCATCCCGATGCTTTGGTGGATTGAGTTTCACCAGCCAAAAGCATGAATTTTAAGT
+CATAAGAACCTCTTTACAACTTGTCATCAACAAAGCGTTGAGCCTTGTCATGAGCCTCTT
+GAGAGGTGCTCTTGTCCTCGTCAGAGGTAAAAGCAGAGGCGACCTTGTCGTAGGCACCAG
+TAATGGATTCCTTGGCCTTGTCGAGGGTAGACTTGGAGGAGTCAGGAGTCATTTTCTCCT
+TGCCTTGTTCAGTAAAAGACTTTCTTGCGGGATCAGACATTTTGAATATTTAAGACAATT
+AAATTG
+>TRINITY_DN522_c0_g1_i1 len=1220 path=[1198:0-1219] [-1, 1198, -2]
+GTCGTATAGAACACACACACAAATTAGCAAAATGGGAATTCTCGATATTGTACCTACTGG
+TGTTATTACAGGTGACAACGTTTTAAAGTTGTTCACCTACGCTCGTGAGCACGGATTCGC
+CATCCCTGCCATTAACGTCACCTCCTCCTCCACTGCTATTGCTGCTCTTGAGGCTGCTCG
+TGAGGCTCGTTCCCCCATCATCTTGCAAACCTCCAACGGTGGTGCTCACTTCTTTGCTGG
+TAAGGAATCCTCCAACGAGGGCCAAAAGGCCTCCATTGCCGGTTCCATCGCCGCTGCCCA
+CTACATCCGTTCCATCGCTCCTTTCTTCGGTGTCCCCGTCGTCATGCACTCTGACCACTG
+CGCCAAGAAGCTTCTCCCCTGGATGGACGGTATGTTCGAAGCCGATGAGGCCTACTTCAA
+GATTCACGGTGAGCCTCTTTTCTCTTCTCACATGCTTGACTTGTCCGAGGAGCCCAAGAA
+GGAGAACATTGCTCAAGTTAAGGAGTACTGCAAGCGTGCCGTTCCCATGAAGATCTGGAT
+CGAGATGGAGATCGGTATCACTGGTGGTGAGGAAGACGGTGTCGACAACTCTCACGTCTC
+CCACACCGAGCTCTACACTCAACCCGAGGACATCTGGGATGTCTACCGTGAGCTCTCCTC
+CGTTACCCCTTACTTCTCCATTGCCGCCGCTTTCGGTAACGTCCACGGTGTCTACAAGCC
+CGGTAACGTCAAGCTCCAACCCGCTCTTTTGGGTCAACACCAAGCCTATGTTAAGGAGCA
+ACTCAAGACCACCAACGACAAGCCCGTTTTCTTCGTCTTCCACGGTGGTTCCGGTTCCTC
+TGTCAACGAGTTCCGTACTGGTATCAAGTGCGGTGTCGTCAAGGTCAACATTGACACTGA
+TACCCAATTCGCCTACGTCGAGGGTGTCCGTGACTATGTCTTGAAGTACAAGGACTACCT
+TATGACCCCCGTCGGTAACCCCGAGGGAGCTGACAAGCCCAACAAGAAGAAGTTCGACCC
+TCGTGTCTGGATCCATGAGGGTGAGAAGACCATGACCAAGCGTGTTCTTACCGCTCTTGA
+GGACTTCTACACTGTCAACACTCTCTAAATTTGTGGTTTTTGAAAGATGGAAATGATTGA
+ATAGACGGTGGGCTTCATTAAAATTATATTTTTTTGTCCCCTTAATGAGAGTTCATACTG
+TTTTGAAATTACGTGTTTGA
+>TRINITY_DN523_c0_g1_i1 len=772 path=[750:0-771] [-1, 750, -2]
+CCAAACTTGGCCGGAGCAGATAATCAGCTTTTCAATCTTTTCAGGTGGTAAAATAGATTT
+TCCATGCTCCTCCTCTTCAAGAATCAGCTTAAATCCATGCTTTTCGTCAAACTCATCGAT
+AGTGGAACGGGCAGCAGGGTGACGAAGTAATGATTTTGAGAAAAAGATAACTAATGGTTT
+ACGGAATTGCCGGTGAATGTTACGCCTAAGAGCATGGAAATACTGCGATGGCTTAGTAAC
+ATAAATGGCTTGAATATTACAATCTTGATGTTGACGTTGCAACTTCTCTTCGGAAGGGAA
+CTCTCGAGGGTCTTCATTACATAATTGTAAATATCTTTCCATACGAGCAGAAGAGTGCTC
+AGGACCTTGACCATCATAACCATGTGGTAAAGAAAGTACGATACCGGTACGTTGAAGCCA
+CTTAGTTTCACCAGCTGCAATAAATTGATCTATGATACATTGAGCATTGTTAGCAAAATC
+ACCAAATTGAGCTTCCCAGACGACAAGAGCATTAGGTGATGACAAAGAGTAACCATACTC
+AAAACCTAAAACACCATATTCAGACAGAGAAGAGTTACGAATAACAAAGCTTGCTTGATT
+AGGGCTTAGATGATTCAATGGAATGTAAACGTTTTCGGAACTCTGATCGTGTAAAACAGC
+GTGTCTTTGGGAAAATGTGCCACGTTCGACATCTTGACCGCTCACACGAACGTGATGACC
+TTCTTCTAAAAGAGTACCAAAGGCCAATGCCTCGGCGGTTGGCATATCGATA
+>TRINITY_DN524_c0_g1_i1 len=875 path=[853:0-874] [-1, 853, -2]
+TAAGCGTCTTTCCAAATCCGACCCTTGTGTTTTGTGTACCACCAGTGAATCTGGTGAACA
+CATTGTTGCTGGTGCTGGTGAGCTCCACTTGGAGATTTGCTTGAAGGATTTGCAAGAAGA
+CCATGCTGGTATCCCTCTTAAGATTTCTCCTCCCGTCGTTTCTTACCGTGAGTCCGTTAG
+CGAGCCCTCTAGCATGACCGCTCTCTCTAAGTCTCCCAACAAGCACAACCGTATCTTCAT
+GACTGCTGAGCCCATGAGTGAAGAACTCTCTGTCGCCATTGAGACTGGTCACGTCAATCC
+TCGTGATGATTTCAAGGTTCGTGCTCGTATCATGGCTGACGAGTTTGGATGGGATGTCAC
+TGATGCTCGTAAGATTTGGTGTTTCGGTCCTGACACCACTGGTGCCAATGTTGTTGTTGA
+TCAAACCAAGGCTGTTGCTTACTTAAACGAAATCAAGGATTCCGTTGTTGCTGCTTTTGC
+CTGGGCTTCCAAGGAGGGTCCCATGTTTGAGGAGAACTTGCGTTCTTGCCGTTTCAACAT
+TCTTGATGTTGTTTTGCACGCTGATGCTATTCACCGTGGTGGTGGTCAAATTATTCCTAC
+TGCTCGTCGTGTCGTCTACGCTTCTACCCTTTTGGCTTCTCCCATCATCCAGGAGCCCGT
+TTTCTTGGTCGAAATCCAAGTTTCCGAAAACGCTATGGGTGGTATTTACTCTGTCCTTAA
+CAAGAAGCGTGGTCATGTCTTTTCTGAGGAGCAACGTGTTGGTACTCCCTTGTACAACAT
+CAAGGCGTACCTTCCCGTCAACGAGTCTTTCGGTTTCACTGGTGAACTTCGTCAAGCTAC
+TGCTGGTCAAGCTTTCCCTCAATTGGTATTTGACC
+>TRINITY_DN525_c0_g1_i1 len=232 path=[210:0-231] [-1, 210, -2]
+CGGAGACACGGGGGAGATCGACACCGACCATAGAGGAGTGAGCACGGTGAGCGGTACCGA
+AAGCATCGTTGACAAAGATGTCACCGAGAGAAGTCAAAGACTTACGGAAAGCCTCGACGG
+CAGAAGCGTCAGCCTTAACCTTCTTACCGTCAACCTTGGCGGAACCCTCCTCCTCGATGT
+GGAAACGCAAGTTCTCCAAAAGGATGACCTCACCACCCTTGGCTTCCTTGCA
+>TRINITY_DN526_c0_g1_i1 len=215 path=[193:0-214] [-1, 193, -2]
+TTTCATTTGATTTGATTTGATTACTCTCTTGTCTATAGTACATTTCTACCTCAATTTGTA
+CTAAACGATTTCTCATACTCTTATACTATACTATACTATACTATTTTAATTTTTCTTTTT
+TCATTCAGCCCTCATAACACGACTATTCTTCTACCCTCTACTACATAGTCTTGTTATAAT
+TCTCTCCTATACATAAAAGTCATAGTCAAAAAGTT
+>TRINITY_DN527_c0_g1_i1 len=297 path=[275:0-296] [-1, 275, -2]
+CGAGTACAACAGTGTTAAGGGTAGCAAATTGTATACCACCGAACCCGTTCATCCACACGC
+CGTTACCACTAATGAACCTACTGATGTTAGTACTAAGAGCAAGTCCGCCGCCTATCACTA
+TCCTGCCACCACTGAGACTGTTTCAAGCAAAGCAGCCCGCTCTGCCACCACTCCTGCTTA
+TGTTGGCGGTGCCACTAAAACTCCTAGTACGACAAAGGCTGTTGAATCTACTCCCAGCAC
+CTTGCCTACTTCAGCTTCCACAAATGCTGCTGCTACTACTACCACTAAAAAGCCCAA
+>TRINITY_DN528_c0_g1_i1 len=417 path=[395:0-416] [-1, 395, -2]
+GTCGGAATTCCAGAAGGTCGTTGTGATTGACGCTAAGGGACATCTCCTTGGACGTTTGGC
+ATCTGTTGTCGCCAAGCAACTTTTGGGCGGCCAGAAGGTTGTTGTAGTTCGCTGTGAAGA
+ATTGAATATTTCCGGCCATTTCTTCCGTAACAAGCTCAAGTACCTTGCCTATTTGCGTAA
+GGCTTGCCGTTACAACCCCAGCCGTGGTGCCTTCCACTTCCGTGCTCCCTCTCGCATTTT
+CCAAAAGGCTGTTCGTGGTATGCTTCCCCACAAGACTGCTCGTGGCCAAGCTGCCTTGGA
+ACACTTACAAGCTGTTGAAGGTATTCCCCCTCCTTTCGACAAGCAAAAGCGTGTTGTCGT
+CCCTGCTGCCCTCCGTGTTTTACGCCTTAAGCCTGGACGTAAATACTGCACCGTCGG
+>TRINITY_DN529_c0_g1_i1 len=238 path=[216:0-237] [-1, 216, -2]
+CGTCGGTCTAAGTTCCTTGGAACAGGACGTCAGAGAGGGTGAGAACCCCGTCTTTGGTCG
+ATTGGATATGCCATATAAAGCGCTTTCGAAGAGTCGAGTTGTTTGGGAATGCAGCTCTAA
+ATGGGTGGTAAATTTCATCTAAAGCTAAATATTGGCGAGAGACCGATAGCGAACAAGTAG
+AGTGATCGAAAGATGAAAAGAACTTTGAAAAGAGAGTTAAATAGTACGTGAAATTGCT
+>TRINITY_DN530_c0_g1_i1 len=678 path=[656:0-677] [-1, 656, -2]
+ATGATTCGTCGTGCTATGCGTGGTGTCATCAACGATATGCCTGAGCTTGAGCGTCTTTTG
+CCTGTTGTTCGTGGTAACGTTGGTTTCGTCTTCACCAACGCTGATTTGAAGGAAGTCCGT
+GAGACCATTATTGCTAATGTTATTGCTGCTCCTGCTCGTCCTAACGCCATTGCTCCCTTG
+GATGTCTTTGTCCCTGCCGGTAACACTGGTATGGAACCCGGTAAGACCTCTTTCTTCCAA
+GCTCTTGGTATCCCCACCAAGATTACTCGTGGTACCATTGAAATTACTTCCGATGTCCAT
+TTGGTCTCCAAGGATGCTAAAGTTGGTCCTTCCGAGGCTACTTTGCTTAACATGTTAAAC
+ATCTCTCCCTTCACCTATGGTATGGATGTTCTCACGATCTATGACCAAGGAAACGTCTTT
+AGTCCTGAGATTCTTGACGTCTCTGAGGAGGATCTTATCGGTCACCTCTTGTCTGCTGCC
+AGTATTATCACTGCCATTTCCTTGGGCGCTAACTACCCTACTATCTTATCCGTTATGCAC
+TCTGTTGTCAACGCTTACAAGAACTTGGTCGCTGTCTCTTTGGCCACTGAGTACACCTTC
+GAGGGTACTGAACAGACTAAGGCTTTCCTTGCTGATCCCTCTGCTTTCGTAGTCGCCGCT
+GCTCCTGCTGCTGCTGCT
+>TRINITY_DN531_c0_g1_i1 len=682 path=[660:0-681] [-1, 660, -2]
+CTACATTTCAATAGTAGAACTAGGATCAAAATGGCACGTAAATTCTTTGTCGGTGGTAAC
+TTTAAGATGAATGGCTCTTTGGAGTCCATGAAGACTATTATTGAGGGTTTGAACACCACC
+AAGCTTAACGTTGGTGATGTCGAAACTGTCATCTTCCCTCAAAACATGTACCTCATCACC
+ACCCGCCAACAAGTCAAGAAGGATATTGGCGTTGGTGCCCAAAACGTCTTCGACAAGAAG
+AACGGTGCCTACACTGGTGAGAACAGTGCTCAATCTTTGATTGATGCTGGTATTACCTAC
+ACTTTGACTGGTCACTCCGAGCGTCGTACCATCTTCAAGGAGTCTGACGAGTTCGTTGCC
+GACAAGACCAAGTTTGCCCTTGAACAAGGTCTTACTGTCGTTGCCTGCATTGGTGAGACT
+TTGGCCGAGCGTGAGGCTAACGAGACCATCAACGTTGTTGTTCGTCAATTGAACGCCATC
+GCTGACAAGGTCCAGAACTGGTCCAAGATTGTCATTGCTTATGAGCCTGTCTGGGCCATT
+GGTACTGGTAAGACTGCCACCCCTGAGCAAGCTCAAGAGGTTCACGCTGAGATCCGCAAG
+TGGGCTACCAACAAGCTTGGTGCATCTGTTGCCGAGGGTCTCCGTGTCATCTACGGTGGT
+TCCGTTAACGGTGGTAACTGCA
+>TRINITY_DN532_c0_g1_i1 len=306 path=[284:0-305] [-1, 284, -2]
+TTGGGCAAGATACGGCGTTGAGCGATGAAAATTACATGACGGTCAGCAAACTTCTTCTCG
+AGCTCACGGGTCAAACGAGCTTGGCATTTGTGGAAAGCCTTAAGAAGGGGTTGGGGCACA
+AAAACAACGATTGCCTTCTTTCCACCTCCAACTTCAACTTCGCGAGCAGAAGTAATTTGG
+AGAGGGCGGAGCTCCTTGGCCATGTCCTTAGAAGAACTCTCTAAATCATAGAGACATTGA
+GCAACAAGGAGGTCGGTTTCAGTGGGCTGGGAGCTCGAACGCTTGACAATCTTGTTGAGA
+GCAGAC
+>TRINITY_DN533_c0_g1_i1 len=316 path=[294:0-315] [-1, 294, -2]
+CGCTCCCGAGGCAGTTCCCAAGGCTTTAGAGAAGACATTGAAAGACTTAAAGTTAGACTA
+CTTGGATGAATATCTTATCCATTGGCCTGTCAGCTTTAAGACTGGTGAGGATAAATTCCC
+CAAAGACAAGGATGGAAATCTCATTTACGAGAAAAACCCCATTGAGGAAACCTGGAAGGC
+AATGGAGAAGCTTTTGGAAACTGGCAAGGTACGTCACATTGGTCTTTCCAACTTCAACGA
+TACAAACTTGGAGCGTATCTTAAAGGTTGCCAAGGTTAAGCCAGCCGTTCATCAAATGGA
+GCTTCATTCCTTCTTA
+>TRINITY_DN534_c0_g1_i1 len=494 path=[472:0-493] [-1, 472, -2]
+AGGATGTGAGGGACAATGGTGGACTTGTAGTAGGGCAAGACACGCTCGGCGGTGTCCTTC
+AAGGACTCACCGTTGGGAGGAGCAATGTCATAAGAACGGCGCCAGATTTGGACTTGCTCA
+GCACCCCATTTCTTACGAGCATCATCCTTGTTCAAACCTTGCAAGTCACCGTAGTAACGC
+TCGTTGAGCTTCTCGCTCTTGATGGTCTCCAAGTTGGGCTCACCAACCTCCTCCAAGATG
+ATTTGGCAGGTCTTTTGGGCACGTTGAAGAGCAGAGGTGAAGGCAATGTCAAACTTGTAG
+CCACGAGACTTCAAGCGCTCACCACCGAGCTTGGCCTCCTTAATACCAGTCTCGGACAAG
+GCAGGGTCCTTCCAACCAGTGAACAAGTTCAACTTGTTCCATTCGGATTCACCGTGACGG
+GTAAGGACGAGCAAGTTAGGTGCAGCTTCGGTAGTCATCGTTAACGTTGTATAGTGTGGT
+GTAAGTAAAGTGAC
+>TRINITY_DN535_c0_g1_i1 len=520 path=[498:0-519] [-1, 498, -2]
+GTACTGGTAAGACTCAAAAGATTACCATTACCAATGACAAGGGTCGTCTTTCCAAGGAAG
+AAATTGATCGTATGGTATCTGAAGCCGAGAAGTACAAGGCTGAAGATGAAGCAGAAACTT
+CTCGTATTCAAGCCAAGAATCACCTGGAGTCTTATGCATATTCTCTTCGTAATTCCTTGG
+ACGATCCTAATCTCAAGGATAAGGTCGATGCTTCAGATAAGGAAGCCATTGATAAGGCTG
+TCAAAGAAACCATTGAATGGTTGGATCACAACACCACTGCTGCCAAAGATGAGTATGAGG
+ACAAGCAAAAAGAACTTGAAGGTGTCGCGAATCCCATCATGGCCAAGATTTATCAAGCAG
+GAGGCGCACCTGGTGGTGCACCTGGTGGTATGCCTGGCGGTGCCCCTGGTGGTGCTCCGG
+GCGGTGCTGACAATGGACCTGAGGTTGAAGAAGTGGATTAGGTTTAAACACTTATTACAG
+CTTAAAAATTGCCAGAAAAATTTTGGAGGTTTGGTCACTC
+>TRINITY_DN536_c0_g1_i1 len=284 path=[262:0-283] [-1, 262, -2]
+TAGAAGTACGCTTCAAACCAACATCCAAGAAAACCTTGAAAGGACGAGGACCATCCTCGA
+TGGCCTCGGTAAGCTCAAATTCACCTTCGGGTTCAGTGACACCCTCATATTTGTCAGCGA
+GGCCAACCTTGGCAAGAGCACGACGAGCGACCAAAAGACCGGTAGCGTAGGCGGCAGTCC
+AGTTGGCCAAACCCCATTTGATACCGTAGCGAGGGAGCTCAGAAGAGTGAGCATGAGCAA
+GAACATAGTCACCGTTTACTCTAGAAGAAACTATTTGGCATGTG
+>TRINITY_DN537_c0_g1_i1 len=268 path=[246:0-267] [-1, 246, -2]
+GGACCAAGGAGTCTAGCATCTATGCGAGTGTTTGGGTGATGAAAACCCATCCGCGAAATG
+AAAGTGAATGCAGGTGGGAACGCCCTTGTGGCGTGCACCATCGACCGACCCGGAAGTTTG
+TCAATGGAAGGGTTTGAGTAAGAGCATAGCTGTTGGGACCCGAAAGATGGTGAACTATGC
+CTGAATAGGGTGAAGCCAGAGGAAACTCTGGTGGAGGCTCGTAGAGATTCTGACGTGCAA
+ATCGATCTTCAAATTTGGGTATAGGGGC
+>TRINITY_DN538_c0_g1_i1 len=593 path=[571:0-592] [-1, 571, -2]
+AGGATATCAAATTGTAAATTGTCATATAAACAGAGTAATAATTTTTAACGTAAAGTTACT
+AAAACAAAAGCTAAACGTAGTTGTCATTAAGACATCTAAGCATCATAGGTAGTAGCACTG
+ATGTTACCACCGTGACCGGTCCAGTTAATGTGGATATCCTTGTCAGCAGGTAAGCTCTTA
+TCAGCAGCTTCAGGCAAAACACGGAAAGTATGGGCACCAAAGTAGTCACGTTGAGCTTGC
+AATAAGTTAGCAGGCAAAACAGCACTACGATAACCGTCGTAGAAGGAAAGACCGGTAGAA
+GTGGCAGGGACTGGAATGCCCAACATAGCGGCTTGGGCAACAACTCTACGCCAACCAGCT
+TGAGCCTTTTCAACACCATTAGTGAAGAAAGGATGGAAAAGGATAGACTCGAGGTTAGGA
+TCCTCACGGAAAGCCTCAGTGATATCCTTAAGGAAGACGGAACGGATAATACAACCACCA
+CGCCACATCAAAGCGATACCGGCGTTGTTAAGCTTCCAGCCGTACTCCTTAGCAGCCTCA
+CGCATAAGCATGAAACCTTGAGCATAAGAGATAATCTTGGAAGCGTACAAGGC
+>TRINITY_DN539_c0_g1_i1 len=227 path=[205:0-226] [-1, 205, -2]
+GTAAATCCACAGTGCTCATTCCCTCAGAAACAGCTTGCTTCAAGACTGCAAAAACAATGT
+GACGAGAAATTTCGCGAGCATTGTTCAAATCTGGCAAGAGGGCTTCATCAGCAGCAAATA
+AAGATCTGGGAACAGTGGCCAAAGCATCGGAAGCTGCTTTCAGCATACCATCACTCAATA
+ACTTGCAACGGGATAACACACATGCAACACCAAGAGCAGGGTAAAGG
+>TRINITY_DN540_c0_g1_i1 len=650 path=[628:0-649] [-1, 628, -2]
+CAACGTAGAACTCGGAGGAGGCAACATCAAGACCAATCTTGATCTTACCCTCGTAACCAG
+CCTTGTTGATGGCCTCAACAATAAGGTCAAGAGCCTCTTGAGGGGTTTGCAAATCGGGAG
+CAATACCACCCTCATCACCGACATTGCCGGCAGAAGAACCATAACGCTTCTTGGCAATGG
+ACTTGAGAGTGTGGTAGGTCTCAGCACCCCAACGCATAGCCTCGGAGAAAGAGGGAGCAC
+CGGTGGGGAGGATCATGAATTCTTGGAAAGCCAAGTCACCACCAGCGTGGGAACCACCGT
+TCAAGACGTTGAAAGAGGGAACGGGGAGGACATAGGGACCCTTGGTGCCAAAGTTCTCGG
+CAATGTACTTCCAGAGAGGGAGCTTCTTTTGGGCAGCACCGGCACGGCAGATAGCCATGG
+AGACACCCAAGATGGCGTTAGCACCCAACTTGGACTTGTTCTCAGTACCGTCGAGCTTAA
+GCAAGAACTCGTCGGCGGCCTTTTGGTCGGTAACGTCAAGGTTGGCCTTAACGACGGCAG
+GGGCAATGATGTTGTTGACATTGCCAACAGCCTTCAAAACACCCTTACCACCCCACTTGG
+TCTTGTCACCATCACGCATCTCAAGAGCCTCCCATATACCAGTGGAGGCA
+>TRINITY_DN541_c0_g1_i1 len=331 path=[309:0-330] [-1, 309, -2]
+CCGGATTGAAGGACATTGATGACGGGAGCAACCTCAGTGTTCTTGCCCAAATACTTGTCA
+CGAGCCTCGTTGGGGAGTAAAGTCCAGAGACGGTCCAAGTTGACAGTGGGACGCCATAAG
+GGATTCTTCATGAGGTGGAAACGGCGCATACCGACCTTACCAAAGTAACCAGGATGGTAC
+TTATCGAAGTGACTACGGAGGTGTTGTAAACCACCAGCCTTACCACGACCACCGGGATGC
+TTCCTGTGCTTGCCAATACGACCGTGACCAGCTGAAACGTGTCCACGAAGCTTACGAGTC
+TTAGATACGTGAGTTGGCATTTTGATGTCCT
+>TRINITY_DN542_c0_g1_i1 len=418 path=[396:0-417] [-1, 396, -2]
+TGTCTTTGAAGTTTTGGCTACCGCTGGTGACACTCACTTGGGTGGTGAAGATTTTGATAA
+CGCTTTGGTCGAGCACTTTATTCAAGAATTCAAGCGCAAGCAAAAGATTGACATCTCTGA
+CGATCCTCGTGCTCTTCGTCGTCTTCGCTCTGCTTGTGAGCGTGCTAAGCGTGCCTTGTC
+TTCTGTTACTCAAACCACCGTTGAGGTCGACTCTCTTTCCAACGGTATCGACTTCTCTTC
+TAGCATTACCCGTGCTCGTTTCGAGGACATCAACGCTACCACATTCAAGGCTACCATTGA
+TCCAGTCGCTAAGGTCTTGAAGGACTCCAAGGTCCCTAAGGCTGATGTTCACGACATTGT
+CCTTGTCGGTGGTTCCACCCGTATTCCCAAGGTTCAAAGACTCGTTTCTGATTTCTTT
+>TRINITY_DN543_c0_g1_i1 len=241 path=[219:0-240] [-1, 219, -2]
+AAAGAAATCAGAAACGAGTCTTTGAACCTTGGGAATACGGGTGGAACCACCGACAAGGAC
+AATGTCGTGAACATCAGCCTTAGGGACCTTGGAGTCCTTCAAGACCTTAGCGACTGGATC
+AATGGTAGCCTTGAATGTGGTAGCGTTGATGTCCTCGAAACGAGCACGGGTAATGCTAGA
+AGAGAAGTCGATACCGTTGGAAAGAGAGTCGACCTCAACGGTGGTTTGAGTAACAGAAGA
+C
+>TRINITY_DN544_c0_g1_i1 len=522 path=[500:0-521] [-1, 500, -2]
+AAAGAATAAAAGAAAAGAACTATAGGCATGTATTCATTAGGAATTAAAAGTGGATCACAT
+TCTCATTCCCTTACTTGGAAAGGTCCAAGACGATACGGCCGGCAATCTTGTTCTCATGCA
+TGAGACGGTAGACGTCGGGAAGAGTAGAGAAGGGTTGGACCTTGTAGTAAGGCTTGACGA
+GACCACGGGAAACGTATTCAAGAGCCTCGATAGAGTCAATACGGTTACCGACGTGAGAAC
+CGCAGATCTTAAGCATCTTAACGGTCAACCAGAAGATATCAGCACCGAGCTTGGCACCGG
+CAGGCATGGAAACAGTGACCATGGTGGAACCGGGACGGGCAAAGCCAGCAGCTTGCTCGT
+AAGACTTGGGGGAGGTGGATAAGACCAAGGTACCGTGGGCACCACCGTTGGTGGCAGCCT
+TGACAGCCTCAATCATGTCGGCTTCCTTCTTGAAGTCAAGGAAGACCTCAGCACCAAAGG
+ACTTGACGAGCTCAGCCTTGTCATCACCAGTATCAATGGCAA
+>TRINITY_DN545_c0_g1_i1 len=264 path=[242:0-263] [-1, 242, -2]
+TGAGCAGGTCAAAAAAACAGACACGCTGTTCAGTCAACCTAACCCATTTTCTTAAAGACA
+ACGCCAACAAATTCACGAATGTTAGAGAACTCTAACAGTAATTAAATCCATTATAGAATA
+GAGTCAGATGAGAAAGGCATTGAGAAGGAAGTGGCATCTTACTTGGAAGAAAGAGCAACG
+ACACCGGGAAGAGCCTTACCCTCCAAGAGTTCAAGAGAAGCACCACCACCGGTAGAGACG
+TGGGAAAGAGCATCCTCCTTACCG
+>TRINITY_DN546_c0_g1_i1 len=404 path=[382:0-403] [-1, 382, -2]
+TTTTGAACGAGTTCCCTCATGGAGCAAGAAGAAGTTTGGTTTTGGATAACTTGGAACATC
+TTCTGGCGGATGGCACGGATTTGAGAAGATTGAGCATAAGTAGTCTTCTTAACTTGGTTA
+GCACGACGACGTGTGAAGCCAATGACAAAGACACGGCAAAGATAACCATCAGTAGTCTTG
+ATAGTTTGATCAGCCTCGATGGTTGTTTGCCATTTGCGGACAAGAGAGCGCAACTTGTCA
+GAAGTGATGCTTAAACCATTGAAGCTGGTAAGGCAAGACTTGCCTTGGATATCTTCGACA
+CGAAGCTTAACCTTGCGGAATGCGTGCTCCTCATCCTTTTGCAAGTCAGCAAGGGAAACC
+TCCAAGATACGTCCCTTGAGGGAGTCATTGGCATTCTTTAGACC
+>TRINITY_DN547_c0_g1_i1 len=288 path=[266:0-287] [-1, 266, -2]
+TTTGGAAACCTTGACCAGTGGGCCAGTTGGTGGTGTTGGTGGTGTAAGAACCAGTGCTGG
+TGTCAACAGTGTCCAAGTATTGGGTAACGGTGGGATAAACAGCAAAGTTGGTCAAGTAAA
+GAGCAGCACTGGGTTCATCAGTGGAAACGACATTCCAGGTGATTTGCTCCTCGCCGTTGG
+TTTGCCAAGTGTCACCATTGGTGGGAGAGTTAATCGACATAGCGAGAGCAGAAGCAATCA
+AAGCCAAAAAGGAAATTTTGAACAACATTGTAGGTATCGTAAAAGAGA
+>TRINITY_DN548_c0_g1_i1 len=347 path=[325:0-346] [-1, 325, -2]
+TTGGGATTTATTTCCCATATTCTAGCGTTAAAGTTTCTTCGCGAACTGATCCGCGTTGAT
+GACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGTAAAAAGATAACGCAGGTG
+TCCTAAGGGGGACTCATCGAGAACAGAAATCTCGAGTAGAATAAAAGGGTAAAAGTCCCC
+TTGATTTTGATTTTCAGTGTGAATACAAACCATGAAAGTGTGGCCTATCGATCCTTTGTT
+CCCTCGAAATTTGAGGACAGAGGTGCCAGAAAAGTTACCACAGGGATAACTGGCTTGTGG
+CAGCCAAGCGTTCATAGCGACGTTGCTTTTTGATTCTTCGATGTCGG
+>TRINITY_DN549_c0_g1_i1 len=447 path=[425:0-446] [-1, 425, -2]
+CAGAAATCCATACATTTCACACAAAGTTTCGTATAACCAAAAGTTTTCTTTTTTTATTCC
+ATTTTTTTTTATTCTTTATTAATTAAAAATGGCTTTGACTGGCAGTGATATTTTCAAGGT
+AATTTTCGCCATTATTCTCCCTCCCTTGGGCGTTTTCTTGGAACGTGGCTGTGGTGCTGA
+CGTTATTATCAACATTCTTCTTTGTTGTCTTGGTTACGTTCCCGGTATTATTCACGCTCT
+CTATATCATCTTAAAATACTAAGCATCCCTCTATTTCAATCCTCTAATATTTGTTCTTTT
+CGCTACTTATCATGTTTATAAAGGAAAGTGAAATAGACATGTGTATTCTTTGCTTCTTCT
+CTTGTCTGTTCTAGGAATTTATTATTCGCTTCATTTAATACCAAATGTTGTGAGGATATC
+ATGGCTTTTGTATTAGTAAACAAAAAA
+>TRINITY_DN550_c0_g1_i1 len=275 path=[253:0-274] [-1, 253, -2]
+CGAGGATGATGCCCAAAGTGACGCTCGTTCCTGGAACGAGTATGAGGCTCAAGGTGAGCC
+CGTCCCCGTTGAGCAAGTCACCCACTTACAAGACGACGTTCAATCCGACACTAGCGAGAT
+CATTGAGAACGAGCCTGGCATGCACCCTCATGTCCATGCTGAGCGTATGTCTCGCATTGC
+TTCTGAGTCTAGCGATGCCGTTCCTCAGCAAACCGCCGTCCAGGTTGCTTAAAAAAACTC
+TTTACTTTTTTTCTATTTGTCGTCTTGGAGAGGGA
+>TRINITY_DN551_c0_g1_i1 len=304 path=[282:0-303] [-1, 282, -2]
+CTTCCCTCTCTCTCTTCCCGGACAAAGCGTCGAATTGGCTTGGGATGCTCCCGGTATGGC
+TGTCGGTCCTAACAGCTCCTACATCACTTCCACCTCTGCCGGAACTCCTCGTTATGCTGC
+TTGGATTTCCCAATTGAACGTTACTTACGCTTCCTTAAACATCACCGGCAACAACAGCGG
+TGTTACCTACCAACCCAGCTCTCACCTTTACAACGACTCTACCCAGCAAGTCATTAACGG
+TACCAACTTCTTGGTTCTCGTTGACGAAGCTATCCCCGTCAGATCGGAAGAGCGTCGTGT
+AGGG
+>TRINITY_DN552_c0_g1_i1 len=212 path=[190:0-211] [-1, 190, -2]
+ACCATCATCAACGTAGATGATACGGCCAGGTTGAATGACCTTGGTGATGTTCTTGTAGTC
+AATGTACATGACCTTGTCGTTACACTTCTCGGCATAAGCATCGTCGGTGGTGAAGATCAT
+CTCGTGACCAGAGGAGATGGGGTAGTCAGTACCGCCAACGGTGAGACCAGTACGAATCTC
+AGGTCCCTTAGTATCCAAGGCAATGGCCAAGG
+>TRINITY_DN553_c0_g1_i1 len=207 path=[185:0-206] [-1, 185, -2]
+CTTGCTGTCATCGTTGACATTGTTGATCACAAAAGGGCTCTTATCGACTCTCCTTGCTCC
+GAGTTCCCTCGTCAAGTCATCCGCTACGGCAGTGTTGTTCTTACTCACATTGTCATGAAG
+CTTCCTCGTGGTGCCCGTTCCGGCATTGTCGCCAAGAAGTGGAAGGCTCAAGATGTTTGC
+AACAAGTGAGCCTCTTCTGCTTGGGCC
+>TRINITY_DN554_c0_g1_i1 len=207 path=[185:0-206] [-1, 185, -2]
+TGAAGCGTATTTACCTACATTCTCATTTTCAGAGACACTGGGTTTTTGAGTACAAGAAAA
+TGCCATAAATGGACTGGAACACCATATTCTGCAAGTTTCACAATGACAACAACTAAGTTT
+AGGTTCTTCAATTATTGCCTTTAGGTGAATAGCTTTGCACAAACAGTTGCCTTCGTATTC
+AGGCATGATTTGTTGCTAAAATGTTCG
+>TRINITY_DN555_c0_g1_i1 len=250 path=[228:0-249] [-1, 228, -2]
+CGGAATCAGTTTGGAAAACAGGTTCTCCAGTGCAGTTATTGCTGGAATAAACATAAACGG
+TACAAACAGCGCCATCAGTGAGGGCATTAATGGAATTAATATTAGGATATGCCTGGCATT
+TGTTGAAGGAAATGGTATAAGAGGTAGATCCCTTGCAGTTAACATCATCGTAGGCCTTCA
+TTCCGAAATAAATAGTCTTTCTGTCTAGTAAAGCATCAGCTTCGGTACTAAGTGGAATAG
+CAGTTGAAAG
+>TRINITY_DN556_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2]
+AACGCCAGGACGGATTGGAGCATCTTGACGACCTTCATTGATATGAGATTCAATCATAAC
+ACCAACAATGGAAGAGTCGCCATTTCTGATTTGTTCGGCGATGCTCTTGGAGACCTTTGG
+TTGGTTCAAATGATTCTTGCTTGAGTTGCCATGAGAGCAATCGATCATGATACGAGGAGG
+AAGGTTGGCCTTCTCAAGATCTTTGCGAACGGCGGC
+>TRINITY_DN557_c0_g1_i1 len=237 path=[215:0-236] [-1, 215, -2]
+CCTCATAAATGGGAACAGTGTGGGTAACACCATCACCAGAGTCCAAGACGATACCAGTGG
+TACGACCAGAGGCATACAAAGACAAAACAGCTTGAATAGCAACATAAAAGGCAGGTGCAT
+TAAAGGTTTCGAAAATAATTTGAGTCATCTTCTCACGGTTGGATTTGGGGTTCAAAGGAG
+CCTCAGTCAACAAGCAAGGGTGCTCCTCAGGAGCAACACGAAGCTCGTTGTAGAAAG
+>TRINITY_DN558_c0_g1_i1 len=236 path=[214:0-235] [-1, 214, -2]
+ATTAAATCTAAGAAGTATCGTACGATCCCTGTCGGTTATGCTGGTGCCGATATTCCCGTC
+GTTCGTACTGAACTCGCCGCTTATTTGTCTTGCAATGCTACCAAGCTGAACAATGACACC
+AACTCTGAGACCGATTTCTTGGGTTACAACATGTACGAGTGGTGCGGTCATTCTGACTTC
+TACACTTCTGGTTATGCTGCCCGTACTCAAGAGCTTGAGAACTTTACTATTCCTAT
+>TRINITY_DN559_c0_g1_i1 len=787 path=[765:0-786] [-1, 765, -2]
+ACAGATTTGAATTGAATTCATATAATTTCAAGTTACTCGCAATTGTTTAAATTTTAAAAA
+ATGTCTTTGCAACCTTTTTTCGGCTTTCCCCCTACTGTCAACGACTTGTTCTCTGACTTT
+GTTAGTTACTCCCCTCGTTTGAACAACCAAATTCCTGGGGAGTTGTCTCCTTCGATTGAT
+GTGCATGAGGGTAAAGACACTGTTAGCGTTGATGTAGAACTCCCTGGTGTTAAGAAAGAG
+GACGTTCAAGTCCATTATGATAGCGGAAAACTTACTATTTCTGGCGAAGTCGTCAATGAG
+AGAAAGAATGAAAGCACCGAGGGTAACCAACGCTGGTCAGAGCGTCGCTTTGGCTCATTC
+TCTCGTACCATTACTATTCCAGCCAAGATTGATGCAGATCGCATTGAGGCCAACTTCAGT
+AATGGCCTATTGACTGTCACCTTGCCCAAGGTCGAGAAGTCCCAAACTAAGAAACAAATT
+GCTATTAAGTAAAATCGTCTCTTCCGATTTTAATATGATAGTTTCGAAATGGTTATGAGA
+CCAATCTTGTTGGATTGTGAGCATATATTATTGTTTGATTTAACAATCAATCATAACATA
+TGCAATTAATGATCCGCTTGCCATTGGATTGATGAATTTTGATAATGAATTGAACACGGT
+CTTCTAAACAGTAAAAGAGCATTTAAATTCCACATCAAGCAATTTATGGCCAGCTGTCAG
+ACAGTGTTTTAATGATCTTGACTACCACTTGTTACGATTCTCCAATGATGAGCAAGTGAT
+CTCTAGC
+>TRINITY_DN560_c0_g1_i1 len=301 path=[279:0-300] [-1, 279, -2]
+GGAACGGCTAGATTGGGAGGAAAGGGGTTGAGCGCCCTCGTAAGTGGAAGTAGTGTCTTT
+AGAGGCGTAGCCACCGGTTTGAGTGCTGGGAGGAGAGACGTTGGAAGTGTCGACGGCGGC
+ACGTTGAGGAGCGGCGTAGGCAGTACGCTCTGAAGAGGTAGCGCCAATGTCGGCATTGCC
+AGAAGGGTTTTTGCTAGAGGCATAGCTACTGTCGCCGTCATTAGCGGTGTTGCCGGCGGT
+GTAGCTACCGGGAACGGGATTGCCCATAACATCTCTAGCGGTTTTGCTGCTAGATTGACC
+G
+>TRINITY_DN561_c0_g1_i1 len=225 path=[203:0-224] [-1, 203, -2]
+GGTAGAAGAGTAAATACCACCGCTAATGGTGCTAGCAGCCAAAGTGGAATCACTACCTTC
+AAAGTCGAATTGCTCAGATTGAGCCAAACTACCTTGGTTTTGAGAAGTAGCTCCGTTGAA
+GTAAATTTGCCATCCGTCAGTGGGGAGATCAGAAGAGATGGAGATGTCGGTATCCAAAGA
+TCCAGCGGAGGATTGGACAGTTCCGAGATTAAAGTTTTGGTTGGG
+>TRINITY_DN562_c0_g1_i1 len=248 path=[226:0-247] [-1, 226, -2]
+ACGACCTCTTCAACTACGGTCTCACTAAATTCTCTGATGCCGAGTTTGACGAGGCCGGCA
+TTGACGCCGAGTACCGTCACTTGATTCGCTTCATGGCCCAACAAGAAATCGGCCACATCG
+AGCTTGTCACCAACATGCTTGGCCCCAACGCCCCCAAGGCTTGCTCTTACCAGTACAACT
+TTGACACTGTGGGCTCCTTCATTGACTTTGCTCAAACCCTTACTAAGTGGAGTGAATCCG
+GTGTCTAT
+>TRINITY_DN563_c0_g1_i1 len=203 path=[181:0-202] [-1, 181, -2]
+CGTAAAAGAGAAATATGTTGTGTAACAAACAAAAAAAAAGAGTAAATAAAACTAAGTTTG
+ATGTTATTTCGAGATGCTGGGTAAAAAATTCAAAAAAAAAAGTGAATTTTATCAGCAAAA
+AAGAGTTGGTGGGACAGGCGACAAGTAAATAAGGAAAGTATAACTAGCGCAGTAGGAAAA
+ACAGAAGATTGTATGAGATTTCC
+>TRINITY_DN564_c0_g1_i1 len=921 path=[899:0-920] [-1, 899, -2]
+CCCGACCAGTCAACATGCCAGAACAACTTGTGCTCCGTGCAACTCTCGAAGGTCACTCTG
+GATGGGTTACATCTCTTTCTACTGCCCCCGAGAACCCTGATATTCTTCTTTCCGGTTCTC
+GTGACAAGTCCATCATTTTGTGGAACTTGGTCCGTGATGACGTGAATTATGGAGTCGCAC
+AGAGACGTTTGACCGGCCACAGCCACTTCGTTTCTGACTGTGCCCTTTCCTTCGATAGTC
+ACTATGCCTTGTCTGCCTCTTGGGATAAGACCATCCGTTTGTGGGATCTTGAGAAGGGTG
+AGTGCACTCACCAATTCGTTGGCCACACCAGCGATGTCTTATCTGTCTCCATTTCTCCTG
+ACAACCGCCAGGTTGTTTCTGGTTCCCGTGACAAGACCATTAAGATTTGGAACATTATTG
+GTAACTGCAAGTACACTATCACCGATGGTGGTCACTCTGACTGGGTTTCTTGTGTGCGCT
+TCTCTCCTAACCCCGATAACCTTACCTTCGTCTCTGCTGGTTGGGACAAGGCCGTTAAGG
+TTTGGGATTTGGAAACCTTCTCCCTTCGCACTTCTCACTATGGCCATACTGGTTACGTAT
+CTGCAGTCACCATCTCCCCTGATGGATCTCTTTGTGCTTCCGGTGGAAGAGACGGTACCT
+TGATGCTTTGGGATCTTAACGAGTCTACCCACCTCTACTCTTTGGAAGCCAAGGCTAACA
+TTAATGCCCTTGTTTTCTCCCCTAACCGTTACTGGCTTTGTGCCGCCACTGGTTCTTCCA
+TTCGTATCTTCGATTTGGAGACTCAAGAGAAGGTTGATGAACTTACTGTTGACTTTGTTG
+GTGTTGGCAAGAAGAGCTCTGAGCCTGAGTGTATTTCTCTTACCTGGTCTCCTGATGGCC
+AAACTTTGTTCTCTGGCTGGA
+>TRINITY_DN565_c0_g1_i1 len=339 path=[317:0-338] [-1, 317, -2]
+TAGTCAAAGGCTCGAAATAAGCAAAAGCGGCAGAAGCCGACAACAGCTGCAAAGTAAATT
+TGGTAAAGGAGACCATGTTAATAAAGAGTGGCGACTGGTATTTATAAAGACTCTCTTTTT
+TTAAAGATTGAGAAATGTACTATTTATATATAGGATAGACACAAAAAGGAATGTGTTGGG
+CAAGAGAGAAATGAATCAAAAATTTGCGGGTATGAACAAAAATGATATTTCACTTTACCA
+AATGACTGTGATGAGGAATTGGCGACTGTATAAAAGAAAGTTTCTTGATAGCTCAAAGCA
+ATTGTGGCTAATCAACAAGTCTCGAGTAGTACGCCGAAC
+>TRINITY_DN566_c0_g1_i1 len=212 path=[190:0-211] [-1, 190, -2]
+GGGAAAACAAGCCCGAAGAGGTTGTTGAATTCCCTTCTCAAGGCAAATTCATCATTGTCG
+GTGTTCCCGGCGCTTTCACTCCTCCTTGTTCTTCTCAAGTTCCTGGCTATATTGCAAATG
+AGAAGCAATTTGCTGCCAAGGGCATCAGCGGAATCTATGTCGTTGCCGTAAATGACGTTT
+TCGTCACCAAGGCTTGGAAGAAGTCTTTCGAC
+>TRINITY_DN567_c0_g1_i1 len=892 path=[870:0-891] [-1, 870, -2]
+CGGTGATCAAACTGACAGGGGTACCCATTTCCAAAGCGTTTTGAGCAGTCCACTTACCAG
+TACCCTTCTGTCCAGCAGCGTCGAGAATCTTCTCAACCAAGGGCTTGCCGTCATCAGCCT
+TGTAACGCAAAACATCGCGAGTGATTTCAATTAAGAAAGAGTCAAGTTTACCAGTGTTCC
+ACTTCTCAAAAACATCGGCAATCTCATCACAAGACATACCAAGGCCACGTTTCATAATGT
+CATAAGTTTCGCAAATCAATTGCATGTCACCATATTCGATACCATTGTGAACCATCTTAA
+CATAATGACCAGCACCTTGTTCACCAACCCAGTCACAGCAAGGCTCGTTGTTTCCGGCTT
+TGGCGGCCAAAGTTTGGAAGATGGGCTTGATACGAGGCCAGGCAGCGGGATTACCACCAG
+GCATCAAAGAGGGACCGTAACGAGCACCCTCTTCACCACCAGAAACACCGGAACCAACAA
+AAAGAATGCCCTTCTTGGCCAACTCCTCGCAACGGCGGGTAGTATCAGGGTAATGGGAGT
+TACCACCGTCAACAATGATATCGCCCTTCTCGAGGAGAGGAGCCAATCCCTCAATAAGGT
+AATCAACAGGCTTACCAGCCTTAACAAGCAAAATACAAACACGAGGCTTCTTAAGCTTGG
+AAACAAATTCCTCAAGGGAGTGAGCACCAACAATAGATTTACCTTTGGCTTCGTTTGCCA
+AAAACTCGTCAACTCTGGAAGTTGTACGGTTGTAGCAACAGACGGTAAAGCCCTTGTCGG
+CACCGTTGAGAATCAAGTTTTGACCCATGACGGCCAAACCGATGAGACCAAAATCGGCAA
+CTTCTTTTTGTGACATGATTCTTCTTTTCGTAGTGTGGTTAATGAATGTTTG
+>TRINITY_DN568_c0_g1_i1 len=903 path=[881:0-902] [-1, 881, -2]
+GTCAGATTCCCCTTGTCCGTACCAGTTCTAAGTTGGTTGTTAAACGTACGCCAGTAAGAG
+CATAATCCCCGAGAAGGAGAAAAGCCCGACCAAGGACTTCCCGGCCGCCAAGGTCCAAGC
+AGGTCCAACATCCCTTCTCACCCCGAAAGGCGAGAAAAGACATCGGTCCACGCTCAGTCC
+AGCAACCGTTCAGGTTCCAAGGCCCAACGTACCCAACCCTTAGAGCCAATCCTTATCCCG
+AAGTTACGGATCCATTTTGCCGACTTCCCTTATCTACATTGTTCTATCAACTAGAGGCTG
+TTCACCTTGGAGACCTGCTGCGGTTATGAGTACGACCAGATGTGAAAACAAGGACCCGAA
+GGTCCATTCTTCCGTTGGATTTTCAAGGGCCGTCGAGAGCGCACCGGATTCAGCATGAGG
+CGCTGAACTCTTCCAAACACCATACCCTAGCTCCGGATAAACCGATTTCAGGGTAGTTCA
+ATGGTTTGTTAAAAAGAAAAGAGAACTCTTCCCAGGGCTCCCGCCGACGTCTCCAACTTC
+ATTTACGTTGCCGTGTTGATTCCACCTTCTGGTTCCGGAATATTAACCGGATTCCCTTTC
+GATAGGAGGCACGAAAAATCGTGCAACTTTCATACGGAGCTTCCCTATCTCTTAGGATCG
+ACTAACCCATGTCCAACTGCTGTTCACATGGAACCTTTCCCCACTTCAGTCTTCAAAGTT
+CTCATTTGAATATTTGCTACTTCCACCAAGATCTGCACTAGAGGCTGTTCGACCCAGGCT
+CACGCCCAAGGCTTCGTCACAAACCTCCACGCCTGCCTACTCGTCTGAGCTTCTCAAAGC
+TAACCCAGACGGTGAGGTATGGGTAGTACGCTTAAGCGCCATCCATTTTCAGGGCTAGTT
+CAT
+>TRINITY_DN569_c0_g1_i1 len=306 path=[284:0-305] [-1, 284, -2]
+GCTCAGACTCATTTGGTTGCTCCCTATGATCAATATTTACACCGTTTCCCTGCCTACTTA
+CAACAATTGAGTATGGAGTCTAACGGTAAGGCCATCACTCGTTCTGGCGATATGGTTAAC
+TACACAACTGGCAAAATCCTTTGGGGTGAGCCTGGTACCAACTCTCAACACTCATTCTTC
+CAATTAATCCATCAAGGTACCAAATTGATTCCCGCCGATTTCTTGATTCCCATTGAATCT
+CACAACCCTATTGATAACAACAAGCATCATCGTATGTTGTTCTCAAACTTTGCCGCTCAA
+ACCGAG
+>TRINITY_DN570_c0_g1_i1 len=341 path=[319:0-340] [-1, 319, -2]
+AGTCTTTAAGGCTGTTGGCGTTGCTCCTGATACTGCCAAGTACCCCAACGGTGCTCGTTG
+GTACAAGCAAATTGCCACTTATGACCTTGCCACTCTTCCTGGTACCGCCAAGGAGGTTTC
+TGCCTATGGTCCTGAGGGTGCTGCTGCCGCTGAAGAAGATGAGATCGATCTCTTTGGCTC
+TGACGAAGAGGAGGATCCTGAAGCTGAGCGCATTAAGGCCGAGCGTGTTGCCGAATACAA
+CAAGAAGAAGGCTGCTAAACCCAAGGCCGTTCACAAGTCTCTTGTCACCTTGGATGTTAA
+GCCTTGGGATGATGAAACCCCTATGGACGAATTGGAGAAGG
+>TRINITY_DN571_c0_g1_i1 len=432 path=[410:0-431] [-1, 410, -2]
+CATCAAAATGCCAACTCACGTATCTAAGACTCGTAAGCTTCGTGGACACGTTTCAGCTGG
+TCACGGTCGTATTGGCAAGCACAGGAAGCATCCCGGTGGTCGTGGTAAGGCTGGTGGTTT
+ACAACACCTCCGTAGTCACTTCGATAAGTACCATCCTGGTTACTTTGGTAAGGTCGGTAT
+GCGCCGTTTCCACCTCATGAAGAATCCCTTATGGCGTCCCACTGTCAACTTGGACCGTCT
+CTGGACTTTACTCCCCAACGAGGCTCGTGACAAGTATTTGGGCAAGAACACTGAGGTTGC
+TCCCGTCATCAATGTCCTTCAATCCGGTTATGGCAAAGTTTTGGGTAAGGGACGTCTTCC
+TGAGACCCCTGTCATTGTTCAAACTCGCTACGTTTCTCGCAGAGCTGAGGAAAAGATTAA
+GCAAGCCGGCGG
+>TRINITY_DN572_c0_g1_i1 len=378 path=[356:0-377] [-1, 356, -2]
+CCAGTATCTCAACATGTCTCTGGTTGTTCCCGACAATTTCCAACACATTCTCCGTCTCCT
+CAACACCAACGTTGATGGCAAGGTCAAGGTCATGTTCGCCATGACCCAAATCAAGGGTGT
+TGGTCGTCGTTACGCTAACATTGTTTGCAAGAAGGCCGATATTGACATGTCGAAGCGCGC
+TGGTGAGCTTACCACTGAAGAATTGGAGCGTATTGTTACCATTATTCAAAACCCTTCTCA
+ATTCAAGATTCCTTCCTGGTTCCTTAACCGTCAAAAGGATATAAACGATGGCAAGTCCTT
+CCAATTGCTTGCCAACAACGTTGACAGCAAGCTTCGTGAGGATCTTGAGCGTCTCAAGAA
+GATTCAAACTCACCGTGG
+>TRINITY_DN573_c0_g1_i1 len=452 path=[430:0-451] [-1, 430, -2]
+TGATCAAGAAGTAAATCATAACGAGTGGAGTGAAGGCAAGAGAAATCAGTTGCTCCCCAT
+TCCATGTTGATAAGCATATGATCACCAGTACACTTGCCAGCAAGCTTGGGAATTTGGTTC
+ATTTGCTCGACGTAAGCACCGTTGGTACCGGTTCCGAAAATGATACCCATAAAGGTGTCG
+CTCTCCTTTGAAGTATAAGCACGGGTAACGAGAGTACCGACGGTATCGTTGATGACAGCC
+TCGATTCTAATAGGAAGGTTACGAGCCTTGAAACCTTCAGTCAAAAATTGGGCAAAGTCC
+TTGTTGATGGCCTCAGGAATGTTAAGACCCTTGGTCCAACGAAGCAAGTAGCTCTCGGTG
+ATGGAAACTTGGTTGGCGGGATAAGAAAAGGTGAAACCCATAGGAAGGTATTCCTCCTCA
+GGGCAGCCAAACTTGGAAGGGAAGTGCTCCTT
+>TRINITY_DN574_c0_g1_i1 len=224 path=[202:0-223] [-1, 202, -2]
+CGATAAAATGCAGTCTCATCTGGTGAATTGTTAAAAACTTGCAGAAAGGGGCTACGTCGT
+AAGTAATACATAAATTGAGGGTAAAGGGTAAATTGTGAAGAGAGACGGAAACTTGACGGA
+TCATCTTTTCTATACTCAGCAAACTTTTGACAAAGTTTGATCAGCATTCGGTCGGTCCAT
+CGAAGGACGTCAGGTCCATCATCGACTTCCGCTTTGAAAGCTGC
+>TRINITY_DN575_c0_g1_i1 len=538 path=[516:0-537] [-1, 516, -2]
+GACAGAACGGCCAACGGGGAGATCATTGATGGTGATTTGACGCAAAACACCCTTGGGGTC
+GATCAAGAAAAGACCACGGAAAGCAACACCGGCATCCTCGATCAAGACACCATAGTCACG
+GGAAACCTTATGGCTAGGGTCGGCCAAAAGGGGAATGTTAATGCCACCAAGGCCACCTTC
+CTTACGAGGAGTGTTGATGAAGGCAAGGTGAGAGTACTCGGAATCGGTGGAGGTCAAGAT
+GACTTGAGCATTACGTTCAGCAAACTTGGAGGCGGCCTCAGAGAAAGCAACAATCTCAGT
+GGGACAAACAAAGGTAAAGTCAAGGGGATAGAAGCCCAAGAAGACCCATTTACCCTTGTA
+ATCGGCCAACTTGATTTCCTCGAAAGCACCGTTAACAACGGCAGTACCCTTGAAGTCGGG
+AGCAGGTTTACCGATTTGCAAACTCATGATTATAGATTAATGATATGGAATTTAGGTAGG
+TTTGGAACAAGTTAAGACAGTTGCTGAGCCCAAAGAGAATCGTACTATTTGGATGTTG
+>TRINITY_DN576_c0_g1_i1 len=702 path=[680:0-701] [-1, 680, -2]
+ACAACATCCAAATAGTACGATTCTCTTTGGGCTCAGCAACTGTCTTAACTTGTTCCAAAC
+CTACCTAAATTCCATATCATTAATCTATAATCATGAGTTTGCAAATCGGTAAACCTGCTC
+CCGACTTCAAGGGTACTGCCGTTGTTAACGGTGCTTTCGAGGAAATCAAGTTGGCCGATT
+ACAAGGGTAAATGGGTCTTCTTGGGCTTCTATCCCCTTGACTTTACCTTTGTTTGTCCCA
+CTGAGATTGTTGCTTTCTCTGAGGCCGCCTCCAAGTTTGCTGAACGTAATGCTCAAGTCA
+TCTTGACCTCCACCGATTCCGAGTACTCTCACCTTGCCTTCATCAACACTCCTCGTAAGG
+AAGGTGGCCTTGGTGGCATTAACATTCCCCTTTTGGCCGACCCTAGCCATAAGGTTTCCC
+GTGACTATGGTGTCTTGATCGAGGATGCCGGTGTTGCTTTCCGTGGTCTTTTCTTGATCG
+ACCCCAAGGGTGTTTTGCGTCAAATCACCATCAATGATCTCCCCGTTGGCCGTTCTGTCG
+ACGAGGCTCTCCGTCTTCTCGATGCCTTCCAATTCGTTGAGGAGCACGGTGAGGTTTGCC
+CTGCCAACTGGCACAAGGGTTCCGATACCATTGACACCAAAAACCCCGAGAAGTACTTTT
+CCAAGCACTAGATCAATTTTCTGAGCAAGTGTAGTCAACGAG
+>TRINITY_DN577_c0_g1_i1 len=259 path=[237:0-258] [-1, 237, -2]
+TTCGAATACTTGAATCAACACACCGGGTTGATTATCGGCGTAGGTGGAAAAGACTTCGGA
+TTTCTTGGTAGGAATAGTCGTGTTACGCTTAATAAGAGGAGTCATGACTCCACCAGCGGT
+CTCAATACCTAAAGAAAGAGGGGCAACGTCAAGAAGCAACAAATCCTGGGTCTTTTCAGA
+AGTATCACCCACCAAAATAGCGGCTTGGACAGCAGCACCATACGCGACAGCCTCATCAGG
+GTTAATAGACTTGCAGGGC
+>TRINITY_DN578_c0_g1_i1 len=425 path=[403:0-424] [-1, 403, -2]
+ACGACGACGACGAGATGGCATTAAAGACCTTTGAACTTCGTAAGCAATCGCAAGAGAACT
+TGGCTGAGCAATTACAAGAGCTCCGTCAAGAGCTTGCCTCTCTTCGCGTACAAAAGATTG
+CCGGTGGTTCTGGTTCTAAATTGTCTAAGATTAAGACTACCCGCAAGGACATTGCTCGTA
+TCTTGACTGTTATCAACGAGTCCAACCGTCTTGCCGCTCGTGAGGCTTACAAGAACAAGA
+AGTACATTCCTCTTGATCTCCGTCAAAAGAAGACTCGTGCTATCCGTCGCGCTCTTACTC
+CCTATGAGCAAAGCCGCAAGACTCTTAAGCAAATTAAGAAGGAGCGCTACTTCCCCCTTC
+GCAAGTATGCTCTTAAGGCCTAAAATGTTTTTGTAGCTAAATAAAACTTGCCATTTTTAC
+CTTGC
+>TRINITY_DN579_c0_g1_i1 len=693 path=[671:0-692] [-1, 671, -2]
+GCAGGGTAAAGGAGGGCATTGTTGCATTGGGAAATCACGTATTTTTTACCATTGCGATTG
+AGAGGAGGAAGTGGGGAACCAGTGGCTATCAAAGCCTTTCCATCTGACCATTTGTCAATT
+TGATCGGGCTTCGCTTCCATAAGAGTAGTGGGATTAGAGATTGGGAAAATGATGGGGCGC
+TCGACGTGCTTGCTCATTTCACGAATGGCTTTCTCTGTAAATTTACCCGGTTGACCGGAA
+CATCCCAAAAGAATGGTGGGCTTGACGAGTGCAATAGCACTCTCTAAATTAATGTCTCCA
+GAAGGGACTTCCTTAAAGTCAGAGTCCTTCTTCAAAAATGGCTTTTGTCCATCAGTAGCA
+ATCTTAGCATGTCTCTCCAAAAGCAAACCGCAACGATCAATCATGAAAAGATTACCTCTA
+GCCTTATCTAATGAAAGGCCATCTGTCACCATACCGGCAACAATTTGGTTGGCGATACCA
+ACACCAGCAGTACCTGCACCAAAGATCATGATGCGCTGCTCGGTTAAGGGAGATTTCGTA
+ACGTGAAGGGCGCCAATAATGGCGGCCAATGCTACGGCACCAGTTCCCTGGATATCATCG
+TTAAAGCAGGCAATGTCAGGACGATAGTGGTCTAAAATGCGCTTGGCGTTGGCAAGACCA
+AAATCCTCAAAATGAATAAAGGCCTCAGGAAAG
+>TRINITY_DN580_c0_g1_i1 len=351 path=[329:0-350] [-1, 329, -2]
+AACTTGAGGAACTCCTTGCAGTTACCACCGTTAACGGAACCACCGTAGATGACACGGAGA
+CCCTCGGCAACAGATGCACCAAGCTTGTTGGTAGCCCACTTGCGGATCTCAGCGTGAACC
+TCTTGAGCTTGCTCAGGGGTGGCAGTCTTACCAGTACCAATGGCCCAGACAGGCTCATAA
+GCAATGACAATCTTGGACCAGTTCTGGACCTTGTCAGCGATGGCGTTCAATTGACGAACA
+ACAACGTTGATGGTCTCGTTAGCCTCACGCTCGGCCAAAGTCTCACCAATGCAGGCAACG
+ACAGTAAGACCTTGTTCAAGGGCAAACTTGGTCTTGTCGGCAACGAACTCG
+>TRINITY_DN581_c0_g1_i1 len=272 path=[252:0-97 253:98-271] [-1, 252, 253, -2]
+GTTGTTTCCTCCATAGGAGTTGTCATTGCTGCCATAGGAAGAATTGTTGTTGTTTCCACC
+ATAGGAGTTATCGTTGTTGTTTCCTCCATAGGAGTTGTTATCGTTGTTATTTCCTCCATA
+GGAGTTATTATCACTATTGTTGTTATTGTTATTGCTGCTATTATTGTTGCTGTCATTGTT
+GTTGTACTTTTGGTACTCGTTGTAGGCCTTGCCGGCAAAACTCTTCAAGTTATCGAAATT
+CATGATGGCTGAATAATTCCAAAAATAATGTG
+>TRINITY_DN582_c0_g1_i1 len=280 path=[258:0-279] [-1, 258, -2]
+GATAGATTCTATTGCTCCCAAGCGTGAAAAAACGAATGGTGAAGTTGAACGACGTGTTGT
+TTCACAATTATTGACTTTAATGGATGGTATGAAAGCTCGTAGTAATGTTGTAGTAATGGC
+CGCTACCAATCGTCCTAACTCTATCGATCCGGCATTGAGACGTTTTGGTCGTTTTGATCG
+TGAAGTCGATGTTGGTATTCCTGATCCCACCGGCCGCTTAGAGATCCTTCGTATTCACAC
+AAAGAACATGAAGCTTGCTGATGACGTTGATCTTGAGCAA
+>TRINITY_DN583_c0_g1_i1 len=253 path=[231:0-252] [-1, 231, -2]
+CAATAAAACCATAGAGGAGATTTCCTCTGGTGTAAAGGTCTTGGTCTCACCCTTGAACTC
+TACCTGAATCAAAGGCTTACCATCCTTCTCGATGACCTTAAAAGGCCAATGTTTCATATC
+AGATTGGACTTCGGGATCGTTAAATCTGCGGCCAATCAATCGTTTGGCATCGAAAATAGT
+GTTGTGAGGATTCATAGCAACTTGATTTTTTGCAGCATCACCGATCAATCGTTCTGTGTC
+AGTGAATGCAACA
+>TRINITY_DN584_c0_g1_i1 len=304 path=[282:0-303] [-1, 282, -2]
+GGGTAAAGGTCTTGGTCTCACCCTTGTACTCAACCTGCAAAACAGGCTTGCCATCCTTGG
+AGATGACCTTGAAGGGCCAGTGCTTCATGTCAGACTGAACCTCAGGATCATCAAATTTAC
+GGCCGATCAAACGCTTGGCATCAAAGATGGTGTTGTGGGGGTTCATGGCGACTTGGTTCT
+TAGCAGCGTCACCAATGAGACGCTCGGTATCGGTAAAGGCAACATAAGAAGGGGTAGTGC
+GGTTACCTTGATCGTTGGCGATAATTTCGACACGGTTGTTGGAAAAGTGTCCAACACAAG
+AGTA
+>TRINITY_DN585_c0_g1_i1 len=567 path=[545:0-566] [-1, 545, -2]
+GAGTTTTTGACTAACGTCTTAACTGATATTTCCTATTTGCTTGTGTTCGCTTCTTACAAG
+TCGCGTTCTTTTTTTATTGCTTGTCAATTAAATTCCTCATCTTGCTAATTAAATTAAAAA
+ACGATTTTGGTTTCAATTGCATTTGGATTACTTCACTGTTGAACTAATTAATTTATTATC
+AATTTAAACCTAATTATTTGTTGAAGTTCCAATTGTTTCCTCCTTTCTCCTGAAATTTAG
+AGAATCTTTTTGATCCCGTCAAATTTATTTTATTTTTTCCTTTATTAAAACCCCGTTTTC
+TCTTTTCGCACAAGATTAACCGACGTTTGTTGTTTACCCATTCATTTTTGGAAATCTCAT
+ACAATCTTCTGTTTTTCCTACTGCGCTAGTTATACTTTCCTTATTTACTTGTCGCCTGTC
+CCACCAACTCTTTTTTGCTGATAAAATTCACTTTTTTTTTTGAATTTTTTACCCAGCATC
+TCGAAATAACATCAAACTTAGTTTTATTTACTCTTTTTTTTTGTTTGTTACACAACATAT
+TTCTCTTTTACGATACCTACAATGTTG
+>TRINITY_DN586_c0_g1_i1 len=417 path=[395:0-416] [-1, 395, -2]
+CTCTTAAGGGTGGTTATGTCATGTTGGAGAACAAGGAGGCCGATATTACTCTTGTCGGTA
+CTGGTTCTGAAGTCTCTCTTTGCATTGACACTGTCAAGACCCTTGAGACCGAGTACAACT
+TGAAGGCTCGTGTCGTTTCATTGCCTTGCTGGGAAGTTTTCGAACAACAACCAGAAAGCT
+ACCGTCTTTCTGTCATTCCTGACGGTATTCCTGCTATGTCCGTCGAGGTTTGGGCTACCA
+ATGGTTGGAGACGTTACGTTCACGAGGCCTTTGGTATGCACACTTTTGGTGACTCTGGCC
+CTGCTCCCAAATTATACGAGAAATTCCATTTCACCACCTCTGGTGTTGCTCAACGTGCCA
+AAAAGACTGTTGATGCTTACAAGGATATCCCTTATATTCGTTCCCCTGTCCGCCGTG
+>TRINITY_DN587_c0_g1_i1 len=241 path=[219:0-240] [-1, 219, -2]
+CTCCAACCATTGGTAGCCCAAACCTCGACGGACATAGCAGGAATACCGTCAGGAATGACA
+GAAAGACGGTAGCTTTCTGGTTGTTGTTCGAAAACTTCCCAGCAAGGCAATGAAACGACA
+CGAGCCTTCAAGTTGTACTCGGTCTCAAGGGTCTTGACAGTGTCAATGCAAAGAGAGACT
+TCAGAACCAGTACCGACAAGAGTAATATCGGCCTCCTTGTTCTCCAACATGACATAACCA
+C
+>TRINITY_DN588_c0_g1_i1 len=232 path=[210:0-231] [-1, 210, -2]
+GTTTCATGCTTATGCGTGAGGCTGCTAAGGAGTACGGCTGGAAGCTTAACAACGCCGGTA
+TCGCTTTGATGTGGCGTGGTGGTTGTATTATCCGTTCCGTCTTCCTTAAGGATATCACTG
+AGGCTTTCCGTGAGGATCCTAACCTCGAGTCTATCCTTTTCCATCCTTTCTTCACTAATG
+GTGTTGAAAAGGCTCAAGCTGGTTGGCGTAGAGTTGTTGCCCAAGCCGCTAT
+>TRINITY_DN589_c0_g1_i1 len=241 path=[219:0-240] [-1, 219, -2]
+GTCGAAAGACTTCTTCCAAGCCTTGGTGACGAAAACGTCATTTACGGCAACGACATAGAT
+TCCGCTGATGCCCTTGGCAGCAAATTGCTTCTCATTTGCAATATAGCCAGGAACTTGAGA
+AGAACAAGGAGGAGTGAAAGCGCCGGGAACACCGACAATGATGAATTTGCCTTGAGAAGG
+GAATTCAACAACCTCTTCGGGCTTGTTTTCCCAAAGAGTAACTTTAGGCAAAGTAGATCC
+G
+>TRINITY_DN590_c0_g1_i1 len=230 path=[208:0-229] [-1, 208, -2]
+CTTCCTCGTCTGTGGGGTCTTTCCACCGTCATTGGTATTGTTTTGGCTATCGGTACCTGG
+ATTACCAACACTACTATGATTGCTCAAGGTCAAAACCGTGGTATCGTTCAAAACTTCGGT
+GTTCAAGATGAAGTTCTTTTCCTCGAAATCTCTCTTACTGAGAATTGGTTGATTTTCGTT
+ACTCGTTGCAACGGTCCCTTCTGGTCTTCTATTCCATCTTGGCAATTGTC
+>TRINITY_DN591_c0_g1_i1 len=203 path=[181:0-202] [-1, 181, -2]
+TTGCACCCCCTCGCCTTTTTTTGTCTTTGTCTTTTTATTTTATTTTTTTACTAGTCTTAA
+CATACTACTATTGTTACTAGTACTTCTACTGACTGACTGAGTGAATTTTTGTATTTATTC
+AATTCTTCCTCGTTTCCTTCCTTGATTTACTGTTTGTACCCCTAAAAAAAACACATTTTC
+ATCTCCTTTTTTTTGTGTTCAAG
+>TRINITY_DN592_c0_g1_i1 len=337 path=[315:0-336] [-1, 315, -2]
+CAGTAAATACCGAGTTTCTCGCTGATAACCTCAGAGTAAAGGCGGACGCCTTCCTTGCTG
+ACAGCAACACCCTTGATACAGGAAATACCAACGGCACCAGGGCGAATGAGACCGACCATT
+TGGTCGCAAACGCGTTCAATAAATTGATGAGGAACGACAAAGACAAGGATGTCGGCACGT
+CTAGCGACCTCACGAACATCGGGGACGGCAATAACGTTGGGAGGGCATTCGATGCCGGGT
+AAGTATTTGACATTCTCGTGAGCTTCGTTGAATACTTCGGTGAGCTTTCTCTTCTCACCC
+TTGTACTCAATCTCCTCCTCAAAGACCCACATGCGGA
+>TRINITY_DN593_c0_g1_i1 len=402 path=[380:0-401] [-1, 380, -2]
+GTGGTCACCGCTGTCTACAAAATGAGTCAAGTCGCCAAAGATCAAAAGGAACAACAAATT
+CCCTCTACTGTTCACCGCATTCGCATTACCCTTACTTCTCGTAACGTTCGTAACTTGGAG
+AAGGTTTGCTCTGACTTGGTCAACCGTGCCAAGGACAAGCAATTGCGTGTTAAGGGTCCT
+GTTCGTCTTCCCACCAAGATCTTGAAAATCACTACCCGTAAGACTCCTAACGGTGAAGGT
+TCCAAGACCTGGGAAACCTATGAGATGCGTATCCACAAGCGTCTCATCGACCTCCACTCT
+CCTTCCGAGATTGTCAAGCAAATTACTTCCATCCACATCGAGCCTGGTGTTGAGGTTGAG
+GTTACCATTGCCCAGTAAGGTGCTTGTTCCATTTGGTCGGGG
+>TRINITY_DN594_c0_g1_i1 len=250 path=[228:0-249] [-1, 228, -2]
+CTCGTTAATACGGAAAGCAGGAGAGACGTGGGCAGCCAAGTTCTTGTGGCGCTTCTCATA
+ACGATTGTACTTGGGAATGAAATGCAAGTACTCACGACGGATAATGATGGTACGGTGCAT
+CTTGGTGGAAACAACGGTACCGGTCAAGATACGGCCACGGATAGAGACTTGACCAACGAA
+AGGGCACTTCTTGTCAACATACTCACCGTAGATAGCTTCGGCAGGGGTCTTGAATCCCAA
+ACCGACATCC
+>TRINITY_DN595_c0_g1_i1 len=282 path=[260:0-281] [-1, 260, -2]
+AACATGTCCAACTGCTTTTTTGACGTTATTGCCAACGGCCAACCTTTAGGACGTATCGTC
+TTCAAATTATTCGACGATGTCGTTCCCAAGACTGCTGCTAACTTCCGTGCTCTCTGCACC
+GGCGAGAAGGGCTATGGCTATGCTGGCTCCACCTTCCACCGTGTCATTCCCCAATTCATG
+CTCCAAGGTGGTGATTTCACTCGCGGTAACGGTACCGGTGGAAAGTCCATTTATGGCGAG
+AAATTTCCTGATGAAAACTTTGCCTTGAAGCATAACAAGCCT
+>TRINITY_DN596_c0_g1_i1 len=465 path=[443:0-464] [-1, 443, -2]
+TCGGGCGGTGTGTACAAAGGGCAGGGACGTATTCAACGCAAGCTGATGACTTGCGCTTAC
+TAGGAATTCCTCGTTGAAGAGCAATAATTGCAATGCTCTATCCCCAGCACGACGGAGTTT
+AACAAGATTACCCAGACCTTCCGGCCAAGGATAAAAAATCAAAAGATTTTTTTCAACTCG
+TTGGCTCCGTCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGT
+TATTGCCTCAAACTTCCATTGGCTTTATGCCAATAGTCCCTCTAAGAAGCTAATGATCAG
+CCAAAATGGCTGATCCAGCTATTTAGCAGGTTAAGGTCTCGTTCGTTATCGCAATTAAGC
+AGACAAATCACTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAG
+AGCTCTCAATCTGTCAATCCTTACTATGTCTGGACCTGGTGAGTT
+>TRINITY_DN597_c0_g1_i1 len=260 path=[238:0-259] [-1, 238, -2]
+GCCTTAAGAGCATACTTGCGAAGGGGGAAGTAGCGCTCCTTCTTAATTTGCTTAAGAGTC
+TTGCGGCTTTGCTCATAGGGAGTAAGAGCGCGACGGATAGCACGAGTCTTCTTTTGACGG
+AGATCAAGAGGAATGTACTTCTTGTTCTTGTAAGCCTCACGAGCGGCAAGACGGTTGGAC
+TCGTTGATAACAGTCAAGATACGAGCAATGTCCTTGCGGGTAGTCTTAATCTCAGACAAT
+TTAGAACCAGAACCACCGGC
+>TRINITY_DN598_c0_g1_i1 len=204 path=[182:0-203] [-1, 182, -2]
+CTTGGCTTCCTTGCAGGCCTTTTCGACCTCAGGGCCAACACAGTCGTCAAGGAACTTGAC
+GGGCTTGCCCAAAAGCTTGCTGAGCTCAGCAGCAACAGGCTTCAAGGAGTACTTGGCAAC
+ACGAGCACCGTTGGGACGGCCCAAGTGAGACATCAAGATGACAGCCTTGGGTTGTTGCTC
+AAGAGCGTACTTGATGGTGGGGAG
+>TRINITY_DN599_c0_g1_i1 len=359 path=[337:0-358] [-1, 337, -2]
+ATTTTGCAAACTCAATTGAGACATACGCCTGTTGCTGAAGATGTTGACTTGCGTGCAGTT
+GCTAAGGCGACCCATGGCTTCTCAGGTGCTGATTTGGAGTTTGTTGTACAAAGAGCTGTT
+AAATTGGCCATCAAGGACAGCATTGAAGAAGACATCAAGCGCGAAAATGAGACTGGAGAG
+GCTCCTGCTGACGATGTTGTTATGGACGAAGATGCATCTGTGTCTCAAGTTCAGCGTCAT
+CATGTGGAGGAGGCCATGAAAATGGCACGCCGCTCTGTCAGTGATGCAGAAGTCCGTCGT
+TATGAAGCTTATGCCCATCAACTCCTTACCTCGCGTGGTCTTACAGGATTCCAGTTTGA
+>TRINITY_DN600_c0_g1_i1 len=393 path=[371:0-392] [-1, 371, -2]
+TCACCACCATCTAACCATCACTTATAAAAGTATCAAAAAATGGTGAACATTCCCAAGACC
+CGTAAGACTTACTGTCCTGGTAAGAACTGCCGCAAGCACACTGTCCACAGAGTCACCCAA
+TACAAGAAGGGACCTGATTCCAAGCTTGCTCAGGGTAAGCGTCGTTATGACCGCAAGCAA
+AGTGGTTTTGGTGGTCAAACTAAGCCCGTTTTCCACAAGAAGGCTAAGGTTACCAAGAAG
+GTTGTCCTTCGTTTGGAATGCGTCTCTTGCAAATACAAGAATCAATTGGTTTTGAAGCGT
+TGCAAGCATTTCGAGCTTGGTGGTGAAAAGAAGACTAAGGGTGCTGCTATCCAATTCTAA
+GTGTTTTAGCAAATACAATTTTCTTCTTTTACG
+>TRINITY_DN601_c0_g1_i1 len=371 path=[349:0-370] [-1, 349, -2]
+ATGCCATCAAGGTCAGCAATGCTCTTGAAGCCGGTACTGTTTGGGTGAATTGTTATAACT
+TACTTCATCACCAAATTCCCTTTGGTGGTTATAAGGAGAGTGGCATCGGTCGCGAATTGG
+GCTCTTACGGTCTTACCAATTATACTCAAACAAAAGCTGTTCACATCAACCTGGGAATGG
+ATTCTCCCATTTAAGGAAATCAGACGCAAATATTTTTTGTAAAAAAAATAAAAAAATATG
+CATTCAATGGATAAAGAATGAAGAAAAACTCTAGTGAAGAGAATTATTGGATTTTTCTCT
+TTATGTTATGAATGTTTACAGTTTTTCTTGAAACTCTTCTATGACGGATTTTCTTTATTA
+TGAATCAAAAC
+>TRINITY_DN602_c0_g1_i1 len=554 path=[532:0-553] [-1, 532, -2]
+GGAGTAACAAAATCCATTAATACAAATAAGTCTTTAACGGTTACTCTTGGCAACACGCTC
+AAGCTCATCCTTCTTCTTGATGGCGTAAGAGTTGGAAGAGCCCTTAGCAGCATTGATGAT
+TTCTTCAGCCAAGCATTCAGAAATGGACTTGACGTTACGGAAAGCAGCCTCACGAGCACC
+GATAGTGATAAGAGCAAGAGCTTGGTTGACACGACGAAGAGGAGAAACATCAACGGCTTG
+ACGACGAACAGTACCAGCACTACCAATACGAGTGGAGTCTTCACGAGGACCACAGGCAGC
+AACGGCATCAACCAAAACTTGGAGAGGGTTTTGGTCGGTCAAGAGAGCAATGATCTCAAA
+AGCATGCTTGACAATGCGAGTGGCCAAGAGCTTCTTACCGTTGTTACGGCCGTTCATCAT
+CAAACTGTTGGTCAAACGTTCGACAATGAAGCAGCGGGCCTTACGGAACCTCTTGGTCTG
+GAAACGGCCAGCGGTGTGAGGGAGAGGTTGACCATTGCCAATGGTAATGTAATCAACCAA
+GGAGATGTCCTTAA
+>TRINITY_DN603_c0_g1_i1 len=281 path=[259:0-280] [-1, 259, -2]
+TGCCGTCAACGCTAGCTTGAACCATGACAAATGTATGGAGGCTTTCCGTAACGAAAGCAT
+CTACGTCTTTTTGGATCTTGCCAACCCCAAGACCGGTATCGATCGTGATACCCCTACATG
+GAACACCGATCAATTCTCATCCTATCAATCTGTTATTGATACTTTCCAAAAGTACAACAA
+CACTGGTGCCTTCTTTGCCGGTAACGAAGTTGTCAACAATGCCTCGAATGCTCCCGCTGT
+CGCTTACGTTCGTGCTGCCGTTCGTGATTCCAAGAACTACA
+>TRINITY_DN604_c0_g1_i1 len=211 path=[189:0-210] [-1, 189, -2]
+GTGAGTTTGAATCTTCTTGAGACGCTCAAGATCCTCACGAAGCTTGCTGTCAACGTTGTT
+GGCAAGCAATTGGAAGGACTTGCCATCGTTTATATCCTTTTGACGGTTAAGGAACCAGGA
+AGGAATCTTGAATTGAGAAGGGTTTTGAATAATGGTAACAATACGCTCCAACTCTTCAGT
+GGTAAGCTCACCAGCACGCTTAGACATGTCA
+>TRINITY_DN605_c0_g1_i1 len=313 path=[291:0-312] [-1, 291, -2]
+GCGGCGCATCCAAACAACAGCAGAGGGCATACGAGCTTCGGCAGTACCCTTACGCTTACC
+GTAACCGGTGTGACGACCAAGACGCTTGGCGGCATGGGTCTTACGAATGCGGAAGCGAGA
+ATGCATCAAGTTAGGCTTGCGAATAACCAAACCGTCCTTAATCAACTTACGGACGTTTTG
+ACGGCTGTTGGCATTGCTGATTTCGCTGATTTCATTAGGATCCATCCAAACTTTGCGTTT
+GCCGCATTTAAGGACGGATGCAGCAAGTCGCTTCTGCGTTCTAAGATTGGCCATTTTTCT
+TGCTGTTTTTGGT
+>TRINITY_DN606_c0_g1_i1 len=254 path=[232:0-253] [-1, 232, -2]
+CGAAGAGAATATGCATAAGACTCCAGGTGATTCTTGGCTTGAATACGAGAAGTTTCTGCT
+TCATCTTCAGCCTTGTACTTCTCGGCTTCAGATACCATACGATCAATTTCTTCCTTGGAA
+AGACGACCCTTGTCATTGGTAATGGTAATCTTTTGAGTCTTACCAGTACCCTTTTCAAGG
+GCAGAAACGTTCAAAATACCATTAGCGTCAACATCGAAGGTGACCTCGATTTGTGGAACA
+CCACGAGGAGCAGG
+>TRINITY_DN607_c0_g1_i1 len=219 path=[197:0-218] [-1, 197, -2]
+TCAAGGCCAAGTTGCTTCTTTTGGCTCTTCAAGAATTGATAAACAGGGTCGACGTTGTCG
+CCATTAACATTGATCTTGGCCAGTACAGGGAAGGTTACGCCATAGTTCTTTTGGCAAAAT
+TGAGCGATTTCTTCGTCAGAACCGGGTTCTTGGTTTCCAAATTGATTGCAAGGGAATCCA
+AGGATGATAAATCCTCTATCCTTGTATTTCTGATACAAC
+>TRINITY_DN608_c0_g1_i1 len=369 path=[347:0-368] [-1, 347, -2]
+TAAGGCCAAGGTCTTTGGTATCTGGATTCGTTATGACTCTCGTTCCGGTACTCACAACAT
+GTACAAAGAGTTCCGCGACACTACTCGTGTTGGTGCTGTCGAGGCTATGTATGCCGATAT
+GGCTGCCCGTCATCGTGCTCGTTTCCGCAGCATCCGTATCCTTAAGGTTGTTGAGGTTGA
+AAAGAAGGAGGATGTTCGTCGTAACTATGTCAAGCAACTCCTCAACCCTCACTTGAAGTT
+CCCTCTTCCTCACAGACGTACTGGCGTTGTCGGTTTGGCTGGTAAGAAGGTTTTTGCTCC
+TCATCGCCCCAGCACTTTCTACTAAGGGATATGGGTCTTTTCTATTAGTAAAAAAAATTA
+GTTTTCCCG
+>TRINITY_DN609_c0_g1_i1 len=412 path=[390:0-411] [-1, 390, -2]
+AAATTTCTTTAAAAAAAAAATTTACCACAGAAGAAGAGTGATGTCTAAGTAAAGGAAAAA
+AGGAAAGGTTCCATTCTGGAAGGATAAATAATAGGTTTTAAATTGCTTTAGGGAAATATA
+AACATTCCTTACAAAGGGAGGAGAAGAGAAACAAACAAATAAGGGATAAACAACATCCTC
+CTATAGCGCTAGATTTGCACAAGCTATACAATATCAAAAGACACACAACTTTGTAGAGAT
+AAAGTGAAAAGCGTGTAAAACAATTGGCACGTTTTTCAGAGTGGAGAGCGGTGGTGATTA
+GAAAAGAGAAAAAAAAAGAGAATATGAAAAAAATGCTGGTTGGTTGGCTGACTAGACTAA
+ACTAGACTGGCTTGGCTGCCAAAGAGTAGTAAATTTTTGTTTAAAAAAAAAT
+>TRINITY_DN610_c0_g1_i1 len=218 path=[196:0-217] [-1, 196, -2]
+CCGGTACCGTTACCGCGAGTGAAATCACCACCTTGGAGCATGAATTGGGGAATGACACGG
+TGGAAGGTGGAGCCAGCATAGCCATAGCCCTTCTCGCCGGTGCAGAGAGCACGGAAGTTA
+GCAGCAGTCTTGGGAACGACATCGTCGAATAATTTGAAGACGATACGTCCTAAAGGTTGG
+CCGTTGGCAATAACGTCAAAAAAGCAGTTGGACATGTT
+>TRINITY_DN611_c0_g1_i1 len=202 path=[180:0-201] [-1, 180, -2]
+GCACACTTACATAGCTGAGTACGCCGTAAGTGTTGTACTTGGTTTATTATATTTTTTTTT
+CTTTTTCTTTGTAGTTTGCTTCTCTTCGGAGTCACTTTAACCACCCCCTCCCAACTCAAC
+TTAATTATTCATTCTTTGCGGCCTCTGTTGATCCTATCCATTTCTTCAACTGACCGAATA
+TTATTTTACCCCTGATATATTT
+>TRINITY_DN612_c0_g1_i1 len=210 path=[188:0-209] [-1, 188, -2]
+ATAGCTTGTGCAAATCTAGCGCTATAGGAGGATGTTGTTTATCCCTTATTTGTTTGTTTC
+TCTTCTCCTCCCTTTGTAAGGAATGTTTATATTTCCCTAAAGCAATTTAAAACCTATTAT
+TTATCCTTCCAGAATGGAACCTTTCCTTTTTTCCTTTACTTAGACATCACTCTTCTTCTG
+TGGTAAATTTTTTTTTAAAGAAATTTTTTG
+>TRINITY_DN613_c0_g1_i1 len=201 path=[179:0-200] [-1, 179, -2]
+CTTTGATATAGTCAACGCTGGAGACCATTGGTCACGAAGGATATCCAAACAAATGCTACC
+GTTTGAATTGATGTTGGGATGATAGATTCTGGTTGTAAAGTTTACCTTTGGTGGCTTGAA
+TGGGTAGTCCGTAGGGAAATGAATGGACAAGAAGAAGACACCACCCGCATAAGGGCTGTC
+AGCAGGACCCATGATTGTAGC
+>TRINITY_DN614_c0_g1_i1 len=314 path=[292:0-313] [-1, 292, -2]
+TGATCAAGTAATTTGTGATTACGCTTCGTGATAGCGGCATTAATATCGGGAAAGTAACTG
+CAGAACCTTGAGATGGGATCCAACACCGTTGTCCGGAAAGGACCGTCCAACTCTTTTACG
+GTATCGGCGTCCAAGTCTTCGACGACTTGTCGATAGTATGCACTGACACCATCCTTCGAT
+CCAGCATCACCGTAAAATGCATCGATTGTGTTAGCGATTCTAGTTTGAGACGCAGTCATG
+GCTCTCAAAGCATCGAGATAACCTTTGGCTTCTTTTTGAAGCTTCTTTGCAGCTGATTCC
+ATAGTTCTATAACG
+>TRINITY_DN615_c0_g1_i1 len=226 path=[204:0-225] [-1, 204, -2]
+TTCCTTCTTCACGAACTTATCTACTTCGGTCGTTGCATTCCTTGGATGATTATCGATGCC
+ATGCCCTACTTCCGCCGCTGGAAAATCCAACCCAAGAAAGTTCCCACCCTTGCTGAACAA
+TGGGAGTGCACACGCTTGGTTCTTCTTTCTCATTTTACCGTGGAGCTTCCTCAAATCTGG
+CTCTTTGACCCTATGTGCGCTACCTTTGGTCTTTCTACCTCTGTTC
+>TRINITY_DN616_c0_g1_i1 len=248 path=[226:0-247] [-1, 226, -2]
+AAAAGAAGCAACTTGGCCTTGAGCGTATTAAGTGGAATTTTGAAAAGTTCTTGGTCAATC
+GTCAAGGTCAAGTCATCGAACGCTATTCCAGTATTAGCAAGCCTGAACATCTCGAAAACG
+ATATCGAGAGTGTCCTTTAAAAAAATACTGGAACAAATTTGCAGTGTAAGCGATCATTTC
+TTCCCGCTTTTAATTTCAGTGGCACACTAATTCTTCTGATCCTTTGGAAGTTTAATGAAC
+TTCACGAT
+>TRINITY_DN617_c0_g1_i1 len=226 path=[204:0-225] [-1, 204, -2]
+CAAAAATTGGTGGTCCGCTTCTCTCGTTCCAGTCGCCTGCGGCTGGTTCATTGGGAATTC
+CTACAAGCCAAGAAAGGATTATGAGAACAAAAAGCAACCAAAGTTCCACCCCCCTGCATC
+TGCCTTTGGACCAGCATGGACACTACTATACCTAACAATGGGATATGCATCCCATTTGGC
+GTACAAGGCTGACCCTTTGATGATTACGAATGCCTCTCGAAATGGA
+>TRINITY_DN618_c0_g1_i1 len=211 path=[189:0-210] [-1, 189, -2]
+GAACAGCACTGGTCAAAATGTCTGCATCTGAACTTGCTACCAGTTATTCAGCTCTCATTT
+TGGCTGACGAGGGTATTGAAATCACCTCTGACAAGCTCTTGTCTTTAACCAAGGCTGCCA
+ACGTCGATGTTGAACCCATTTGGGCTACCATTTTCGCTAAGGCTCTTGAGGGCAAGGACC
+TTAAGGAACTTTTATTAAACATTGGCTCTGG
+>TRINITY_DN619_c0_g1_i1 len=224 path=[202:0-223] [-1, 202, -2]
+TGGGTAAATAAGAAGAGATGGTAGTAATAATAAAAATAAGTGGTAGTAGTAGTAGTATAT
+TAGTATGTGATGATACTAATAAGAACAATTATAGTGAGAATAATTTAGTAGAGAGAGGAC
+GAGTTATAAGTAAAAAAAAAAGAGTAGGACGAAAAATGTTTAACACTTTACCAAAGGGCG
+ATACGAAATTTCGTGGGTATATAGTTAAATAGGATAGATAGTTA
+>TRINITY_DN620_c0_g1_i1 len=241 path=[219:0-240] [-1, 219, -2]
+GTCGGCAACGAACTCGTCAGACTCCTTGAAGATGGTACGACGCTCGGAGTGACCAGTCAA
+AGTGTAGGTAATACCAGCATCAATCAAAGATTGAGCACTGTTCTCACCAGTGTAGGCACC
+GTTCTTCTTGTCGAAGACGTTTTGGGCACCAACGCCAATATCCTTCTTGACTTGTTGGCG
+GGTGGTGATGAGGTACATGTTTTGAGGGAAGATGACAGTTTCGACATCACCAACGTTAAG
+C
diff --git a/sample_data/test_DE_analysis/Makefile b/sample_data/test_DE_analysis/Makefile
new file mode 100644
index 0000000..5208ab6
--- /dev/null
+++ b/sample_data/test_DE_analysis/Makefile
@@ -0,0 +1,30 @@
+
+
+test: test_edgeR test_DESeq2 test_voom test_ROTS
+
+test_edgeR:
+ ../../Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method edgeR -s samples.txt -o edgeR_outdir
+ cd edgeR_outdir && ../../../Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt
+
+test_DESeq2:
+ ../../Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method DESeq2 -s samples.txt -o DESeq2_outdir
+ cd DESeq2_outdir && ../../../Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt
+
+test_voom:
+ ../../Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method voom -s samples.txt -o voom_outdir
+ cd voom_outdir && ../../../Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt
+
+test_ROTS:
+ ../../Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method ROTS -s samples.txt -o ROTS_outdir --ROTS_B 50 # make it go faster, use more in practice
+ cd ROTS_outdir && ../../../Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt
+
+clean:
+ rm -rf ./edgeR_outdir
+ rm -rf ./DESeq2_outdir
+ rm -rf ./voom_outdir
+ rm -rf ./ROTS_outdir
+ rm -f ./Trinity_trans.counts.matrix.*
+ rm -f ./Trinity_trans.TMM.EXPR.matrix.*
+ rm -f ./*.pdf
+
+
diff --git a/sample_data/test_DE_analysis/Trinity_trans.TMM.EXPR.matrix b/sample_data/test_DE_analysis/Trinity_trans.TMM.EXPR.matrix
new file mode 100644
index 0000000..0eb8706
--- /dev/null
+++ b/sample_data/test_DE_analysis/Trinity_trans.TMM.EXPR.matrix
@@ -0,0 +1,7240 @@
+ wt_37_1 wt_37_2 wt_37_3 wt_GSNO_1 wt_GSNO_2 wt_GSNO_3 wt_ph8_1 wt_ph8_2 wt_ph8_3
+TR24|c0_g1_i1 35.060 38.638 25.627 15.718 14.737 19.820 70.390 75.390 84.680
+TR2779|c0_g1_i1 67.417 60.128 39.248 62.822 64.280 60.952 293.399 305.166 310.675
+TR127|c1_g1_i1 64.384 37.709 103.699 0.000 4.315 10.790 4.686 4.433 13.865
+TR2107|c1_g1_i1 136.060 178.180 199.556 19.395 21.573 23.242 3.110 6.018 9.361
+TR2011|c5_g1_i1 5.409 15.517 5.273 7.438 9.994 14.455 5.106 10.335 3.972
+TR4163|c0_g1_i1 87.458 78.780 79.649 48.282 45.367 47.237 44.739 39.249 43.988
+TR5055|c0_g2_i1 66.721 92.833 43.566 19.226 7.877 13.217 10.272 27.596 10.381
+TR1449|c0_g1_i1 51.548 50.783 52.652 30.582 23.794 21.944 27.810 24.026 28.281
+TR1982|c2_g1_i1 5.003 6.082 5.535 2.740 7.021 4.454 6.768 8.519 12.647
+TR1859|c3_g1_i1 5.322 0.000 0.000 0.000 0.000 0.000 13.365 24.827 6.508
+TR1492|c0_g1_i2 1526.347 1568.410 1432.877 1096.470 1103.333 1171.357 663.758 679.332 675.664
+TR1122|c0_g1_i1 0.000 12.065 21.057 0.000 0.000 23.473 7.505 0.000 7.285
+TR2278|c0_g1_i1 68.933 59.594 64.190 50.794 49.948 51.230 40.053 34.798 33.841
+TR4084|c0_g1_i1 16.159 18.573 25.483 22.651 25.055 19.310 32.282 26.688 30.014
+TR4761|c0_g1_i1 1299.169 1507.411 1138.438 131.593 120.301 143.398 240.272 259.491 256.659
+TR3638|c0_g1_i1 436.933 413.422 388.737 123.145 112.308 95.857 186.923 190.554 186.051
+TR2090|c0_g1_i1 0.000 0.000 0.000 0.000 0.012 10.426 0.000 2.929 3.376
+TR3854|c0_g1_i1 379.967 398.251 324.168 481.117 460.267 482.927 373.649 395.209 412.633
+TR131|c0_g1_i1 16.980 18.246 14.324 736.059 695.721 731.977 719.566 730.642 758.630
+TR5075|c0_g1_i1 11.146 7.190 10.898 4.626 5.587 4.248 56.485 68.963 80.582
+TR2182|c3_g2_i6 21.548 8.386 18.137 0.000 0.000 25.220 15.593 17.439 8.503
+TR3788|c0_g1_i1 13.348 10.740 17.055 87.372 79.792 73.744 11.814 15.053 18.162
+TR4859|c0_g1_i1 43.309 33.694 77.116 6.213 17.548 29.080 6.837 12.676 6.653
+TR2487|c0_g1_i1 202.279 191.689 169.981 449.958 404.176 438.810 412.991 449.128 426.426
+TR2122|c0_g2_i2 14.266 15.813 12.917 17.869 22.117 21.689 35.426 32.296 35.150
+TR4277|c0_g1_i1 4729.946 5139.686 4993.670 162.163 190.920 174.019 165.231 176.899 183.036
+TR4669|c0_g2_i1 0.000 0.000 0.000 0.000 157.490 192.042 0.034 0.116 0.090
+TR3091|c0_g1_i1 6.983 8.416 5.778 123.145 109.647 122.643 109.337 105.345 112.862
+TR2130|c1_g3_i1 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
+TR3807|c0_g1_i1 5.525 17.297 11.646 0.000 2.938 0.000 2.939 0.000 0.000
+TR1894|c2_g1_i1 18.622 37.086 23.545 3.737 8.953 2.257 4.943 1.647 1.688
+TR5212|c0_g1_i1 16.265 13.885 17.028 22.194 23.644 20.317 18.745 15.765 19.624
+TR939|c0_g1_i1 17.067 17.218 15.631 16.667 15.928 16.567 15.156 16.727 16.826
+TR1891|c0_g1_i1 21.085 20.343 21.472 25.655 19.792 21.907 59.629 58.637 56.544
+TR2672|c0_g1_i1 41.136 27.315 54.419 8.267 3.956 0.000 7.394 12.854 26.467
+TR2844|c0_g1_i1 33.815 32.804 36.742 44.149 44.465 40.829 39.787 36.382 34.509
+TR1837|c2_g1_i1 0.000 5.123 0.000 5.636 21.272 6.615 18.206 11.323 0.000
+TR1678|c0_g1_i1 1.661 1.731 0.000 0.000 3.505 0.000 16.107 9.676 13.251
+TR3249|c0_g1_i1 2.241 2.344 4.597 2.487 0.000 11.991 2.287 15.739 13.928
+TR1479|c0_g1_i1 24.214 24.299 27.989 60.419 63.806 63.500 53.212 46.593 57.474
+TR989|c0_g1_i1 75.868 80.283 80.352 63.904 59.040 51.060 56.810 54.408 58.882
+TR1084|c0_g1_i1 4.868 2.542 2.515 5.407 2.580 6.505 2.519 24.632 10.182
+TR1054|c0_g1_i1 26.571 18.859 28.845 13.170 13.337 17.744 15.490 13.308 11.293
+TR1514|c2_g1_i1 118.114 127.723 127.623 100.951 95.801 103.989 24.571 17.679 23.668
+TR5344|c0_g1_i1 64.200 75.981 81.858 48.595 48.375 65.272 43.060 39.783 49.494
+TR2134|c2_g1_i1 13.812 3.600 3.768 7.763 3.690 9.248 3.872 7.389 3.845
+TR1339|c1_g1_i1 31.043 29.708 29.386 39.823 41.053 39.433 37.765 32.465 35.836
+TR1869|c3_g1_i1 17.810 6.151 28.737 20.536 6.431 0.000 30.765 14.190 7.465
+TR4389|c0_g1_i1 41.609 38.905 40.302 20.981 24.072 24.152 33.293 40.352 36.288
+TR496|c1_g1_i1 9.745 8.218 8.636 94.546 111.753 97.314 57.650 49.094 53.827
+TR2569|c0_g1_i1 65.523 55.520 73.267 253.512 243.552 237.070 108.386 112.191 116.319
+TR173|c0_g1_i1 40.856 35.137 38.950 39.991 35.674 37.794 37.731 36.943 39.167
+TR439|c0_g1_i1 239.667 265.890 278.349 236.341 239.179 187.212 195.345 175.635 146.758
+TR4041|c0_g1_i1 29.961 23.735 29.350 16.342 23.297 17.392 15.618 17.385 15.264
+TR3271|c0_g1_i1 16.873 8.782 14.306 33.454 22.626 39.591 19.902 4.691 14.687
+TR588|c0_g1_i1 656.114 694.680 645.073 12.004 15.651 10.365 2.296 6.552 9.099
+TR3330|c0_g1_i1 19.472 18.998 20.679 18.986 15.338 13.533 13.768 10.691 10.119
+TR2326|c0_g1_i1 33.641 33.427 39.392 25.042 21.643 23.060 30.329 23.839 28.678
+TR2210|c0_g1_i1 805.753 747.302 777.230 318.497 341.817 299.563 371.979 365.886 362.381
+TR1364|c0_g1_i1 14.855 16.614 16.442 20.993 20.833 13.217 21.804 19.148 10.254
+TR4000|c0_g1_i1 27.285 29.491 40.555 25.956 22.869 25.572 21.890 23.439 24.291
+TR3821|c0_g1_i1 2.608 2.720 0.000 0.000 5.541 3.495 38.399 32.029 35.918
+TR3400|c0_g1_i1 69.232 65.716 69.364 1519.487 1463.195 1493.470 847.580 880.221 841.225
+TR4121|c0_g1_i1 20.969 22.518 21.066 54.591 51.163 56.194 98.474 99.043 90.909
+TR3630|c0_g1_i1 10.789 18.760 12.575 3.965 5.703 9.612 10.589 8.795 5.425
+TR1571|c0_g1_i1 32.694 29.560 28.963 35.557 28.444 29.092 7.137 9.872 9.424
+TR4609|c0_g1_i1 93.881 93.644 67.751 16.511 20.104 28.680 131.646 142.395 149.014
+TR2867|c0_g1_i1 25.170 29.758 30.207 22.206 24.766 24.055 21.316 22.833 17.711
+TR1399|c2_g1_i1 71.019 86.810 90.124 37.624 28.421 32.709 165.762 180.023 166.454
+TR870|c0_g1_i1 8.403 8.772 17.740 3.124 8.942 7.501 8.970 2.893 3.006
+TR1825|c0_g1_i1 13.551 8.080 3.903 12.834 14.344 20.693 1.928 20.991 1.968
+TR1394|c2_g1_i1 4.153 8.663 4.210 13.783 6.593 11.093 6.263 0.000 0.000
+TR3881|c0_g1_i1 13.783 9.484 12.250 45.663 43.655 39.178 18.488 22.825 19.317
+TR1278|c0_g1_i1 34.355 36.987 36.616 10.070 18.196 14.758 21.641 21.872 20.030
+TR3135|c0_g1_i1 305.470 295.489 277.520 111.549 124.558 117.133 134.097 149.463 138.426
+TR2204|c0_g1_i1 57.092 49.893 55.852 17.917 21.527 17.586 9.835 12.614 7.420
+TR4196|c0_g1_i1 17.665 22.677 19.885 13.434 18.647 16.336 2.570 7.789 5.326
+TR2146|c1_g1_i1 39.359 31.112 36.426 18.325 18.519 24.905 21.744 20.741 16.627
+TR3771|c0_g1_i1 113.942 99.795 117.824 60.695 52.238 67.008 50.188 44.928 38.725
+TR1833|c0_g1_i1 62.616 58.398 59.061 25.042 28.537 23.266 14.008 12.285 11.392
+TR4967|c0_g2_i1 31.873 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
+TR1922|c0_g1_i1 2.743 2.858 14.405 9.157 2.915 0.000 14.539 11.288 11.690
+TR2901|c0_g1_i1 18.235 18.029 19.912 19.359 28.271 18.254 23.903 19.112 24.093
+TR3584|c0_g1_i1 55.923 53.186 52.832 23.805 25.414 21.725 30.012 33.801 34.708
+TR1595|c0_g1_i1 85.150 71.561 109.495 58.124 60.405 56.157 53.598 50.634 59.171
+TR1103|c0_g1_i1 8.104 6.339 6.148 4.482 4.292 5.413 24.349 14.047 8.278
+TR1074|c0_g1_i1 34.259 20.343 28.467 33.502 10.549 13.132 12.011 11.216 11.753
+TR1703|c4_g1_i1 33.138 31.281 17.145 6.958 10.006 4.212 3.041 3.053 4.703
+TR2939|c0_g1_i1 823.708 744.068 658.270 49.304 62.742 75.698 829.529 854.415 845.910
+TR1973|c0_g1_i1 4.984 3.896 14.017 10.190 7.866 9.989 8.285 7.442 8.169
+TR3064|c0_g1_i1 80.881 74.320 64.686 294.092 257.826 290.181 161.187 155.899 171.274
+TR2137|c2_g1_i1 39.359 31.637 47.433 16.583 20.347 21.203 22.772 12.739 19.471
+TR3859|c0_g1_i1 205.321 207.779 192.904 65.550 62.915 58.961 123.559 130.636 131.322
+TR1495|c0_g1_i1 24.349 24.051 21.923 28.587 22.718 28.886 27.244 26.385 30.628
+TR4258|c0_g1_i1 248.292 261.786 311.476 164.710 158.739 174.929 114.049 108.577 112.880
+TR1654|c2_g1_i1 9.156 11.462 1.830 20.212 17.432 9.782 5.406 3.587 1.841
+TR4474|c0_g1_i1 1176.602 1164.432 943.290 8058.929 7622.533 8084.016 2672.348 2928.142 2921.025
+TR1308|c0_g1_i1 10.161 8.060 11.340 16.571 18.288 17.113 27.424 27.044 30.574
+TR4857|c0_g1_i1 26.204 8.545 11.358 32.481 24.245 21.883 4.755 7.941 9.794
+TR2175|c0_g1_i4 33.882 33.516 28.566 35.004 30.179 28.485 34.698 38.732 33.092
+TR2430|c0_g1_i1 26.426 27.503 33.217 16.102 17.768 19.759 8.242 8.305 10.390
+TR77|c0_g1_i1 111.459 122.136 84.697 103.787 84.535 100.069 93.813 100.529 102.580
+TR3301|c0_g1_i1 89.409 86.177 84.995 19.935 23.771 24.104 46.915 57.221 48.402
+TR2003|c0_g1_i1 4.849 4.045 12.043 12.737 14.309 11.664 12.397 5.448 8.341
+TR3913|c0_g1_i1 1770.225 1796.363 1785.620 8679.881 8430.875 8766.717 3691.455 3922.094 3975.887
+TR967|c0_g1_i1 1.681 5.251 1.668 0.000 3.551 2.245 4.892 11.421 10.056
+TR2128|c1_g1_i1 2.753 5.360 4.128 208.138 206.432 199.494 324.173 346.462 374.305
+TR0|c0_g1_i1 61.390 81.500 28.512 32.457 21.978 33.850 51.653 56.723 66.356
+TR4516|c0_g1_i1 157.434 138.978 149.663 118.026 107.635 108.917 126.292 131.090 134.391
+TR4536|c0_g1_i1 2.106 4.074 3.056 373.329 346.710 370.370 95.269 108.016 111.968
+TR3971|c0_g1_i1 156.874 144.852 195.932 154.172 143.297 142.184 111.145 131.739 120.246
+TR2235|c0_g1_i1 27.459 24.269 24.023 73.265 81.805 83.356 58.121 48.480 51.714
+TR3446|c0_g1_i1 513.650 473.659 512.249 17.304 19.375 17.878 8.687 10.486 11.807
+TR4967|c0_g5_i1 0.000 54.323 29.080 0.000 0.000 0.000 0.000 0.000 0.000
+TR765|c0_g1_i1 11.484 11.294 7.788 6.958 4.025 4.260 5.098 3.525 4.784
+TR1842|c0_g1_i1 89.650 89.846 89.286 45.170 52.331 58.730 124.330 110.580 109.008
+TR4401|c0_g1_i1 19.298 17.475 19.489 176.438 174.564 177.369 110.828 99.470 106.579
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diff --git a/sample_data/test_DE_analysis/Trinity_trans.TPM.not_cross_norm b/sample_data/test_DE_analysis/Trinity_trans.TPM.not_cross_norm
new file mode 100644
index 0000000..42ffc50
--- /dev/null
+++ b/sample_data/test_DE_analysis/Trinity_trans.TPM.not_cross_norm
@@ -0,0 +1,7240 @@
+ wt_37_1 wt_37_2 wt_37_3 wt_GSNO_1 wt_GSNO_2 wt_GSNO_3 wt_ph8_1 wt_ph8_2 wt_ph8_3
+TR24|c0_g1_i1 36.3 39.07 28.43 13.08 12.74 16.33 82.16 84.69 93.81
+TR2779|c0_g1_i1 69.8 60.8 43.54 52.28 55.57 50.22 342.46 342.81 344.17
+TR127|c1_g1_i1 66.66 38.13 115.04 0 3.73 8.89 5.47 4.98 15.36
+TR2107|c1_g1_i1 140.87 180.17 221.38 16.14 18.65 19.15 3.63 6.76 10.37
+TR2011|c5_g1_i1 5.6 15.69 5.85 6.19 8.64 11.91 5.96 11.61 4.4
+TR4163|c0_g1_i1 90.55 79.66 88.36 40.18 39.22 38.92 52.22 44.09 48.73
+TR5055|c0_g2_i1 69.08 93.87 48.33 16 6.81 10.89 11.99 31 11.5
+TR1449|c0_g1_i1 53.37 51.35 58.41 25.45 20.57 18.08 32.46 26.99 31.33
+TR1982|c2_g1_i1 5.18 6.15 6.14 2.28 6.07 3.67 7.9 9.57 14.01
+TR1859|c3_g1_i1 5.51 0 0 0 0 0 15.6 27.89 7.21
+TR1492|c0_g1_i2 1580.31 1585.93 1589.58 912.47 953.83 965.12 774.75 763.13 748.51
+TR1122|c0_g1_i1 0 12.2 23.36 0 0 19.34 8.76 0 8.07
+TR2278|c0_g1_i1 71.37 60.26 71.21 42.27 43.18 42.21 46.75 39.09 37.49
+TR4084|c0_g1_i1 16.73 18.78 28.27 18.85 21.66 15.91 37.68 29.98 33.25
+TR4761|c0_g1_i1 1345.1 1524.25 1262.94 109.51 104 118.15 280.45 291.5 284.33
+TR3638|c0_g1_i1 452.38 418.04 431.25 102.48 97.09 78.98 218.18 214.06 206.11
+TR2090|c0_g1_i1 0 0 0 0 0.01 8.59 0 3.29 3.74
+TR3854|c0_g1_i1 393.4 402.7 359.62 400.38 397.9 397.9 436.13 443.96 457.12
+TR131|c0_g1_i1 17.58 18.45 15.89 612.54 601.45 603.1 839.89 820.77 840.42
+TR5075|c0_g1_i1 11.54 7.27 12.09 3.85 4.83 3.5 65.93 77.47 89.27
+TR2182|c3_g2_i6 22.31 8.48 20.12 0 0 20.78 18.2 19.59 9.42
+TR3788|c0_g1_i1 13.82 10.86 18.92 72.71 68.98 60.76 13.79 16.91 20.12
+TR4859|c0_g1_i1 44.84 34.07 85.55 5.17 15.17 23.96 7.98 14.24 7.37
+TR2487|c0_g1_i1 209.43 193.83 188.57 374.45 349.41 361.55 482.05 504.53 472.4
+TR2122|c0_g2_i2 14.77 15.99 14.33 14.87 19.12 17.87 41.35 36.28 38.94
+TR4277|c0_g1_i1 4897.17 5197.1 5539.79 134.95 165.05 143.38 192.86 198.72 202.77
+TR4669|c0_g2_i1 0 0 0 0 136.15 158.23 0.04 0.13 0.1
+TR3091|c0_g1_i1 7.23 8.51 6.41 102.48 94.79 101.05 127.62 118.34 125.03
+TR2130|c1_g3_i1 0 0 0 0 0 0 0 0 0
+TR3807|c0_g1_i1 5.72 17.49 12.92 0 2.54 0 3.43 0 0
+TR1894|c2_g1_i1 19.28 37.5 26.12 3.11 7.74 1.86 5.77 1.85 1.87
+TR5212|c0_g1_i1 16.84 14.04 18.89 18.47 20.44 16.74 21.88 17.71 21.74
+TR939|c0_g1_i1 17.67 17.41 17.34 13.87 13.77 13.65 17.69 18.79 18.64
+TR1891|c0_g1_i1 21.83 20.57 23.82 21.35 17.11 18.05 69.6 65.87 62.64
+TR2672|c0_g1_i1 42.59 27.62 60.37 6.88 3.42 0 8.63 14.44 29.32
+TR2844|c0_g1_i1 35.01 33.17 40.76 36.74 38.44 33.64 46.44 40.87 38.23
+TR1837|c2_g1_i1 0 5.18 0 4.69 18.39 5.45 21.25 12.72 0
+TR1678|c0_g1_i1 1.72 1.75 0 0 3.03 0 18.8 10.87 14.68
+TR3249|c0_g1_i1 2.32 2.37 5.1 2.07 0 9.88 2.67 17.68 15.43
+TR1479|c0_g1_i1 25.07 24.57 31.05 50.28 55.16 52.32 62.11 52.34 63.67
+TR989|c0_g1_i1 78.55 81.18 89.14 53.18 51.04 42.07 66.31 61.12 65.23
+TR1084|c0_g1_i1 5.04 2.57 2.79 4.5 2.23 5.36 2.94 27.67 11.28
+TR1054|c0_g1_i1 27.51 19.07 32 10.96 11.53 14.62 18.08 14.95 12.51
+TR1514|c2_g1_i1 122.29 129.15 141.58 84.01 82.82 85.68 28.68 19.86 26.22
+TR5344|c0_g1_i1 66.47 76.83 90.81 40.44 41.82 53.78 50.26 44.69 54.83
+TR2134|c2_g1_i1 14.3 3.64 4.18 6.46 3.19 7.62 4.52 8.3 4.26
+TR1339|c1_g1_i1 32.14 30.04 32.6 33.14 35.49 32.49 44.08 36.47 39.7
+TR1869|c3_g1_i1 18.44 6.22 31.88 17.09 5.56 0 35.91 15.94 8.27
+TR4389|c0_g1_i1 43.08 39.34 44.71 17.46 20.81 19.9 38.86 45.33 40.2
+TR496|c1_g1_i1 10.09 8.31 9.58 78.68 96.61 80.18 67.29 55.15 59.63
+TR2569|c0_g1_i1 67.84 56.14 81.28 210.97 210.55 195.33 126.51 126.03 128.86
+TR173|c0_g1_i1 42.3 35.53 43.21 33.28 30.84 31.14 44.04 41.5 43.39
+TR439|c0_g1_i1 248.14 268.86 308.79 196.68 206.77 154.25 228.01 197.3 162.58
+TR4041|c0_g1_i1 31.02 24 32.56 13.6 20.14 14.33 18.23 19.53 16.91
+TR3271|c0_g1_i1 17.47 8.88 15.87 27.84 19.56 32.62 23.23 5.27 16.27
+TR588|c0_g1_i1 679.31 702.44 715.62 9.99 13.53 8.54 2.68 7.36 10.08
+TR3330|c0_g1_i1 20.16 19.21 22.94 15.8 13.26 11.15 16.07 12.01 11.21
+TR2326|c0_g1_i1 34.83 33.8 43.7 20.84 18.71 19 35.4 26.78 31.77
+TR2210|c0_g1_i1 834.24 755.65 862.23 265.05 295.5 246.82 434.18 411.02 401.45
+TR1364|c0_g1_i1 15.38 16.8 18.24 17.47 18.01 10.89 25.45 21.51 11.36
+TR4000|c0_g1_i1 28.25 29.82 44.99 21.6 19.77 21.07 25.55 26.33 26.91
+TR3821|c0_g1_i1 2.7 2.75 0 0 4.79 2.88 44.82 35.98 39.79
+TR3400|c0_g1_i1 71.68 66.45 76.95 1264.5 1264.93 1230.52 989.31 988.8 931.92
+TR4121|c0_g1_i1 21.71 22.77 23.37 45.43 44.23 46.3 114.94 111.26 100.71
+TR3630|c0_g1_i1 11.17 18.97 13.95 3.3 4.93 7.92 12.36 9.88 6.01
+TR1571|c0_g1_i1 33.85 29.89 32.13 29.59 24.59 23.97 8.33 11.09 10.44
+TR4609|c0_g1_i1 97.2 94.69 75.16 13.74 17.38 23.63 153.66 159.96 165.08
+TR2867|c0_g1_i1 26.06 30.09 33.51 18.48 21.41 19.82 24.88 25.65 19.62
+TR1399|c2_g1_i1 73.53 87.78 99.98 31.31 24.57 26.95 193.48 202.23 184.4
+TR870|c0_g1_i1 8.7 8.87 19.68 2.6 7.73 6.18 10.47 3.25 3.33
+TR1825|c0_g1_i1 14.03 8.17 4.33 10.68 12.4 17.05 2.25 23.58 2.18
+TR1394|c2_g1_i1 4.3 8.76 4.67 11.47 5.7 9.14 7.31 0 0
+TR3881|c0_g1_i1 14.27 9.59 13.59 38 37.74 32.28 21.58 25.64 21.4
+TR1278|c0_g1_i1 35.57 37.4 40.62 8.38 15.73 12.16 25.26 24.57 22.19
+TR3135|c0_g1_i1 316.27 298.79 307.87 92.83 107.68 96.51 156.52 167.9 153.35
+TR2204|c0_g1_i1 59.11 50.45 61.96 14.91 18.61 14.49 11.48 14.17 8.22
+TR4196|c0_g1_i1 18.29 22.93 22.06 11.18 16.12 13.46 3 8.75 5.9
+TR2146|c1_g1_i1 40.75 31.46 40.41 15.25 16.01 20.52 25.38 23.3 18.42
+TR3771|c0_g1_i1 117.97 100.91 130.71 50.51 45.16 55.21 58.58 50.47 42.9
+TR1833|c0_g1_i1 64.83 59.05 65.52 20.84 24.67 19.17 16.35 13.8 12.62
+TR4967|c0_g2_i1 33 0 0 0 0 0 0 0 0
+TR1922|c0_g1_i1 2.84 2.89 15.98 7.62 2.52 0 16.97 12.68 12.95
+TR2901|c0_g1_i1 18.88 18.23 22.09 16.11 24.44 15.04 27.9 21.47 26.69
+TR3584|c0_g1_i1 57.9 53.78 58.61 19.81 21.97 17.9 35.03 37.97 38.45
+TR1595|c0_g1_i1 88.16 72.36 121.47 48.37 52.22 46.27 62.56 56.88 65.55
+TR1103|c0_g1_i1 8.39 6.41 6.82 3.73 3.71 4.46 28.42 15.78 9.17
+TR1074|c0_g1_i1 35.47 20.57 31.58 27.88 9.12 10.82 14.02 12.6 13.02
+TR1703|c4_g1_i1 34.31 31.63 19.02 5.79 8.65 3.47 3.55 3.43 5.21
+TR2939|c0_g1_i1 852.83 752.38 730.26 41.03 54.24 62.37 968.24 959.81 937.11
+TR1973|c0_g1_i1 5.16 3.94 15.55 8.48 6.8 8.23 9.67 8.36 9.05
+TR3064|c0_g1_i1 83.74 75.15 71.76 244.74 222.89 239.09 188.14 175.13 189.74
+TR2137|c2_g1_i1 40.75 31.99 52.62 13.8 17.59 17.47 26.58 14.31 21.57
+TR3859|c0_g1_i1 212.58 210.1 214 54.55 54.39 48.58 144.22 146.75 145.48
+TR1495|c0_g1_i1 25.21 24.32 24.32 23.79 19.64 23.8 31.8 29.64 33.93
+TR4258|c0_g1_i1 257.07 264.71 345.54 137.07 137.23 144.13 133.12 121.97 125.05
+TR1654|c2_g1_i1 9.48 11.59 2.03 16.82 15.07 8.06 6.31 4.03 2.04
+TR4474|c0_g1_i1 1218.2 1177.44 1046.45 6706.55 6589.67 6660.69 3119.21 3289.34 3235.95
+TR1308|c0_g1_i1 10.52 8.15 12.58 13.79 15.81 14.1 32.01 30.38 33.87
+TR4857|c0_g1_i1 27.13 8.64 12.6 27.03 20.96 18.03 5.55 8.92 10.85
+TR2175|c0_g1_i4 35.08 33.89 31.69 29.13 26.09 23.47 40.5 43.51 36.66
+TR2430|c0_g1_i1 27.36 27.81 36.85 13.4 15.36 16.28 9.62 9.33 11.51
+TR77|c0_g1_i1 115.4 123.5 93.96 86.37 73.08 82.45 109.5 112.93 113.64
+TR3301|c0_g1_i1 92.57 87.14 94.29 16.59 20.55 19.86 54.76 64.28 53.62
+TR2003|c0_g1_i1 5.02 4.09 13.36 10.6 12.37 9.61 14.47 6.12 9.24
+TR3913|c0_g1_i1 1832.81 1816.43 1980.9 7223.3 7288.48 7223.19 4308.73 4405.9 4404.54
+TR967|c0_g1_i1 1.74 5.31 1.85 0 3.07 1.85 5.71 12.83 11.14
+TR2128|c1_g1_i1 2.85 5.42 4.58 173.21 178.46 164.37 378.38 389.2 414.66
+TR0|c0_g1_i1 63.56 82.41 31.63 27.01 19 27.89 60.29 63.72 73.51
+TR4516|c0_g1_i1 163 140.53 166.03 98.22 93.05 89.74 147.41 147.26 148.88
+TR4536|c0_g1_i1 2.18 4.12 3.39 310.68 299.73 305.16 111.2 121.34 124.04
+TR3971|c0_g1_i1 162.42 146.47 217.36 128.3 123.88 117.15 129.73 147.99 133.21
+TR2235|c0_g1_i1 28.43 24.54 26.65 60.97 70.72 68.68 67.84 54.46 57.29
+TR3446|c0_g1_i1 531.81 478.95 568.27 14.4 16.75 14.73 10.14 11.78 13.08
+TR4967|c0_g5_i1 0 54.93 32.26 0 0 0 0 0 0
+TR765|c0_g1_i1 11.89 11.42 8.64 5.79 3.48 3.51 5.95 3.96 5.3
+TR1842|c0_g1_i1 92.82 90.85 99.05 37.59 45.24 48.39 145.12 124.22 120.76
+TR4401|c0_g1_i1 19.98 17.67 21.62 146.83 150.91 146.14 129.36 111.74 118.07
+TR536|c0_g2_i1 6.62 6.96 4.16 7.87 12.77 5.03 12.83 8.09 11.41
+TR4425|c0_g1_i1 100.98 108.12 97.86 66.42 61.61 63.14 88.2 87.24 78.79
+TR2953|c0_g1_i1 2132.43 2302.74 1901.96 873.74 848.59 931.29 305.75 294.95 294.94
+TR2697|c0_g1_i1 20.11 20.4 6.26 13.83 0 21.47 6.94 0 0
+TR2282|c0_g1_i1 25.16 21.91 25.04 27.6 27.4 27.48 35.45 28.2 26.48
+TR4511|c0_g1_i1 249.99 256.5 306.02 52.16 56.33 48.92 116.31 102.8 99.14
+TR2154|c0_g1_i1 2566.97 2414.23 2417.96 4103.67 4226.92 4105.71 3963.82 3964.75 3932.38
+TR3066|c0_g1_i1 141.89 149.06 127.42 20.25 19.67 21.09 42.01 44.83 39.51
+TR2182|c3_g2_i1 172.35 243.63 84.2 148.72 190.68 221.77 1031.86 946.34 1029
+TR1614|c1_g1_i1 5.83 0 0 5.23 20.71 9.31 14.04 6.54 0
+TR347|c0_g1_i1 52.38 46.11 56.07 18.55 19.04 15.38 24.04 25.49 23.63
+TR4030|c0_g1_i1 6.79 8.74 9.46 112.88 120.35 101.94 140.23 129.66 132.3
+TR1840|c0_g1_i1 21.17 18.48 33.38 25.4 28 16.08 40.62 34.67 36.66
+TR2058|c5_g1_i1 0 7.9 0 21.11 13.88 8.28 15.03 18.31 9.41
+TR1794|c2_g1_i1 3.75 0 0 3.39 3.34 0 9.57 8.77 9.01
+TR1584|c2_g1_i1 4.6 10.15 7.76 5.39 7.42 6.52 20.91 14.63 13.93
+TR2049|c0_g1_i1 120.06 119 106.42 48.43 42.39 53.7 90.8 80.82 96.42
+TR1950|c3_g1_i1 12.73 10.24 14.3 11.61 8.84 12.96 24.14 24.18 19.52
+TR1544|c1_g1_i1 3.72 2.27 6.01 7.84 10.47 9.49 11.25 8.95 10.5
+TR1453|c0_g1_i1 8.78 5.97 9.94 10.5 2.6 3.12 3.53 0 0
+TR1431|c0_g1_i1 34.82 38.97 47.78 1.53 1.53 2.78 1.77 0 0.88
+TR3367|c0_g1_i1 40.52 46.44 34.24 58.08 69.48 60.82 28.27 22.45 19.97
+TR1533|c0_g1_i1 26.4 22.15 27.81 34.34 38.36 28.07 15.07 22.71 18.06
+TR1242|c1_g1_i1 15.08 16.92 12.98 10.02 14.15 7.74 29.32 29.38 30.52
+TR3802|c0_g1_i1 75.21 65.28 80.45 7.61 8.69 11.8 3.88 2.53 8.95
+TR2831|c0_g1_i1 16.68 14.38 15.68 14.35 13.3 12.35 18.1 19.04 16.34
+TR3892|c0_g3_i1 648.94 607.31 564.92 695.91 689.55 693.47 4176.67 4255.58 4323.47
+TR2456|c0_g1_i1 18.54 18.19 16.42 72.64 69.24 61.46 161.76 149.64 141.15
+TR1644|c1_g1_i1 18.29 22.36 33.24 34.07 24.23 25.29 32.31 27.13 35.38
+TR981|c1_g1_i1 103.8 89.77 93.92 66.28 67.62 68.28 67.35 81.93 66.72
+TR2870|c0_g1_i1 102.76 99.05 105.86 78.42 88.82 85.18 122.58 113.36 119.41
+TR1027|c1_g1_i1 25.99 19.69 13.73 5.35 3.13 6.5 25.68 24.73 21.78
+TR3500|c0_g1_i1 237.75 197.17 272.35 85.06 98.48 91.72 289.34 274.88 277.89
+TR1843|c0_g1_i1 2.54 2.58 5.26 8.95 18.99 9.43 13.34 7.83 5.27
+TR4365|c0_g1_i1 5.19 5.27 19.51 0 4.67 5.54 0 6.49 6.71
+TR1950|c1_g1_i1 3.7 0 8.7 6.69 9.91 0 28.3 4.32 4.44
+TR3155|c0_g1_i1 10.15 10.32 9.61 35.09 33.3 40.3 99.97 113.92 114.35
+TR1964|c0_g1_i1 132.22 164.42 179.6 156.1 161.56 155.79 148.56 133.88 145
+TR1967|c0_g2_i1 77.95 48.13 59.12 0 3.86 1.55 2.42 2.85 7.26
+TR127|c0_g1_i1 31.41 47.78 52.54 0 4.71 11.18 0 0 6.77
+TR4700|c0_g1_i1 203.7 186.74 210.01 119.11 122.95 106.01 131.33 123.28 130.15
+TR4318|c0_g1_i1 23.07 23.49 19 5.93 0 3.51 0 0 0
+TR2674|c0_g1_i1 3.38 8.61 8.97 0 1.49 0 7.38 16.01 9.01
+TR994|c0_g1_i1 100.55 99.63 93.85 84.76 98.94 82.31 70.02 81.51 82.06
+TR411|c0_g1_i1 0 0 6.09 11.48 0 6.48 10.66 12.8 9.86
+TR1895|c2_g1_i1 65.5 72.82 80.62 42.08 37.45 38.82 33.21 32.74 32.46
+TR4162|c0_g1_i1 46.27 40.82 36.06 79.15 85.51 77.4 119.57 127.26 125.04
+TR664|c1_g1_i1 15.97 12.03 10.67 10.37 9.87 8.17 14.12 6.47 9.45
+TR2995|c0_g1_i1 323.28 345.93 388.74 106.43 103.2 106.91 216.03 219.5 208.8
+TR2382|c0_g1_i1 36.64 34.35 31.77 45.75 44.34 50.98 109.7 107.05 103.69
+TR1919|c0_g1_i1 11.01 7.24 6.08 7.36 5.4 5.51 35.32 30.21 27.4
+TR3780|c0_g1_i1 732.3 760.08 815.15 138.94 158.05 134.1 239.41 220.92 232.71
+TR2380|c0_g1_i1 199.99 178.92 229.76 167.79 148.15 155.12 223.22 208.32 199.12
+TR5317|c0_g1_i1 11.05 12.63 12.37 24.97 24.23 30.32 166.23 190.11 187.06
+TR4085|c0_g1_i1 116.94 129.87 150.09 54.81 70.25 47.13 94.88 111.41 105.87
+TR3953|c0_g2_i1 2.9 1.5 5.9 54.17 57.07 60 144.31 138.24 143.79
+TR2237|c0_g1_i1 51.81 42.93 42.4 27.43 27.89 27.75 35.92 38.67 32.32
+TR1499|c1_g1_i1 0 0 0 0 9.19 0 0 6.36 13.14
+TR4037|c0_g1_i1 10.22 16.92 22.56 18.04 18.02 19.02 40.39 25 29.23
+TR4719|c0_g1_i1 11.12 11.33 23.47 7.03 9.81 3.38 1.72 3.32 5.05
+TR615|c0_g1_i1 27.96 22.58 27.79 39.26 42.1 40.74 37.43 35.46 35.68
+TR1649|c1_g1_i1 15.16 9.26 6.37 8.04 2.67 6.45 14.66 14.22 9.59
+TR2026|c1_g1_i1 53.95 43.06 41.23 8.58 9.39 7.58 40.76 35.66 42.84
+TR1455|c2_g1_i1 13.72 16.99 20.33 17.26 14.67 11.41 11.28 12.47 10.13
+TR973|c1_g1_i1 68.07 60.05 70.42 41.68 46.37 39.64 54.25 40.06 41.18
+TR541|c0_g1_i1 10.53 7.41 12.24 32.55 33.86 34.42 31.15 20.36 29.4
+TR466|c1_g1_i1 14.55 21.05 15.11 8.33 10.81 11.29 12.77 8.89 10.6
+TR1393|c1_g1_i1 9.05 12.66 20.97 26.89 27.87 28.85 16.47 16.18 12.82
+TR2113|c0_g1_i1 21.17 15.5 17.52 19.58 18.56 17.19 13.62 13.74 16.52
+TR1017|c0_g1_i1 81.36 102.06 93.42 70.78 64.14 46.06 64.4 63.21 64.66
+TR3456|c0_g1_i1 187.81 198.89 180.96 407.92 407 413.73 357.96 362.3 359.78
+TR1763|c2_g1_i1 5.44 6.93 19.87 9.61 14.4 15.92 4.33 7.04 2.84
+TR3015|c0_g1_i1 17.3 19.27 17.54 64.38 58.65 57.77 23.38 37.3 20.84
+TR1881|c1_g1_i1 91.23 73.4 113.74 114.04 138.75 112.85 254.44 221.73 209.13
+TR2957|c0_g1_i1 35.19 38.14 37.62 21.78 28.54 25.85 30.75 32.48 29.08
+TR3960|c0_g1_i1 25.81 25.05 29.81 78.17 89.73 75.77 88.47 76.84 84.12
+TR1546|c0_g1_i1 42.4 37.79 31 17.76 14.35 19.49 15.84 19.16 21.62
+TR3712|c0_g1_i1 138.41 161.34 122.33 26.89 40.17 30.76 52.94 65.04 46.81
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+TR1032|c0_g1_i1 31.31 33.69 31.03 27.94 26.64 30.57 60.29 56.91 59.7
+TR3219|c0_g2_i1 0 1.44 1.68 0 0 0 1.61 0 0
+TR949|c1_g1_i1 40.5 35.09 38.63 7.9 13.84 9.56 25.69 23.31 24.94
+TR2031|c1_g1_i1 11.24 9.16 9.83 0 1.99 11.96 5.14 0 0
+TR4216|c0_g1_i1 40.48 53.23 41.53 21.27 27.48 17.2 58.28 42.84 61.27
+TR585|c0_g1_i1 2.73 2.78 4.27 8.43 7.21 10.15 7.24 7.05 4.28
+TR4747|c0_g1_i1 79.07 82.89 82.11 64.45 67.14 54.77 82.67 91.05 90.62
+TR1539|c2_g1_i1 9.87 1.44 7.37 2.49 11.19 7.5 19.53 16.08 13.3
+TR2657|c0_g1_i1 4.02 3.27 2.39 10.2 10.94 12.39 17.73 19.81 19.07
+TR4558|c0_g1_i1 62.64 60.96 76.57 23.63 25.44 29.34 45.19 32.96 28.38
+TR826|c0_g1_i1 8.73 8.87 7.02 37.1 36.48 38.87 107.23 106.17 100.72
+TR2045|c3_g1_i1 8.02 6.73 7.59 5.18 5.2 6.67 10.88 13.36 14.08
+TR1927|c2_g1_i1 4.66 4.73 5.71 12.76 8.36 0 0 11.38 0
+TR2078|c2_g1_i1 12.78 6.46 8.36 5.94 0 6.84 0 0 0
+TR303|c0_g1_i1 3.56 7.24 16.61 6.42 22.19 11.37 17.94 8.25 4.23
+TR3966|c0_g1_i1 54.63 56.62 55.46 76.93 82.45 71.02 59.81 59.61 58.38
+TR1890|c3_g1_i1 11.31 0 28.82 0 0 6.04 0 0 0
+TR5095|c0_g1_i1 7.7 10.79 10.46 26.67 25.6 26.23 34.21 27.28 30.45
+TR3761|c0_g1_i1 14.13 15.58 14.59 23.87 15.55 12.52 0 2.41 1.22
+TR4058|c0_g1_i1 639.81 654.02 605.28 2559.84 2474.15 2631.42 1293.09 1360.87 1403.18
+TR4924|c0_g1_i1 0 0 0 45.73 24.52 19.45 12.25 5.54 5.71
+TR2183|c5_g1_i1 157.4 150.11 171.09 67.05 73.16 97.85 97.7 75.33 86
+TR3572|c0_g1_i1 14 15.44 36.12 19.53 19.51 16.12 45.04 53.74 34.93
+TR1643|c1_g2_i1 0.03 0.02 0.02 0.1 0.11 0.08 0.37 0.11 0.4
+TR1988|c0_g1_i1 4.17 2.83 5.81 27.03 13.49 19.23 5.92 8.65 10.19
+TR213|c0_g1_i1 54.74 51.02 60.03 22.1 21.43 17.47 17.19 18.84 15.03
+TR483|c0_g2_i1 13.57 20.83 30.84 9.37 13.28 15.41 20.86 15.78 18.29
+TR1537|c0_g1_i1 0 13.83 0 29 0 71.92 0 0 9.47
+TR120|c0_g2_i1 20.72 12.89 26.7 14.56 23.14 24.49 147.42 212.96 235.32
+TR2186|c3_g1_i1 212.32 206.09 255.18 523.83 416.82 527.29 124.11 166.8 138.87
+TR133|c0_g1_i1 72.25 67.64 74.24 39.57 45.03 39.59 56.15 42.67 54.41
+TR1154|c0_g1_i1 45.46 46.66 57.68 25.01 26.5 20.77 51.16 44.41 48.04
+TR760|c0_g1_i1 15.27 14.35 19.25 23.2 22.92 20.75 32.42 29.54 31.84
+TR1366|c0_g1_i1 13.83 35.21 20.09 40.55 33.9 33.16 26 39.91 40.92
+TR1710|c5_g1_i1 0 0 20.73 0 24.62 0 15.43 6.9 14.27
+TR3344|c0_g1_i1 206.5 183.29 212.45 221.71 227.47 195.09 189.45 179.84 184.87
+TR205|c0_g2_i1 73.78 70.79 73.93 39.11 39.64 36.02 21.31 10.72 10.73
+TR323|c0_g1_i1 5.62 5.73 6.33 0 0 0 10.07 0 6.41
+TR1337|c1_g1_i1 33.99 27.8 38.74 18.79 20.56 16.6 16.44 12.7 13.5
+TR706|c0_g4_i1 0 0 0 0 0 0 0 0 0
+TR3121|c0_g1_i1 147.64 118.45 142.99 94.86 94.19 96.83 371.83 372.18 407.79
+TR424|c0_g1_i1 12.42 0 11.91 3.09 0.27 1.11 31.95 0 0
+TR179|c0_g1_i1 14.37 0 0 0 0 0 22.61 0 29.15
+TR1018|c0_g1_i1 188.36 177.2 226.41 114.1 104.35 96.89 55.96 44.43 51.92
+TR1422|c1_g1_i1 20.6 0 6.44 9.45 9.27 11 14.32 0 0
+TR754|c0_g1_i1 37.24 36.71 36.15 7.16 3.92 3.96 25.47 26.38 30.85
+TR2079|c0_g1_i1 8.8 13.44 6.15 7.77 1.29 1.56 25.11 21.34 12.33
+TR4552|c0_g1_i1 212.07 198.2 196.46 162.35 158.78 163.32 248.19 242.68 230.53
+TR143|c1_g1_i1 55.23 36.93 72.32 13.02 17.53 21.61 14.9 10.72 12.18
+TR2181|c1_g2_i1 66.89 64.91 67.34 42.04 38.21 47.05 51.06 54.34 43.07
+TR2477|c0_g1_i1 107.84 126.42 121.02 8.5 14.53 9.5 82.56 79.02 77.09
+TR974|c0_g1_i1 58.81 53.68 64.58 51.1 48.96 48.95 40.27 35.38 41.02
+TR1996|c2_g2_i1 82.62 81.88 124.89 78.52 37 68.11 45.39 113.75 90.35
+TR5227|c0_g1_i1 245.16 230.17 226.69 166.21 176.29 166.64 640.04 611.04 622.45
+TR1562|c1_g1_i1 11.41 17.33 14.57 5.27 20.61 6.1 8.16 7.28 0
+TR2269|c0_g1_i1 34.63 39.37 48.22 15.63 14.47 14.15 32.65 30.6 30.98
+TR790|c0_g1_i1 2.52 7.7 27.91 2.25 0 10.72 2.94 5.53 5.64
+TR3462|c0_g1_i1 15.3 15.74 13.14 20.53 22.8 19.3 85.85 87.84 83.65
+TR162|c0_g1_i1 18.34 19.37 18.87 11.63 12.62 13.37 22.47 15.2 17.72
+TR2058|c1_g1_i1 0 0 0 9.92 3.26 0 9.3 8.53 8.76
+TR2182|c11_g1_i1 5.5 5.6 3.08 0 4.88 2.93 6.54 9.18 9.37
+TR1643|c1_g1_i1 0.03 0.02 0.02 0.1 0.11 0.08 0.37 0.11 0.4
+TR1325|c0_g2_i1 11.27 6.37 0 15.19 16.03 17.84 16.22 14.4 11.62
+TR2280|c0_g1_i1 84.58 95.22 108.84 44.56 42.41 35 48.62 47.18 44.82
+TR5261|c0_g1_i1 14.75 12.53 27.18 6.58 4.36 5.23 2.86 2.69 8.24
+TR5016|c0_g1_i1 47.81 51.03 45.83 101.81 107.77 102.95 81.14 84.88 82.8
+TR2144|c0_g1_i1 33.02 27.6 33.43 34.33 30.9 29.62 26.88 25.99 21.35
+TR5059|c0_g1_i1 148.38 172.38 227.88 57.62 74.4 72.35 97.57 97.55 95.17
+TR177|c0_g1_i1 7.07 9.61 7.78 10.51 6.26 5.02 10.87 12.84 18.31
+TR1500|c2_g1_i1 0 4.62 6.36 5.35 5.33 3.22 26 29.94 7.97
+TR589|c1_g1_i1 202.8 193.69 242.43 79.91 83.87 84.24 140.49 142.55 105.69
+TR1294|c0_g1_i1 19.35 16.78 25.28 14.69 15.7 14.87 15.56 13.28 15.17
+TR3065|c0_g1_i1 6.03 0 23.36 0 10.91 0 8.76 0 8.07
+TR5251|c0_g1_i1 461.88 514.61 384.52 110.76 102.67 106.63 154.53 160.33 169.86
+TR3487|c0_g1_i1 162.08 162.6 176.85 144.11 127.23 136.41 157.05 179.73 160.32
+TR1723|c2_g1_i1 11.23 11.44 10.27 16.12 12.37 19.4 10.46 8.73 7.35
+TR4647|c0_g1_i1 52.82 49.58 46.58 267.33 248.46 262.34 340.3 328.47 343.77
+TR3574|c0_g1_i1 29.29 36.44 31.29 21.8 17.26 19.97 22.76 18.55 18.61
+TR1857|c1_g1_i1 0 0 10.33 19.46 34.48 4.56 0 5.14 5.29
+TR1780|c0_g1_i1 13.45 9.12 12.93 8.63 14.56 14.29 12.34 21.7 15.99
+TR5232|c0_g1_i1 90.89 93.48 82.85 12.96 12.52 10.11 49.15 54.49 53.11
+TR2130|c0_g2_i1 1032.83 1040.55 1099.75 7092.35 7005.69 7593.51 4023.8 4197.18 4148.17
+TR2408|c0_g1_i1 0 0 0 0 0 0 0 0 0
+TR2590|c0_g1_i1 192.85 199.32 352.67 54.78 61.39 44.01 653.61 468.9 503.23
+TR1386|c1_g1_i1 19.17 6.51 11 5.75 11.37 10.21 3.93 0 7.45
+TR3615|c0_g1_i1 6.82 8.67 5.12 17.93 8.99 10.87 60.4 47.45 56.15
+TR1683|c2_g1_i1 0 0 0 0 3.8 2.28 48.7 23.15 32.95
+TR2187|c2_g1_i1 78.9 95.23 29.41 46.65 46.63 43.5 130.18 96.41 98.96
+TR2191|c0_g1_i1 31.85 31.65 36.75 30.78 35.33 27.74 54.07 48.64 45.44
+TR4108|c0_g1_i1 255.17 238.83 278.15 87.48 82.17 76.52 41.53 32.33 41.69
+TR1650|c2_g1_i1 80.5 72.57 103.52 20.39 17.33 20.98 33.51 34.1 29.69
+TR5091|c0_g1_i1 1598.13 1676.26 2043.34 8547.59 8086.63 8562.46 5411.61 5413.77 5393.42
diff --git a/sample_data/test_DE_analysis/Trinity_trans.counts.matrix b/sample_data/test_DE_analysis/Trinity_trans.counts.matrix
new file mode 100644
index 0000000..1ecf85d
--- /dev/null
+++ b/sample_data/test_DE_analysis/Trinity_trans.counts.matrix
@@ -0,0 +1,7240 @@
+ wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2
+TR24|c0_g1_i1 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00
+TR2779|c0_g1_i1 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00
+TR127|c1_g1_i1 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00
+TR2107|c1_g1_i1 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00
+TR2011|c5_g1_i1 11.00 4.00 4.00 8.00 5.00 7.00 3.00 4.00 8.00
+TR4163|c0_g1_i1 368.00 422.00 425.00 172.00 216.00 210.00 234.00 254.00 212.00
+TR5055|c0_g2_i1 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00
+TR1449|c0_g1_i1 196.00 230.00 207.00 66.00 113.00 91.00 124.00 130.00 107.00
+TR1982|c2_g1_i1 7.00 7.00 6.00 4.00 3.00 8.00 16.00 9.00 11.00
+TR1859|c3_g1_i1 0.00 0.00 1.00 0.00 0.00 0.00 1.00 2.00 4.00
+TR1492|c0_g1_i2 1895.00 1906.00 1921.00 1104.00 1263.00 1319.00 899.00 929.00 922.00
+TR1122|c0_g1_i1 2.00 3.00 0.00 3.00 0.00 0.00 1.00 1.00 0.00
+TR2278|c0_g1_i1 497.00 610.00 598.00 333.00 406.00 413.00 323.00 409.00 337.00
+TR4084|c0_g1_i1 95.00 148.00 86.00 77.00 111.00 127.00 175.00 201.00 158.00
+TR4761|c0_g1_i1 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00
+TR3638|c0_g1_i1 647.00 676.00 712.00 117.00 184.00 174.00 324.00 344.00 338.00
+TR2090|c0_g1_i1 0.00 0.00 0.00 22.00 0.00 0.02 10.33 0.00 9.09
+TR3854|c0_g1_i1 1878.00 1734.00 1864.00 1775.00 2173.00 2151.00 2216.00 2142.00 2155.00
+TR131|c0_g1_i1 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00
+TR5075|c0_g1_i1 13.00 22.00 21.00 6.00 8.00 10.00 163.00 121.00 142.00
+TR2182|c3_g2_i6 1.44 2.70 3.84 3.35 0.00 0.00 1.22 2.18 2.63
+TR3788|c0_g1_i1 17.00 30.00 22.00 91.00 132.00 125.00 32.00 22.00 27.00
+TR4859|c0_g1_i1 6.00 12.00 8.00 4.00 1.00 3.00 1.00 1.00 2.00
+TR2487|c0_g1_i1 386.00 383.00 424.00 689.00 866.00 806.00 963.00 989.00 1032.00
+TR2122|c0_g2_i2 145.00 135.00 136.00 155.00 157.00 201.00 369.00 398.00 344.00
+TR4277|c0_g1_i1 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00
+TR4669|c0_g2_i1 0.00 0.00 0.00 209.00 0.00 217.50 0.14 0.06 0.18
+TR3091|c0_g1_i1 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00
+TR2130|c1_g3_i1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
+TR3807|c0_g1_i1 6.00 4.00 2.00 0.00 0.00 1.00 0.00 1.00 0.00
+TR1894|c2_g1_i1 21.00 14.00 11.00 1.00 2.00 5.00 1.00 3.00 1.00
+TR5212|c0_g1_i1 64.00 89.00 78.00 73.00 98.00 108.00 103.00 105.00 84.00
+TR939|c0_g1_i1 96.00 99.00 99.00 72.00 89.00 88.00 107.00 103.00 108.00
+TR1891|c0_g1_i1 115.00 137.96 124.00 96.53 139.00 110.94 364.77 411.00 384.00
+TR2672|c0_g1_i1 14.00 29.00 22.00 0.00 4.00 2.00 14.00 4.00 7.00
+TR2844|c0_g1_i1 166.00 211.00 178.00 161.00 214.00 223.00 199.00 245.00 213.00
+TR1837|c2_g1_i1 1.00 0.00 0.00 1.00 1.00 4.00 0.00 3.00 2.00
+TR1678|c0_g1_i1 1.00 0.00 1.00 0.00 0.00 2.00 8.00 10.00 6.00
+TR3249|c0_g1_i1 1.00 2.00 1.00 4.00 1.00 0.00 6.00 1.00 7.00
+TR1479|c0_g1_i1 136.00 178.00 141.00 277.00 324.00 354.00 367.00 363.00 302.00
+TR989|c0_g1_i1 125.00 139.00 123.00 62.00 95.00 91.00 102.00 104.00 96.00
+TR1084|c0_g1_i1 1.00 1.00 2.00 2.00 2.00 1.00 4.00 1.00 10.00
+TR1054|c0_g1_i1 30.00 51.00 44.00 22.00 20.00 21.00 20.00 29.00 24.00
+TR1514|c2_g1_i1 241.00 269.00 232.00 153.00 182.00 179.00 50.00 55.00 38.00
+TR5344|c0_g1_i1 100.00 119.00 88.00 67.00 61.00 63.00 72.00 66.00 59.00
+TR2134|c2_g1_i1 1.00 1.00 4.00 2.00 2.00 1.00 1.00 1.00 2.00
+TR1339|c1_g1_i1 57.00 63.00 62.00 59.00 73.00 78.00 77.00 86.00 71.00
+TR1869|c3_g1_i1 1.00 4.00 3.00 0.00 3.00 1.00 1.00 4.00 2.00
+TR4389|c0_g1_i1 124.00 145.00 138.00 60.00 64.00 76.00 131.00 128.00 148.00
+TR496|c1_g1_i1 17.00 20.00 21.00 157.00 187.00 229.00 125.00 142.00 116.00
+TR2569|c0_g1_i1 39.00 55.00 48.00 130.00 169.00 169.00 87.00 84.00 86.00
+TR173|c0_g1_i1 167.00 210.00 202.00 140.00 182.00 168.00 212.00 218.00 203.00
+TR439|c0_g1_i1 151.00 166.00 142.00 83.00 127.00 134.00 87.00 119.00 107.00
+TR4041|c0_g1_i1 35.00 48.00 46.00 20.00 23.00 34.00 25.00 27.00 29.00
+TR3271|c0_g1_i1 2.00 3.00 4.00 7.00 7.00 5.00 3.00 4.00 1.00
+TR588|c0_g1_i1 1031.00 1062.00 1014.00 12.00 17.00 23.00 15.00 4.00 11.00
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+TR2326|c0_g1_i1 106.00 141.00 111.00 57.00 76.00 68.00 103.00 116.00 87.00
+TR2210|c0_g1_i1 3146.00 3707.00 3529.00 983.00 1284.00 1426.00 1735.00 1900.00 1779.00
+TR1364|c0_g1_i1 29.00 32.00 27.00 18.00 35.00 36.00 20.00 45.00 38.00
+TR4000|c0_g1_i1 108.00 168.00 104.00 73.00 91.00 83.00 101.00 97.00 99.00
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+TR3400|c0_g1_i1 166.00 197.00 182.00 2941.00 3671.00 3661.00 2396.00 2566.00 2549.00
+TR4121|c0_g1_i1 127.00 135.00 123.00 247.00 295.00 286.00 585.00 677.00 647.00
+TR3630|c0_g1_i1 10.00 7.00 6.00 4.00 2.00 3.00 3.00 6.00 5.00
+TR1571|c0_g1_i1 86.00 95.00 99.00 66.00 99.00 82.00 31.00 25.00 33.00
+TR4609|c0_g1_i1 113.00 90.00 118.00 27.00 19.00 24.00 198.00 184.00 193.00
+TR2867|c0_g1_i1 200.00 231.00 176.00 126.00 143.00 165.00 136.00 175.00 178.00
+TR1399|c2_g1_i1 68.00 76.00 58.00 20.00 28.00 22.00 140.00 145.00 155.00
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+TR3881|c0_g1_i1 41.00 60.00 62.00 132.00 189.00 187.00 95.00 97.00 114.00
+TR1278|c0_g1_i1 119.00 133.00 115.00 37.00 31.00 58.00 73.00 84.00 81.00
+TR3135|c0_g1_i1 618.00 650.00 665.00 191.00 223.00 258.00 325.00 334.00 357.00
+TR2204|c0_g1_i1 131.00 165.00 156.00 36.00 45.00 56.00 22.00 31.00 38.00
+TR4196|c0_g1_i1 16.00 15.00 13.00 9.00 9.00 13.00 4.00 2.00 6.00
+TR2146|c1_g1_i1 117.00 155.00 154.00 73.00 66.00 69.00 71.00 99.00 90.00
+TR3771|c0_g1_i1 191.00 252.00 227.00 100.00 111.00 99.00 83.00 114.00 98.00
+TR1833|c0_g1_i1 190.00 217.00 212.00 59.00 78.00 92.00 42.00 55.00 46.00
+TR4967|c0_g2_i1 0.00 0.00 136.64 0.00 0.00 0.00 0.00 0.00 0.00
+TR1922|c0_g1_i1 1.00 5.00 1.00 0.00 3.00 1.00 4.00 5.00 4.00
+TR2901|c0_g1_i1 38.00 47.00 40.00 30.00 39.00 59.00 57.00 60.00 46.00
+TR3584|c0_g1_i1 245.00 276.00 268.00 78.00 105.00 116.00 182.00 168.00 180.00
+TR1595|c0_g1_i1 134.00 229.00 166.00 82.00 104.00 112.00 124.00 119.00 108.00
+TR1103|c0_g1_i1 3.00 3.00 4.00 2.00 2.00 2.00 4.00 12.00 7.00
+TR1074|c0_g1_i1 4.00 5.00 7.00 2.00 6.00 2.00 2.00 2.00 2.00
+TR1703|c4_g1_i1 19.00 11.00 21.00 2.00 4.00 6.00 3.00 2.00 2.00
+TR2939|c0_g1_i1 1437.00 1421.00 1656.00 114.00 91.00 120.00 1830.00 1902.00 1881.00
+TR1973|c0_g1_i1 6.00 24.00 8.00 12.00 15.00 12.00 14.00 15.00 13.00
+TR3064|c0_g1_i1 181.00 177.00 205.00 551.00 685.00 622.00 470.00 470.00 435.00
+TR2137|c2_g1_i1 44.00 73.00 57.00 23.00 22.00 28.00 30.00 37.00 20.00
+TR3859|c0_g1_i1 963.00 1014.00 990.00 213.00 291.00 289.00 693.00 696.00 700.00
+TR1495|c0_g1_i1 94.00 97.00 99.00 88.00 107.00 88.00 136.00 129.00 119.00
+TR4258|c0_g1_i1 330.00 433.00 326.00 172.00 198.00 198.00 157.00 167.00 154.00
+TR1654|c2_g1_i1 6.00 1.00 5.00 4.00 10.00 9.00 1.00 3.00 2.00
+TR4474|c0_g1_i1 1586.00 1421.00 1669.00 8588.00 10472.00 10275.00 4404.00 4248.00 4500.00
+TR1308|c0_g1_i1 32.00 51.00 42.00 53.00 63.00 72.00 138.00 132.00 124.00
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+TR4216|c0_g1_i1 97.00 77.00 75.00 30.00 45.00 58.00 114.00 109.00 80.00
+TR585|c0_g1_i1 2.00 3.00 2.00 7.00 7.00 6.00 3.00 5.00 5.00
+TR4747|c0_g1_i1 261.00 266.00 253.00 165.00 236.00 245.00 295.00 272.00 297.00
+TR1539|c2_g1_i1 1.00 5.00 7.00 5.00 2.00 9.00 9.00 13.00 11.00
+TR2657|c0_g1_i1 8.00 6.00 10.00 29.00 29.00 31.00 48.00 45.00 50.00
+TR4558|c0_g1_i1 89.00 113.00 93.00 41.00 40.00 43.00 42.00 67.00 49.00
+TR826|c0_g1_i1 21.00 17.00 21.00 88.00 102.00 100.00 245.00 263.00 259.00
+TR2045|c3_g1_i1 19.00 22.00 23.00 18.00 17.00 17.00 41.00 32.00 39.00
+TR1927|c2_g1_i1 1.00 1.00 1.00 0.00 3.00 2.00 0.00 0.00 2.00
+TR2078|c2_g1_i1 1.00 1.00 2.00 1.00 1.00 0.00 0.00 0.00 0.00
+TR303|c0_g1_i1 2.00 4.00 1.00 3.00 2.00 7.00 1.00 4.00 2.00
+TR3966|c0_g1_i1 205.00 207.00 201.00 246.00 324.00 346.00 219.00 227.00 224.00
+TR1890|c3_g1_i1 0.00 4.00 2.00 1.00 0.00 0.00 0.00 0.00 0.00
+TR5095|c0_g1_i1 40.00 40.00 29.00 93.00 115.00 110.00 117.00 133.00 105.00
+TR3761|c0_g1_i1 13.00 12.00 12.00 10.00 23.00 15.00 1.00 0.00 2.00
+TR4058|c0_g1_i1 4051.00 3886.00 4026.00 15590.00 18460.00 17767.00 9060.00 8469.00 8795.00
+TR4924|c0_g1_i1 0.00 0.00 0.00 4.00 11.00 6.00 1.00 2.00 1.00
+TR2183|c5_g1_i1 149.00 169.00 159.00 93.00 77.00 84.00 85.00 96.00 75.00
+TR3572|c0_g1_i1 13.00 30.00 12.00 13.00 19.00 19.00 29.00 37.00 45.00
+TR1643|c1_g2_i1 0.05 0.04 0.06 0.15 0.24 0.25 0.79 0.74 0.22
+TR1988|c0_g1_i1 2.00 4.00 3.00 13.00 22.00 11.00 7.00 4.00 6.00
+TR213|c0_g1_i1 345.00 421.00 376.00 113.00 174.00 168.00 106.00 123.00 133.00
+TR483|c0_g2_i1 65.00 99.00 43.03 46.00 34.00 48.04 59.00 68.00 51.00
+TR1537|c0_g1_i1 18.70 0.00 0.00 93.05 45.43 0.00 12.94 0.00 0.00
+TR120|c0_g2_i1 20.90 43.91 34.16 38.01 27.38 43.44 388.15 244.06 352.77
+TR2186|c3_g1_i1 80.00 91.00 84.00 196.00 232.00 186.00 49.00 42.00 60.00
+TR133|c0_g1_i1 175.00 197.00 190.00 98.00 119.00 135.00 145.00 151.00 114.00
+TR1154|c0_g1_i1 202.00 258.00 200.00 86.00 126.00 133.00 216.00 233.00 200.00
+TR760|c0_g1_i1 162.00 226.00 175.00 224.00 305.00 300.00 376.00 389.00 349.00
+TR1366|c0_g1_i1 10.00 5.00 4.00 9.00 13.00 11.00 10.00 6.00 10.00
+TR1710|c5_g1_i1 0.00 3.00 0.00 0.00 0.00 5.00 2.00 2.00 1.00
+TR3344|c0_g1_i1 434.00 515.00 497.00 442.00 610.00 624.00 450.00 465.00 439.00
+TR205|c0_g2_i1 117.00 124.00 124.00 56.97 75.00 75.87 18.05 36.00 18.12
+TR323|c0_g1_i1 2.00 2.00 2.00 0.00 0.00 0.00 2.00 3.00 0.00
+TR1337|c1_g1_i1 70.00 100.00 87.00 40.00 55.00 60.00 35.00 43.00 33.00
+TR706|c0_g4_i1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
+TR3121|c0_g1_i1 138.00 167.00 175.00 108.00 128.00 127.00 477.00 434.00 438.00
+TR424|c0_g1_i1 0.00 39.98 41.16 3.47 11.70 1.03 0.00 108.94 0.00
+TR179|c0_g1_i1 0.00 0.00 32.37 0.00 0.00 0.00 66.30 51.82 0.00
+TR1018|c0_g1_i1 84.00 101.00 91.00 44.00 62.00 57.00 23.00 24.00 20.00
+TR1422|c1_g1_i1 0.00 1.00 4.00 2.00 2.00 2.00 0.00 2.00 0.00
+TR754|c0_g1_i1 97.00 98.00 100.00 10.00 22.00 12.00 84.00 70.00 72.00
+TR2079|c0_g1_i1 9.00 4.00 6.00 1.00 6.00 1.00 8.00 16.00 14.00
+TR4552|c0_g1_i1 699.00 714.00 760.00 551.00 666.00 649.00 842.00 917.00 888.00
+TR143|c1_g1_i1 100.00 201.00 152.00 56.00 41.00 55.00 34.00 42.00 30.00
+TR2181|c1_g2_i1 72.27 75.01 75.77 50.15 54.20 49.22 48.03 56.77 61.00
+TR2477|c0_g1_i1 473.00 467.00 410.00 34.00 37.00 63.00 299.00 324.00 307.00
+TR974|c0_g1_i1 141.00 174.00 157.00 123.00 156.00 149.00 111.00 110.00 96.00
+TR1996|c2_g2_i1 48.93 71.83 50.31 39.00 54.00 25.53 51.77 25.43 66.00
+TR5227|c0_g1_i1 667.00 675.00 722.00 462.00 560.00 592.00 1862.00 1934.00 1832.00
+TR1562|c1_g1_i1 3.00 2.00 2.00 1.00 1.00 4.00 0.00 1.00 1.00
+TR2269|c0_g1_i1 413.00 526.00 369.00 142.00 191.00 176.00 340.00 364.00 336.00
+TR790|c0_g1_i1 3.00 10.00 1.00 4.00 1.00 0.00 2.00 1.00 2.00
+TR3462|c0_g1_i1 81.00 70.00 80.00 95.00 123.00 136.00 448.00 466.00 471.00
+TR162|c0_g1_i1 53.00 53.00 51.00 35.00 37.00 40.00 50.00 64.00 43.00
+TR2058|c1_g1_i1 0.00 0.00 0.00 0.00 3.00 1.00 2.00 2.00 2.00
+TR2182|c11_g1_i1 2.00 1.00 2.00 1.00 0.00 2.00 3.00 2.00 3.00
+TR1643|c1_g1_i1 0.05 0.04 0.06 0.15 0.24 0.25 0.79 0.74 0.22
+TR1325|c0_g2_i1 7.08 0.00 12.75 18.99 19.55 20.62 12.94 18.00 16.14
+TR2280|c0_g1_i1 492.00 582.00 444.00 173.00 268.00 254.00 241.00 265.00 254.00
+TR5261|c0_g1_i1 5.00 10.00 6.00 2.00 3.00 2.00 3.00 1.00 1.00
+TR5016|c0_g1_i1 270.00 251.00 257.00 521.00 627.00 661.00 456.00 453.00 468.00
+TR2144|c0_g1_i1 74.00 92.00 90.00 76.00 107.00 96.00 59.00 75.00 72.00
+TR5059|c0_g1_i1 376.00 508.00 329.00 151.00 146.00 188.00 213.00 220.00 219.00
+TR177|c0_g1_i1 4.00 3.00 3.00 2.00 5.00 3.00 7.00 4.00 5.00
+TR1500|c2_g1_i1 3.00 4.00 0.00 2.00 4.00 4.00 5.00 16.00 19.00
+TR589|c1_g1_i1 120.00 145.00 128.00 50.00 57.00 60.00 63.00 82.00 86.00
+TR1294|c0_g1_i1 105.00 164.00 123.00 89.00 107.00 113.93 99.00 103.00 86.74
+TR3065|c0_g1_i1 0.00 3.00 1.00 0.00 0.00 2.00 1.00 1.00 0.00
+TR5251|c0_g1_i1 1367.00 1048.00 1247.00 271.00 342.00 316.00 465.00 427.00 440.00
+TR3487|c0_g1_i1 461.00 515.00 467.00 370.00 475.00 418.00 469.00 464.00 527.00
+TR1723|c2_g1_i1 8.00 7.00 8.00 13.00 13.00 10.00 5.00 7.00 6.00
+TR4647|c0_g1_i1 145.00 140.00 157.00 734.00 909.00 842.00 1038.00 1038.00 994.00
+TR3574|c0_g1_i1 82.00 72.00 67.00 43.00 57.00 45.00 43.00 53.00 43.00
+TR1857|c1_g1_i1 0.00 2.00 0.00 1.00 5.00 9.00 1.00 0.00 1.00
+TR1780|c0_g1_i1 20.00 29.00 30.00 30.00 22.00 37.00 36.00 28.00 49.00
+TR5232|c0_g1_i1 174.00 157.00 172.00 18.00 28.00 27.00 101.00 94.00 104.00
+TR2130|c0_g2_i1 872.96 909.82 882.13 6101.34 6874.12 6795.39 3429.80 3292.17 3500.57
+TR2408|c0_g1_i1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
+TR2590|c0_g1_i1 426.00 770.00 419.00 90.00 136.00 152.00 1103.00 1443.00 1031.00
+TR1386|c1_g1_i1 2.00 3.00 6.00 3.00 2.00 4.00 2.00 1.00 0.00
+TR3615|c0_g1_i1 15.00 9.00 12.00 18.00 36.00 18.00 99.00 107.00 84.00
+TR1683|c2_g1_i1 0.00 0.00 0.00 1.00 0.00 2.00 14.00 20.00 10.00
+TR2187|c2_g1_i1 30.59 8.45 25.82 13.37 17.00 17.17 28.00 35.00 27.90
+TR2191|c0_g1_i1 272.00 328.00 278.00 228.00 308.00 352.00 408.00 493.00 437.00
+TR4108|c0_g1_i1 770.00 923.00 836.00 236.00 328.00 307.00 139.00 140.00 108.00
+TR1650|c2_g1_i1 141.00 205.00 159.00 39.00 46.00 39.00 59.00 67.00 68.00
+TR5091|c0_g1_i1 1585.00 1918.00 1538.00 7753.00 9347.00 8844.00 5064.00 5045.00 5122.00
diff --git a/sample_data/test_edgeR_diff_expr/example_DESeq2_analysis_pipeline/Makefile b/sample_data/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/Makefile
similarity index 100%
rename from sample_data/test_edgeR_diff_expr/example_DESeq2_analysis_pipeline/Makefile
rename to sample_data/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/Makefile
diff --git a/sample_data/test_edgeR_diff_expr/example_DESeq2_analysis_pipeline/cleanme.pl b/sample_data/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/cleanme.pl
similarity index 100%
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diff --git a/sample_data/test_edgeR_diff_expr/example_DESeq2_analysis_pipeline/counts.matrix b/sample_data/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/counts.matrix
similarity index 100%
rename from sample_data/test_edgeR_diff_expr/example_DESeq2_analysis_pipeline/counts.matrix
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diff --git a/sample_data/test_edgeR_diff_expr/example_DESeq2_analysis_pipeline/run_DESeq2.sh b/sample_data/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/run_DESeq2.sh
similarity index 100%
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diff --git a/sample_data/test_edgeR_diff_expr/example_DESeq2_analysis_pipeline/samples.txt b/sample_data/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/samples.txt
similarity index 100%
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diff --git a/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/Makefile b/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/Makefile
similarity index 100%
rename from sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/Makefile
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diff --git a/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/Trinity.fa.seqLens b/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/Trinity.fa.seqLens
similarity index 100%
rename from sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/Trinity.fa.seqLens
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diff --git a/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/TMM_info.txt b/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/TMM_info.txt
similarity index 100%
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diff --git a/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_runTMM.R b/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_runTMM.R
similarity index 100%
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rename to sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_runTMM.R
diff --git a/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_run_edgeR.1820.R b/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_run_edgeR.1820.R
similarity index 100%
rename from sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_run_edgeR.1820.R
rename to sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_run_edgeR.1820.R
diff --git a/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_targets.1820.dat b/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_targets.1820.dat
similarity index 100%
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diff --git a/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/all_data_files.list b/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/all_data_files.list
similarity index 100%
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diff --git a/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/cysts.dat b/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/cysts.dat
similarity index 100%
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diff --git a/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/example.matrix.normalized.FPKM b/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/example.matrix.normalized.FPKM
similarity index 100%
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rename to sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/example.matrix.normalized.FPKM
diff --git a/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/myc.dat b/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/myc.dat
similarity index 100%
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diff --git a/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/myc_vs_cysts.eps b/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/myc_vs_cysts.eps
similarity index 100%
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diff --git a/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/myc_vs_cysts.results.txt b/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/myc_vs_cysts.results.txt
similarity index 100%
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diff --git a/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/cleanMe.sh b/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/cleanMe.sh
similarity index 100%
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diff --git a/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/example.matrix b/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/example.matrix
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diff --git a/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/runMe.sh b/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/runMe.sh
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diff --git a/sample_data/test_edgeR_diff_expr/testEdgeRfuncs/Makefile b/sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/Makefile
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diff --git a/sample_data/test_edgeR_diff_expr/testEdgeRfuncs/dataA.dat b/sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/dataA.dat
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diff --git a/sample_data/test_edgeR_diff_expr/testEdgeRfuncs/dataB.dat b/sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/dataB.dat
similarity index 100%
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diff --git a/sample_data/test_edgeR_diff_expr/testEdgeRfuncs/runMe.sh b/sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/runMe.sh
similarity index 100%
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diff --git a/sample_data/test_edgeR_diff_expr/testEdgeRfuncs/run_edgeR_on_sample_data.R b/sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/run_edgeR_on_sample_data.R
similarity index 100%
rename from sample_data/test_edgeR_diff_expr/testEdgeRfuncs/run_edgeR_on_sample_data.R
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diff --git a/sample_data/test_edgeR_diff_expr/testEdgeRfuncs/targets.dat b/sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/targets.dat
similarity index 100%
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diff --git a/sample_data/test_DE_analysis/notes b/sample_data/test_DE_analysis/notes
new file mode 100644
index 0000000..3f4eb46
--- /dev/null
+++ b/sample_data/test_DE_analysis/notes
@@ -0,0 +1 @@
+from Candida data set, used in Aussie workshop 2015
diff --git a/sample_data/test_DE_analysis/samples.txt b/sample_data/test_DE_analysis/samples.txt
new file mode 100644
index 0000000..b6648cd
--- /dev/null
+++ b/sample_data/test_DE_analysis/samples.txt
@@ -0,0 +1,14 @@
+wt_37 wt_37_1 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_1-SRX707647-SRR1582649_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_1-SRX707647-SRR1582649_2.fastq
+wt_37 wt_37_2 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_2-SRX707648-SRR1582650_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_2-SRX707648-SRR1582650_2.fastq
+wt_37 wt_37_3 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_3-SRX707649-SRR1582651_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_3-SRX707649-SRR1582651_2.fastq
+wt_GSNO wt_GSNO_1 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_1-SRX707644-SRR1582646_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_1-SRX707644-SRR1582646_2.fastq
+wt_GSNO wt_GSNO_2 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_2-SRX707645-SRR1582647_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_2-SRX707645-SRR1582647_2.fastq
+wt_GSNO wt_GSNO_3 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_3-SRX707646-SRR1582648_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_3-SRX707646-SRR1582648_2.fastq
+wt_ph8 wt_ph8_1 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_1-SRX707641-SRR1582643_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_1-SRX707641-SRR1582643_2.fastq
+wt_ph8 wt_ph8_2 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_2-SRX707642-SRR1582644_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_2-SRX707642-SRR1582644_2.fastq
+wt_ph8 wt_ph8_3 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_3-SRX707643-SRR1582645_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_3-SRX707643-SRR1582645_2.fastq
+
+--CPU=6
+--max_memory=20G
+--seqType=fq
+--grid_conf=/seq/regev_genome_portal/SOFTWARE/trinityrnaseq/hpc_conf/BroadInst_LSF.hour.10.conf
diff --git a/sample_data/test_GenomeGuidedTrinity/__run_genome-guided_Trinity_use_existing_bam.use_LSF.sh b/sample_data/test_GenomeGuidedTrinity/old/__run_genome-guided_Trinity_use_existing_bam.use_LSF.sh
similarity index 100%
rename from sample_data/test_GenomeGuidedTrinity/__run_genome-guided_Trinity_use_existing_bam.use_LSF.sh
rename to sample_data/test_GenomeGuidedTrinity/old/__run_genome-guided_Trinity_use_existing_bam.use_LSF.sh
diff --git a/sample_data/test_GenomeGuidedTrinity/__run_genome-guided_Trinity_use_existing_bam.use_PBS.sh b/sample_data/test_GenomeGuidedTrinity/old/__run_genome-guided_Trinity_use_existing_bam.use_PBS.sh
similarity index 100%
rename from sample_data/test_GenomeGuidedTrinity/__run_genome-guided_Trinity_use_existing_bam.use_PBS.sh
rename to sample_data/test_GenomeGuidedTrinity/old/__run_genome-guided_Trinity_use_existing_bam.use_PBS.sh
diff --git a/sample_data/test_GenomeGuidedTrinity/__run_genome-guided_Trinity_use_existing_bam.use_SGE.sh b/sample_data/test_GenomeGuidedTrinity/old/__run_genome-guided_Trinity_use_existing_bam.use_SGE.sh
similarity index 100%
rename from sample_data/test_GenomeGuidedTrinity/__run_genome-guided_Trinity_use_existing_bam.use_SGE.sh
rename to sample_data/test_GenomeGuidedTrinity/old/__run_genome-guided_Trinity_use_existing_bam.use_SGE.sh
diff --git a/sample_data/test_GenomeGuidedTrinity/run_Schizo_TrinityGG.SE.sh b/sample_data/test_GenomeGuidedTrinity/old/run_Schizo_TrinityGG.SE.sh
similarity index 100%
rename from sample_data/test_GenomeGuidedTrinity/run_Schizo_TrinityGG.SE.sh
rename to sample_data/test_GenomeGuidedTrinity/old/run_Schizo_TrinityGG.SE.sh
diff --git a/sample_data/test_GenomeGuidedTrinity/run_Schizo_TrinityGG.sh b/sample_data/test_GenomeGuidedTrinity/old/run_Schizo_TrinityGG.sh
similarity index 100%
rename from sample_data/test_GenomeGuidedTrinity/run_Schizo_TrinityGG.sh
rename to sample_data/test_GenomeGuidedTrinity/old/run_Schizo_TrinityGG.sh
diff --git a/sample_data/test_GenomeGuidedTrinity/run_genome-guided_Trinity.sh b/sample_data/test_GenomeGuidedTrinity/old/run_genome-guided_Trinity.sh
similarity index 100%
rename from sample_data/test_GenomeGuidedTrinity/run_genome-guided_Trinity.sh
rename to sample_data/test_GenomeGuidedTrinity/old/run_genome-guided_Trinity.sh
diff --git a/sample_data/test_GenomeGuidedTrinity/run_mouse_TrinityGG.sh b/sample_data/test_GenomeGuidedTrinity/old/run_mouse_TrinityGG.sh
similarity index 100%
rename from sample_data/test_GenomeGuidedTrinity/run_mouse_TrinityGG.sh
rename to sample_data/test_GenomeGuidedTrinity/old/run_mouse_TrinityGG.sh
diff --git a/sample_data/test_Trinity_Assembly/Makefile b/sample_data/test_Trinity_Assembly/Makefile
index 5658a5e..ded6e8e 100644
--- a/sample_data/test_Trinity_Assembly/Makefile
+++ b/sample_data/test_Trinity_Assembly/Makefile
@@ -3,12 +3,33 @@ test_trinity:
./runMe.sh
-test:
+test: test_assembly test_abundance_estimation test_bowtie_PE_read_estimates
+
+
+test_assembly:
./runMe.sh
./misc_run_tests/__test_runMe_include_normalization.sh
./misc_run_tests/__runMe_with_qual_trimming.sh
./misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh
./misc_run_tests/__test_runMe_with_jaccard_clip.sh
+ ./misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh
+
+test_abundance_estimation: test_RSEM test_eXpress test_kallisto
+
+test_RSEM:
+ ../../util/align_and_estimate_abundance.pl --transcripts trinity_out_dir/Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --SS_lib_type RF --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference --output_dir RSEM_PE
+
+
+test_eXpress:
+ ../../util/align_and_estimate_abundance.pl --transcripts trinity_out_dir/Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --SS_lib_type RF --est_method eXpress --aln_method bowtie2 --trinity_mode --prep_reference --output_dir eXpress_PE
+
+test_kallisto:
+ ../../util/align_and_estimate_abundance.pl --transcripts trinity_out_dir/Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --est_method kallisto --trinity_mode --prep_reference --output_dir kallisto_PE
+
+test_bowtie_PE_read_estimates:
+ ../../util/bowtie_PE_separate_then_join.pl --seqType fq --left reads.left.fq --right reads.right.fq --target trinity_out_dir/Trinity.fasta --aligner bowtie
+ ../../util/SAM_nameSorted_to_uniq_count_stats.pl bowtie_out/bowtie_out.nameSorted.bam
+
test_full:
./runMe.sh 1
diff --git a/sample_data/test_Trinity_Assembly/README b/sample_data/test_Trinity_Assembly/README
index b467d4f..822062c 100644
--- a/sample_data/test_Trinity_Assembly/README
+++ b/sample_data/test_Trinity_Assembly/README
@@ -1,6 +1,8 @@
First, execute 'runMe.sh' to run the Trinity assembly example.
-Then, execute 'run_abundance_estimation_procedure.sh' to compute abundance estimations based on mapped read pairs.
+To test abundance estimation as well, execute 'runMe.sh 1'
+
+
diff --git a/sample_data/test_Trinity_Assembly/cleanme.pl b/sample_data/test_Trinity_Assembly/cleanme.pl
index 22d1b29..f6520ab 100755
--- a/sample_data/test_Trinity_Assembly/cleanme.pl
+++ b/sample_data/test_Trinity_Assembly/cleanme.pl
@@ -53,7 +53,13 @@ my %keep = map { + $_ => 1 } @files_to_keep;
`rm -rf ./trinity_w_jaccard` if (-d "trinity_w_jaccard");
`rm -rf ./__test_trinity*`;
+`rm -rf ./trinity_trim_and_norm_outdir`;
+`rm -rf ./RSEM_outdir`;
+`rm -rf ./eXpress_outdir`;
+`rm -rf ./eXpress_PE`;
+`rm -rf ./kallisto_PE`;
+`rm -rf ./RSEM_PE`;
foreach my $file (<*>) {
diff --git a/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_include_long_reads.sh b/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_include_long_reads.sh
index 9df68fd..9dda7b5 100755
--- a/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_include_long_reads.sh
+++ b/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_include_long_reads.sh
@@ -5,7 +5,7 @@
#######################################################
## use jellyfish
-../../Trinity.pl --seqType fq --JM 2G --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU 4 --no_cleanup --long_reads longReads.fa
+../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU 4 --no_cleanup --long_reads longReads.fa
##### Done Running Trinity #####
diff --git a/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh b/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh
index d9a9d6e..9ae8e06 100755
--- a/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh
+++ b/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh
@@ -23,7 +23,7 @@ fi
#######################################################
## use jellyfish
-../../Trinity.pl --seqType fq --JM 2G --left reads.left.fq,reads2.left.fq --right reads.right.fq,reads2.right.fq --SS_lib_type RF --CPU 4 --trimmomatic --normalize_reads --normalize_by_read_set
+../../Trinity --seqType fq --max_memory 2G --left reads.left.fq,reads2.left.fq --right reads.right.fq,reads2.right.fq --SS_lib_type RF --CPU 4 --trimmomatic --normalize_reads --normalize_by_read_set --output trinity_trim_and_norm_outdir
##### Done Running Trinity #####
@@ -32,18 +32,5 @@ if [ ! $* ]; then
fi
-sleep 2
-
-
-###########################################
-# use RSEM to estimate read abundance ####
-###########################################
-
-sleep 2
-
-../../util/RSEM_util/run_RSEM_align_n_estimate.pl --transcripts trinity_out_dir/Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --SS_lib_type RF
-
-###### Done running RSEM ########
-
diff --git a/sample_data/test_Trinity_Assembly/runMe.sh b/sample_data/test_Trinity_Assembly/runMe.sh
index 7d939b8..fb16b44 100755
--- a/sample_data/test_Trinity_Assembly/runMe.sh
+++ b/sample_data/test_Trinity_Assembly/runMe.sh
@@ -23,7 +23,7 @@ fi
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
-../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU 4
+../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU 4 --no_cleanup
##### Done Running Trinity #####
@@ -32,8 +32,6 @@ if [ ! $* ]; then
fi
-sleep 2
-
###########################################
# use RSEM to estimate read abundance ####
@@ -42,13 +40,19 @@ sleep 2
sleep 2
# first try RSEM
-../../util/align_and_estimate_abundance.pl --transcripts trinity_out_dir/Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --SS_lib_type RF --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference
+../../util/align_and_estimate_abundance.pl --transcripts trinity_out_dir/Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --SS_lib_type RF --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference --output_dir RSEM_outdir
# try eXpress
-../../util/align_and_estimate_abundance.pl --transcripts trinity_out_dir/Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --SS_lib_type RF --est_method eXpress --aln_method bowtie2 --trinity_mode --prep_reference
+../../util/align_and_estimate_abundance.pl --transcripts trinity_out_dir/Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --SS_lib_type RF --est_method eXpress --aln_method bowtie2 --trinity_mode --prep_reference --output_dir eXpress_outdir
+
+
+#######################################
+## run bowtie PE to get alignment stats
+#######################################
+../../util/bowtie_PE_separate_then_join.pl --seqType fq --left reads.left.fq --right reads.right.fq --target trinity_out_dir/Trinity.fasta --aligner bowtie
-###### Done running RSEM ########
+../../util/SAM_nameSorted_to_uniq_count_stats.pl bowtie_out/bowtie_out.nameSorted.bam
diff --git a/sample_data/test_Trinity_Coding_Extraction/Makefile b/sample_data/test_Trinity_Coding_Extraction/Makefile
deleted file mode 100644
index 4ab2c6d..0000000
--- a/sample_data/test_Trinity_Coding_Extraction/Makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-test:
- ./runMe.sh
-
-clean:
- ./cleanme.pl
-
diff --git a/sample_data/test_Trinity_Coding_Extraction/Trinity.fasta.gz b/sample_data/test_Trinity_Coding_Extraction/Trinity.fasta.gz
deleted file mode 100644
index 34b64c0..0000000
Binary files a/sample_data/test_Trinity_Coding_Extraction/Trinity.fasta.gz and /dev/null differ
diff --git a/sample_data/test_Trinity_Coding_Extraction/cleanme.pl b/sample_data/test_Trinity_Coding_Extraction/cleanme.pl
deleted file mode 100755
index 3359dab..0000000
--- a/sample_data/test_Trinity_Coding_Extraction/cleanme.pl
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/usr/bin/env perl
-
-use strict;
-use warnings;
-
-use FindBin;
-
-
-## we delete all files we don't need in this directory. Be careful in case users try running it somewhere else, outside this dir.
-chdir $FindBin::Bin or die "error, cannot cd to $FindBin::Bin";
-
-
-
-my @files_to_keep = qw (cleanme.pl
- runMe.sh
- Trinity.fasta.gz
- __test_using_both_strands.sh
- __runMe_incl_PfamSearch.sh
-
- Makefile
-);
-
-
-my %keep = map { + $_ => 1 } @files_to_keep;
-
-
-
-foreach my $file (<*>) {
-
- if (! $keep{$file}) {
- print STDERR "-removing file: $file\n";
- unlink($file);
- }
-}
-
-
-`rm -rf ./transdecoder.tmp.*`;
-
-exit(0);
diff --git a/sample_data/test_Trinity_Coding_Extraction/runMe.sh b/sample_data/test_Trinity_Coding_Extraction/runMe.sh
deleted file mode 100755
index fad9e65..0000000
--- a/sample_data/test_Trinity_Coding_Extraction/runMe.sh
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/bin/sh
-
-if [ -e Trinity.fasta.gz ] && [ ! -e Trinity.fasta ]
-then
- gunzip -c Trinity.fasta.gz > Trinity.fasta
-fi
-
-
-../../trinity-plugins/transdecoder/TransDecoder -t Trinity.fasta -m 50
-
-echo
-echo
-echo See best_candidates.\* for candidate ORFs
-echo
-
-
-
diff --git a/sample_data/test_align_and_estimate_abundance/Makefile b/sample_data/test_align_and_estimate_abundance/Makefile
index b1270bf..2c0d233 100644
--- a/sample_data/test_align_and_estimate_abundance/Makefile
+++ b/sample_data/test_align_and_estimate_abundance/Makefile
@@ -1,6 +1,15 @@
-test:
- ./run_rsem.sh
- ./run_eXpress.sh
+test: test_RSEM test_eXpress test_kallisto
+ ../../Analysis/DifferentialExpression/merge_matrices.pl RSEM-trans.TPM.not_cross_norm eXpress-trans.TPM.not_cross_norm kallisto-trans.TPM.not_cross_norm > combined.TPM.not_cross_norm.matrix
+ ./plot_paired_comparisons.Rscript
+
+test_RSEM:
+ ./align_and_estimate_tester.pl RSEM
+
+test_eXpress:
+ ./align_and_estimate_tester.pl eXpress
+
+test_kallisto:
+ ./align_and_estimate_tester.pl kallisto
clean:
diff --git a/sample_data/test_align_and_estimate_abundance/Trinity.fasta.gene_trans_map b/sample_data/test_align_and_estimate_abundance/Trinity.fasta.gene_trans_map
deleted file mode 100644
index c8bc603..0000000
--- a/sample_data/test_align_and_estimate_abundance/Trinity.fasta.gene_trans_map
+++ /dev/null
@@ -1,124 +0,0 @@
-comp7_c0 comp7_c0_seq1
-comp15_c0 comp15_c0_seq1
-comp20_c0 comp20_c0_seq1
-comp22_c0 comp22_c0_seq1
-comp22_c1 comp22_c1_seq1
-comp23_c0 comp23_c0_seq1
-comp25_c0 comp25_c0_seq1
-comp28_c0 comp28_c0_seq1
-comp29_c0 comp29_c0_seq1
-comp30_c0 comp30_c0_seq1
-comp30_c1 comp30_c1_seq1
-comp31_c0 comp31_c0_seq1
-comp31_c1 comp31_c1_seq1
-comp33_c0 comp33_c0_seq1
-comp34_c0 comp34_c0_seq1
-comp35_c0 comp35_c0_seq1
-comp36_c0 comp36_c0_seq1
-comp36_c1 comp36_c1_seq1
-comp36_c1 comp36_c1_seq2
-comp37_c0 comp37_c0_seq1
-comp37_c0 comp37_c0_seq2
-comp37_c0 comp37_c0_seq3
-comp37_c0 comp37_c0_seq4
-comp37_c0 comp37_c0_seq5
-comp37_c0 comp37_c0_seq6
-comp37_c0 comp37_c0_seq7
-comp37_c1 comp37_c1_seq1
-comp37_c2 comp37_c2_seq1
-comp38_c0 comp38_c0_seq1
-comp38_c0 comp38_c0_seq2
-comp38_c0 comp38_c0_seq3
-comp38_c0 comp38_c0_seq4
-comp38_c0 comp38_c0_seq5
-comp38_c0 comp38_c0_seq6
-comp38_c0 comp38_c0_seq7
-comp38_c0 comp38_c0_seq8
-comp38_c0 comp38_c0_seq9
-comp38_c0 comp38_c0_seq10
-comp38_c0 comp38_c0_seq11
-comp38_c0 comp38_c0_seq12
-comp38_c0 comp38_c0_seq13
-comp38_c0 comp38_c0_seq14
-comp38_c1 comp38_c1_seq1
-comp39_c0 comp39_c0_seq1
-comp39_c0 comp39_c0_seq2
-comp39_c0 comp39_c0_seq3
-comp40_c0 comp40_c0_seq1
-comp40_c1 comp40_c1_seq1
-comp40_c1 comp40_c1_seq2
-comp41_c0 comp41_c0_seq1
-comp41_c1 comp41_c1_seq1
-comp41_c1 comp41_c1_seq2
-comp41_c1 comp41_c1_seq3
-comp41_c1 comp41_c1_seq4
-comp41_c1 comp41_c1_seq5
-comp41_c1 comp41_c1_seq6
-comp41_c1 comp41_c1_seq7
-comp41_c1 comp41_c1_seq8
-comp41_c1 comp41_c1_seq9
-comp41_c1 comp41_c1_seq10
-comp41_c1 comp41_c1_seq11
-comp41_c1 comp41_c1_seq12
-comp41_c1 comp41_c1_seq13
-comp41_c1 comp41_c1_seq14
-comp41_c1 comp41_c1_seq15
-comp41_c1 comp41_c1_seq16
-comp41_c1 comp41_c1_seq17
-comp41_c1 comp41_c1_seq18
-comp41_c1 comp41_c1_seq19
-comp41_c1 comp41_c1_seq20
-comp41_c1 comp41_c1_seq21
-comp41_c1 comp41_c1_seq22
-comp41_c1 comp41_c1_seq23
-comp41_c1 comp41_c1_seq24
-comp41_c1 comp41_c1_seq25
-comp41_c2 comp41_c2_seq1
-comp42_c0 comp42_c0_seq1
-comp42_c1 comp42_c1_seq1
-comp42_c2 comp42_c2_seq1
-comp42_c3 comp42_c3_seq1
-comp42_c3 comp42_c3_seq2
-comp42_c3 comp42_c3_seq3
-comp42_c3 comp42_c3_seq4
-comp42_c3 comp42_c3_seq5
-comp42_c3 comp42_c3_seq6
-comp42_c3 comp42_c3_seq7
-comp42_c3 comp42_c3_seq8
-comp42_c4 comp42_c4_seq1
-comp42_c5 comp42_c5_seq1
-comp42_c6 comp42_c6_seq1
-comp43_c0 comp43_c0_seq1
-comp43_c0 comp43_c0_seq2
-comp43_c0 comp43_c0_seq3
-comp44_c0 comp44_c0_seq1
-comp44_c0 comp44_c0_seq2
-comp44_c1 comp44_c1_seq1
-comp45_c0 comp45_c0_seq1
-comp45_c0 comp45_c0_seq2
-comp45_c0 comp45_c0_seq3
-comp45_c0 comp45_c0_seq4
-comp45_c0 comp45_c0_seq5
-comp45_c0 comp45_c0_seq6
-comp46_c0 comp46_c0_seq1
-comp46_c1 comp46_c1_seq1
-comp46_c2 comp46_c2_seq1
-comp46_c2 comp46_c2_seq2
-comp46_c2 comp46_c2_seq3
-comp46_c2 comp46_c2_seq4
-comp46_c2 comp46_c2_seq5
-comp46_c2 comp46_c2_seq6
-comp46_c2 comp46_c2_seq7
-comp46_c2 comp46_c2_seq8
-comp46_c2 comp46_c2_seq9
-comp46_c2 comp46_c2_seq10
-comp46_c2 comp46_c2_seq11
-comp46_c2 comp46_c2_seq12
-comp46_c2 comp46_c2_seq13
-comp46_c2 comp46_c2_seq14
-comp46_c2 comp46_c2_seq15
-comp46_c2 comp46_c2_seq16
-comp46_c2 comp46_c2_seq17
-comp46_c2 comp46_c2_seq18
-comp46_c2 comp46_c2_seq19
-comp47_c0 comp47_c0_seq1
diff --git a/sample_data/test_align_and_estimate_abundance/Trinity.fasta.gz b/sample_data/test_align_and_estimate_abundance/Trinity.fasta.gz
deleted file mode 100644
index ab16f19..0000000
Binary files a/sample_data/test_align_and_estimate_abundance/Trinity.fasta.gz and /dev/null differ
diff --git a/sample_data/test_align_and_estimate_abundance/align_and_estimate_tester.pl b/sample_data/test_align_and_estimate_abundance/align_and_estimate_tester.pl
new file mode 100755
index 0000000..c59bf9a
--- /dev/null
+++ b/sample_data/test_align_and_estimate_abundance/align_and_estimate_tester.pl
@@ -0,0 +1,93 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+use File::Basename;
+use lib ("$FindBin::Bin/../../PerlLib");
+use Process_cmd;
+
+
+my $usage = "usage: $0 (RSEM|eXpress|kallisto)\n\n";
+
+my $method = $ARGV[0] or die $usage;
+unless ($method =~ /^(RSEM|eXpress|kallisto)$/) {
+ die $usage;
+}
+
+my $utildir = "$FindBin::Bin/../../util";
+
+my $samples_file = "samples.txt";
+my $trinity_fasta = "../test_DATA/Trinity.fasta";
+
+main: {
+
+ &process_cmd("ln -sf $trinity_fasta .");
+
+ $trinity_fasta = basename($trinity_fasta);
+
+ my @samples;
+ {
+ open (my $fh, $samples_file) or die $!;
+ while (<$fh>) {
+ chomp;
+ my ($sample_name, $left_fq, $right_fq) = split(/\s+/);
+ $left_fq = &ensure_full_path($left_fq);
+ $right_fq = &ensure_full_path($right_fq);
+ push (@samples, [$sample_name, $left_fq, $right_fq]);
+ }
+ close $fh;
+ }
+
+ my @trans_results;
+ my @gene_results;
+
+ foreach my $sample (@samples) {
+ my ($sample_name, $left_fq, $right_fq) = @$sample;
+
+ my $cmd = "$utildir/align_and_estimate_abundance.pl --transcripts $trinity_fasta --prep_reference "
+ . " --left $left_fq --right $right_fq --seqType fq --trinity_mode ";
+
+ my $outdir = "$method-$sample_name";
+
+ if ($method eq 'RSEM') {
+ $cmd .= " --est_method RSEM --output_dir $outdir --aln_method bowtie ";
+
+ push (@trans_results, "$outdir/RSEM.isoforms.results");
+ push (@gene_results, "$outdir/RSEM.genes.results");
+
+ }
+ elsif ($method eq 'eXpress') {
+ $cmd .= " --est_method eXpress --output_dir $outdir --aln_method bowtie2 ";
+ push (@trans_results, "$outdir/results.xprs");
+ push (@gene_results, "$outdir/results.xprs.genes");
+ }
+ elsif ($method eq 'kallisto') {
+ $cmd .= " --est_method kallisto --output_dir kallisto-$sample_name ";
+ push (@trans_results, "$outdir/abundance.tsv");
+ push (@gene_results, "$outdir/abundance.tsv.genes");
+
+ }
+ else {
+ # shouldn't ever get here.
+ die "error - method $method not recognized";
+ }
+
+ &process_cmd($cmd);
+
+
+ }
+
+ ## generate matrices.
+ my $cmd = "$utildir/abundance_estimates_to_matrix.pl --est_method $method --out_prefix $method-trans --name_sample_by_basedir @trans_results";
+ &process_cmd($cmd);
+
+ $cmd = "$utildir/abundance_estimates_to_matrix.pl --est_method $method --out_prefix $method-gene --name_sample_by_basedir @gene_results";
+ &process_cmd($cmd);
+
+
+
+ exit(0);
+}
+
diff --git a/sample_data/test_align_and_estimate_abundance/cleanme.pl b/sample_data/test_align_and_estimate_abundance/cleanme.pl
index 51a1978..b768bdc 100755
--- a/sample_data/test_align_and_estimate_abundance/cleanme.pl
+++ b/sample_data/test_align_and_estimate_abundance/cleanme.pl
@@ -11,18 +11,12 @@ chdir $FindBin::Bin or die "error, cannot cd to $FindBin::Bin";
-my @files_to_keep = qw (cleanme.pl
-
- reads.right.fq.gz
- reads.left.fq.gz
-
- run_eXpress.sh
- run_rsem.sh
-
- Trinity.fasta.gene_trans_map
- Trinity.fasta.gz
-
- Makefile
+my @files_to_keep = qw (
+cleanme.pl
+Makefile
+align_and_estimate_tester.pl
+samples.txt
+plot_paired_comparisons.Rscript
);
@@ -32,17 +26,16 @@ my %keep = map { + $_ => 1 } @files_to_keep;
foreach my $file (<*>) {
- if (! $keep{$file}) {
+ if (-f $file && ! $keep{$file}) {
print STDERR "-removing file: $file\n";
unlink($file);
}
}
-`rm -rf ./transdecoder.tmp.*`;
-
-`rm -rf ./eXpress_estimate`;
-`rm -rf ./rsem_estimate`;
+`rm -rf ./RSEM-*`;
+`rm -rf ./eXpress-*`;
+`rm -rf ./kallisto-*`;
exit(0);
diff --git a/sample_data/test_align_and_estimate_abundance/plot_paired_comparisons.Rscript b/sample_data/test_align_and_estimate_abundance/plot_paired_comparisons.Rscript
new file mode 100755
index 0000000..6b7328a
--- /dev/null
+++ b/sample_data/test_align_and_estimate_abundance/plot_paired_comparisons.Rscript
@@ -0,0 +1,14 @@
+#!/usr/bin/env Rscript
+
+pdf("pairs.pdf")
+data = read.table("combined.TPM.not_cross_norm.matrix")
+data = log2(data+1)
+c = colnames(data)
+log_matrix = data[,grep("log", c)]
+pairs(log_matrix)
+plateau = data[, grep("plateau", c)]
+pairs(plateau)
+diauxic = data[, grep("diauxic", c)]
+pairs(diauxic)
+heatshock = data[, grep("heatshock", c)]
+pairs(heatshock)
diff --git a/sample_data/test_align_and_estimate_abundance/reads.left.fq.gz b/sample_data/test_align_and_estimate_abundance/reads.left.fq.gz
deleted file mode 120000
index 8b5eddd..0000000
--- a/sample_data/test_align_and_estimate_abundance/reads.left.fq.gz
+++ /dev/null
@@ -1 +0,0 @@
-../test_Trinity_Assembly/reads.left.fq.gz
\ No newline at end of file
diff --git a/sample_data/test_align_and_estimate_abundance/reads.right.fq.gz b/sample_data/test_align_and_estimate_abundance/reads.right.fq.gz
deleted file mode 120000
index 72c4d39..0000000
--- a/sample_data/test_align_and_estimate_abundance/reads.right.fq.gz
+++ /dev/null
@@ -1 +0,0 @@
-../test_Trinity_Assembly/reads.right.fq.gz
\ No newline at end of file
diff --git a/sample_data/test_align_and_estimate_abundance/run_eXpress.sh b/sample_data/test_align_and_estimate_abundance/run_eXpress.sh
deleted file mode 100755
index 46645c5..0000000
--- a/sample_data/test_align_and_estimate_abundance/run_eXpress.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../util/align_and_estimate_abundance.pl --transcripts Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --gene_trans_map Trinity.fasta.gene_trans_map --aln_method bowtie --est_method eXpress --output_dir eXpress_estimate --SS_lib_type RF
diff --git a/sample_data/test_align_and_estimate_abundance/run_rsem.sh b/sample_data/test_align_and_estimate_abundance/run_rsem.sh
deleted file mode 100755
index 65d7174..0000000
--- a/sample_data/test_align_and_estimate_abundance/run_rsem.sh
+++ /dev/null
@@ -1,14 +0,0 @@
-if [ ! -e Trinity.fasta ]; then
- gunzip -c Trinity.fasta.gz > Trinity.fasta
-fi
-
-if [ ! -e reads.left.fq ]; then
- gunzip -c reads.left.fq.gz > reads.left.fq
-fi
-
-if [ ! -e reads.right.fq ]; then
- gunzip -c reads.right.fq.gz > reads.right.fq
-fi
-
-
-../../util/align_and_estimate_abundance.pl --transcripts Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --gene_trans_map Trinity.fasta.gene_trans_map --aln_method bowtie --est_method RSEM --output_dir rsem_estimate --SS_lib_type RF --prep_reference
diff --git a/sample_data/test_align_and_estimate_abundance/samples.txt b/sample_data/test_align_and_estimate_abundance/samples.txt
new file mode 100644
index 0000000..4bce4f8
--- /dev/null
+++ b/sample_data/test_align_and_estimate_abundance/samples.txt
@@ -0,0 +1,4 @@
+heatshock ../test_DATA/Sp_hs.10k.left.fq.gz ../test_DATA/Sp_hs.10k.right.fq.gz
+plateau ../test_DATA/Sp_plat.10k.right.fq.gz ../test_DATA/Sp_plat.10k.left.fq.gz
+log_growth ../test_DATA/Sp_log.10k.left.fq.gz ../test_DATA/Sp_log.10k.right.fq.gz
+diauxic_shift ../test_DATA/Sp_ds.10k.right.fq.gz ../test_DATA/Sp_ds.10k.left.fq.gz
diff --git a/sample_data/test_edgeR_diff_expr/Makefile b/sample_data/test_edgeR_diff_expr/Makefile
deleted file mode 100644
index a78a220..0000000
--- a/sample_data/test_edgeR_diff_expr/Makefile
+++ /dev/null
@@ -1,17 +0,0 @@
-
-DIRS = example_edgeR_analysis_pipeline testEdgeRfuncs
-#example_DESeq2_analysis_pipeline
-
-
-test:
- @for i in $(DIRS); do \
- echo "Running example in $$i..."; \
- (cd $$i; $(MAKE) test); done
-
-
-clean:
- @for i in $(DIRS); do \
- echo "Running example in $$i..."; \
- (cd $$i; $(MAKE) clean); done
-
-
diff --git a/sample_data/test_full_edgeR_pipeline/cleanme.pl b/sample_data/test_full_edgeR_pipeline/cleanme.pl
index 5635876..78235ce 100755
--- a/sample_data/test_full_edgeR_pipeline/cleanme.pl
+++ b/sample_data/test_full_edgeR_pipeline/cleanme.pl
@@ -22,7 +22,6 @@ my @files_to_keep = qw (cleanme.pl
my %keep = map { + $_ => 1 } @files_to_keep;
`rm -rf edgeR_\*`;
-`find ./trinity_out_dir -type f -delete`;
`rm -rf ./trinity_out_dir`;
`rm -f rnaseq_reads/*fq`;
`rm -rf collectl/`;
diff --git a/sample_data/test_full_edgeR_pipeline/samples_n_reads_decribed.txt b/sample_data/test_full_edgeR_pipeline/samples_n_reads_decribed.txt
index 25d694e..0979301 100644
--- a/sample_data/test_full_edgeR_pipeline/samples_n_reads_decribed.txt
+++ b/sample_data/test_full_edgeR_pipeline/samples_n_reads_decribed.txt
@@ -1,12 +1,12 @@
#sample replicate left.reads right.reads
-heatshock hs_rep1 rnaseq_reads/Sp_hs.10k.left.fq.gz rnaseq_reads/Sp_hs.10k.right.fq.gz
+heatshock hs_rep1 ../test_DATA/Sp_hs.10k.left.fq.gz ../test_DATA/Sp_hs.10k.right.fq.gz
-plateau plat_rep1 rnaseq_reads/Sp_plat.10k.right.fq.gz rnaseq_reads/Sp_plat.10k.left.fq.gz
+plateau plat_rep1 ../test_DATA/Sp_plat.10k.right.fq.gz ../test_DATA/Sp_plat.10k.left.fq.gz
-log_growth log_rep1 rnaseq_reads/Sp_log.10k.left.fq.gz rnaseq_reads/Sp_log.10k.right.fq.gz
+log_growth log_rep1 ../test_DATA/Sp_log.10k.left.fq.gz ../test_DATA/Sp_log.10k.right.fq.gz
-diauxic_shift ds_rep1 rnaseq_reads/Sp_ds.10k.right.fq.gz rnaseq_reads/Sp_ds.10k.left.fq.gz
+diauxic_shift ds_rep1 ../test_DATA/Sp_ds.10k.right.fq.gz ../test_DATA/Sp_ds.10k.left.fq.gz
## Trinity.pl configuration settings:
diff --git a/trinity-plugins/BIN/README b/trinity-plugins/BIN/README
new file mode 100644
index 0000000..7f5b5d9
--- /dev/null
+++ b/trinity-plugins/BIN/README
@@ -0,0 +1,2 @@
+certain binaries, such as samtools, are installed here as part of the plugins-build.
+
diff --git a/trinity-plugins/Makefile b/trinity-plugins/Makefile
index 9988036..4218185 100644
--- a/trinity-plugins/Makefile
+++ b/trinity-plugins/Makefile
@@ -1,17 +1,6 @@
-
JELLYFISH_CODE="jellyfish-2.1.4"
-RSEM_CODE="rsem-1.2.19"
-TRANSDECODER_CODE="TransDecoder_r20140704"
-
-RSEM_LIBCURSES=-lcurses
-
-UNAME_S := $(shell uname -s)
-
-ifeq ($(UNAME_S),Linux)
- RSEM_LIBCURSES += -ltinfo
-endif
-
+HTSLIB_CODE="htslib.github.Aug182015.tar.gz"
#######################
### Required by Trinity
@@ -21,17 +10,30 @@ FASTOOL_CODE=fstrozzi-Fastool-7c3e034f05
PARAFLY_CODE=parafly-code
TRIMMOMATIC_CODE=Trimmomatic-0.32
-trinity_essentials: jellyfish fastool_target parafly_target trimmomatic_target
+trinity_essentials: jellyfish scaffold_iworm_contigs_target fastool_target parafly_target trimmomatic_target samtools
trimmomatic_target:
ln -sf ${TRIMMOMATIC_CODE} Trimmomatic
+samtools:
+ tar xvf samtools-0.1.19.tar.bz2
+ cd samtools-0.1.19 && $(MAKE) LIBPATH=-ltinfo
+ mv samtools-0.1.19/samtools ./BIN/.
+
jellyfish:
tar -zxvf ${JELLYFISH_CODE}.tar.gz && ln -sf ${JELLYFISH_CODE} tmp.jellyfish
cd ./tmp.jellyfish/ && ./configure CC=gcc CXX=g++ --enable-static --disable-shared --prefix=`pwd` && $(MAKE) LDFLAGS="-lpthread -all-static" AM_CPPFLAGS="-Wall -Wnon-virtual-dtor -I"`pwd`"/include"
mv tmp.jellyfish jellyfish
+htslib_target:
+# tar xjvf htslib-1.2.1.tar.bz2
+# cd htslib-1.2.1 && ./configure && $(MAKE)
+ tar xvf ${HTSLIB_CODE} && cd htslib && $(MAKE)
+
+scaffold_iworm_contigs_target: htslib_target
+ cd scaffold_iworm_contigs && $(MAKE)
+
fastool_target:
cd ${FASTOOL_CODE} && $(MAKE)
ln -sf ${FASTOOL_CODE} fastool
@@ -46,20 +48,10 @@ parafly_target:
### Needed for downstream analyses
##################################
-plugins: transdecoder_target slclust_target collectl_target rsem
+plugins: slclust_target collectl_target
@echo "\n\n** Done building plugins **\n\n"
-rsem:
- tar -zxvf ${RSEM_CODE}.tar.gz
- cd ${RSEM_CODE} && $(MAKE) LIBCURSES="${RSEM_LIBCURSES}"
- ln -sf ${RSEM_CODE} rsem
-
-transdecoder_target:
- tar -zxvf ${TRANSDECODER_CODE}.tar.gz
- cd ${TRANSDECODER_CODE} && ${MAKE} simple
- ln -sf ${TRANSDECODER_CODE} transdecoder
-
slclust_target:
cd slclust && $(MAKE) install
@@ -67,11 +59,12 @@ collectl_target:
cd collectl && ./build_collectl.sh
clean:
- rm -rf ./${JELLYFISH_CODE} ./jellyfish # has tar.gz
- rm -rf ./${RSEM_CODE} ./rsem # has tar.gz
- rm -rf ./${TRANSDECODER_CODE} ./transdecoder # has tar.gz
+ rm -rf ${JELLYFISH_CODE} ./jellyfish # has tar.gz
cd ${FASTOOL_CODE} && $(MAKE) clean
+ rm -rf ./samtools-0.1.19
rm -f ./fastool # rm symlink
+ rm -rf ./htslib
+ cd scaffold_iworm_contigs && $(MAKE) clean
cd parafly && $(MAKE) clean
rm -f ./parafly # rm symlink
rm -f ./Trimmomatic # rm symlink
diff --git a/trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool.c b/trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool.c
index e61830c..1209c16 100644
--- a/trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool.c
+++ b/trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool.c
@@ -22,7 +22,12 @@ KSEQ_INIT(int, read)
int print_seq(int ilmn_trinity, char *append, int to_fasta, char *s[]) {
if (ilmn_trinity && (s[0][strlen(s[0])-2] != '/') && s[3] != NULL) {
- printf(">%s/%c\n", s[0], s[3][0]);
+ char read_dir = s[3][0];
+ if (! (read_dir == '1' || read_dir == '2')) {
+ fprintf(stderr, "Error, cannot convert fastq file to fasta since cannot recognize read orientation as /1 or /2 (instead: %c)", read_dir);
+ exit(3);
+ }
+ printf(">%s/%c\n", s[0], s[3][0]);
}
else if (append == NULL) {
printf(">%s\n", s[0]);
diff --git a/trinity-plugins/scaffold_iworm_contigs/Makefile b/trinity-plugins/scaffold_iworm_contigs/Makefile
new file mode 100644
index 0000000..4babd7c
--- /dev/null
+++ b/trinity-plugins/scaffold_iworm_contigs/Makefile
@@ -0,0 +1,10 @@
+CXX = g++
+prefix = ../htslib
+
+ScaffoldIwormContigs:
+ $(CXX) -I$(prefix) -L$(prefix) ScaffoldIwormContigs.cpp error_checker.cpp -lhts -lz -o scaffold_iworm_contigs
+
+clean:
+ rm scaffold_iworm_contigs
+
+
diff --git a/trinity-plugins/scaffold_iworm_contigs/ScaffoldIwormContigs.cpp b/trinity-plugins/scaffold_iworm_contigs/ScaffoldIwormContigs.cpp
new file mode 100755
index 0000000..eb599f6
--- /dev/null
+++ b/trinity-plugins/scaffold_iworm_contigs/ScaffoldIwormContigs.cpp
@@ -0,0 +1,216 @@
+#include <string>
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <map>
+#include <set>
+#include <algorithm>
+#include <vector>
+#include <stdexcept>
+#include "error_checker.h"
+
+#ifndef WIN32
+#define HTS
+#endif
+
+#ifdef HTS
+#include "htslib/sam.h"
+#endif
+
+#ifdef _DEBUG
+ofstream SAM_OFH("scaffolding_entries.sam");
+#endif
+
+using namespace std;
+
+
+void examine_frags(const set<string>& iworm_left, const set<string>& iworm_right, map<pair<string, string>, int>& paired_iworm_contigs)
+{
+ if (iworm_left.size() == 0 || iworm_right.size() == 0)
+ return; // no pairs
+
+ if (iworm_left.size() == 1 && iworm_right.size() == 1)
+ {
+ string k1 = *iworm_left.begin();
+ string k2 = *iworm_right.begin();
+ if (k1 != k2)
+ {
+ if (k2 < k1) swap(k1, k2);
+
+ pair<string, string> key(k1, k2);
+ if (paired_iworm_contigs.find(key) == paired_iworm_contigs.end())
+ paired_iworm_contigs[key] = 1;
+ else
+ paired_iworm_contigs[key]++;
+
+#ifdef _DEBUG
+ SAM_OFH << k1 << k2 << endl;
+#endif
+
+ }
+ }
+}
+
+struct map_key
+{
+ template <typename T>
+ typename T::first_type operator()(T keyValuePair) const
+ {
+ return keyValuePair.first;
+ }
+};
+
+template <typename T>
+struct sort_pred {
+ map<T, int> &_hash;
+ sort_pred(map<T, int>& h) : _hash(h) {}
+ bool operator()(const T &left, const T &right) {
+ return _hash[left] > _hash[right];
+ }
+};
+
+template <typename T>
+void copy_to_out(map<T, int>& paired_iworm_contigs, map<string, int>& iworm_acc_to_fasta_index)
+{
+ vector<T> outvec;
+ const char *my_endl = "\n";
+
+ outvec.reserve(paired_iworm_contigs.size());
+ transform(paired_iworm_contigs.begin(), paired_iworm_contigs.end(), back_inserter(outvec), map_key());
+ sort(outvec.begin(), outvec.end(), sort_pred<T >(paired_iworm_contigs));
+ for (typename vector<T>::const_iterator a = outvec.begin(); a != outvec.end(); ++a)
+ {
+ const int index_A = iworm_acc_to_fasta_index[a->first];
+ const int index_B = iworm_acc_to_fasta_index[a->second];
+
+ cout << a->first << '\t' << index_A << '\t';
+ cout << a->second << '\t' << index_B << '\t';
+ cout << paired_iworm_contigs[*a] << my_endl;
+ }
+}
+
+void index_iworm(string iworm_fasta, map<string, int>& aMap)
+{
+ int counter = 0;
+
+ ifstream fh(iworm_fasta.c_str());
+ while (fh)
+ {
+ string line;
+ fh >> line;
+ if (line[0] == '>')
+ aMap[line.substr(1, string::npos)] = counter++;
+ }
+}
+
+void validate_iworm(string iworm_acc)
+{
+ pair<int, int> a;
+
+ if (iworm_acc[0] == 'a') iworm_acc[0] = ' ';
+ replace(iworm_acc.begin(), iworm_acc.end(), ';', ' ');
+ istringstream iss2(iworm_acc);
+ iss2 >> a.first >> a.second;
+ if (iss2.fail())
+ throw bad_name_exception();
+}
+
+pair<string, int> parse_read_name(string read_acc)
+{
+ pair<string, int> result;
+ size_t s = read_acc.rfind('/');
+ result.first = read_acc.substr(0, s);
+ result.second = read_acc[s + 1] - '1';
+
+ if (s == string::npos || (result.second != 0 && result.second != 1))
+ throw single_read_exception();
+
+ return result;
+}
+
+void process_line(string read_acc, string iworm_acc, set<string>& iworm_left,
+ set<string>& iworm_right, string& prev_core_acc,
+ map<pair<string, string>, int>& paired_iworm_contigs,
+ error_checker& checker)
+{
+ try
+ {
+ validate_iworm(iworm_acc);
+
+ pair<string, int> read = parse_read_name(read_acc);
+ const string core_acc = read.first;
+ int frag_end = read.second;
+
+ if (core_acc != prev_core_acc)
+ {
+ examine_frags(iworm_left, iworm_right, paired_iworm_contigs);
+ iworm_left.clear();
+ iworm_right.clear();
+ }
+
+ if (frag_end == 0)
+ iworm_left.insert(iworm_acc);
+ if (frag_end == 1)
+ iworm_right.insert(iworm_acc);
+
+ prev_core_acc = core_acc;
+ }
+ catch (const bad_name_exception&)
+ {
+ checker.add_bad_name(iworm_acc, read_acc);
+ }
+ catch (const single_read_exception&)
+ {
+ checker.add_single_read(read_acc);
+ }
+}
+
+int main(int argc, char* argv[])
+{
+ string usage = "\n\nusage: ScaffoldIwormContigs nameSorted.sam iworm_fasta_file\n\n";
+ if (argc != 3)
+ {
+ cerr << usage;
+ return -1;
+ }
+
+ string name_sorted_sam_file(argv[1]);
+ map<string, int> iworm_acc_to_fasta_index;
+ index_iworm(argv[2], iworm_acc_to_fasta_index);
+
+ string prev_core_acc;
+ map<pair<string,string>, int> paired_iworm_contigs;
+ set<string> iworm_left;
+ set<string> iworm_right;
+ error_checker errors;
+
+ samFile *in = sam_open(name_sorted_sam_file.c_str(), "r");
+ bam_hdr_t *h = sam_hdr_read(in);
+ bam1_t *b = bam_init1();
+
+ while (sam_read1(in, h, b) > 0)
+ {
+ string read_acc(bam_get_qname(b));
+ if (b->core.tid >= 0)
+ {
+ string iworm_acc(h->target_name[b->core.tid]);
+ process_line(read_acc, iworm_acc, iworm_left, iworm_right, prev_core_acc, paired_iworm_contigs, errors);
+ }
+ }
+
+ int r = sam_close(in);
+ if (r < 0) {
+ throw runtime_error("Error closing input");
+ }
+
+ // get last one
+ examine_frags(iworm_left, iworm_right, paired_iworm_contigs);
+
+ errors.report();
+
+ copy_to_out(paired_iworm_contigs, iworm_acc_to_fasta_index);
+
+ return 0;
+}
+
+
diff --git a/trinity-plugins/scaffold_iworm_contigs/error_checker.cpp b/trinity-plugins/scaffold_iworm_contigs/error_checker.cpp
new file mode 100755
index 0000000..6cdecd7
--- /dev/null
+++ b/trinity-plugins/scaffold_iworm_contigs/error_checker.cpp
@@ -0,0 +1,40 @@
+#include <string>
+#include <iostream>
+#include "error_checker.h"
+
+using namespace std;
+
+void error_checker::add_bad_name(string contig, string entry)
+{
+ num_unrecognized_iworm_contig_names++;
+ if (num_unrecognized_iworm_contig_names <= 10) {
+ cerr << "warning, inchworm contig (" << contig << ") isn't recognized. Ignoring entry: [[" << entry << "]]";
+ }
+ if (num_unrecognized_iworm_contig_names == 11) {
+ cerr << "warning, too many unrecognized inchworm contig names. Will report summary of counts later.";
+ }
+}
+
+void error_checker::add_single_read(string read)
+{
+ // must have mixed in a single read with the pairs...
+ if (num_warnings <= 10) {
+ cerr << "warning, ignoring read: " << read << "since cannot decipher if /1 or /2 of a pair.";
+ }
+ else if (num_warnings == 11) {
+ cerr << "number of read warnings exceeded 10. Turning off warning messages from here out.\n";
+ }
+
+ num_warnings++;
+}
+
+void error_checker::report() const
+{
+ if (num_warnings) {
+ cerr << "WARNING: note there were " << num_warnings << " reads that could not be deciphered as being /1 or /2 of a PE fragment. Hopefully, these were SE reads that should have been ignored. Otherwise, please research this further.\n\n";
+ }
+ if (num_unrecognized_iworm_contig_names) {
+ cerr << "WARNING: note, there were " << num_unrecognized_iworm_contig_names << " inchworm contig names in the SAM file that were ignored due to the inchworm contig accession not being recognized.\n";
+ }
+}
+
diff --git a/trinity-plugins/scaffold_iworm_contigs/error_checker.h b/trinity-plugins/scaffold_iworm_contigs/error_checker.h
new file mode 100755
index 0000000..01e838e
--- /dev/null
+++ b/trinity-plugins/scaffold_iworm_contigs/error_checker.h
@@ -0,0 +1,24 @@
+#ifndef ERROR_CHECKER_H_B91F75504340473B989F054E04E58BE7
+#define ERROR_CHECKER_H_B91F75504340473B989F054E04E58BE7
+
+#include <string>
+
+class bad_name_exception : std::exception
+{
+};
+
+class single_read_exception : std::exception
+{
+};
+
+struct error_checker
+{
+ void add_bad_name(std::string contig, std::string entry);
+ void add_single_read(std::string read);
+ void report() const;
+private:
+ int num_unrecognized_iworm_contig_names;
+ int num_warnings;
+};
+
+#endif
diff --git a/trinity-plugins/slclust/Makefile.bak b/trinity-plugins/slclust/Makefile.bak
deleted file mode 100644
index 188b24b..0000000
--- a/trinity-plugins/slclust/Makefile.bak
+++ /dev/null
@@ -1,10 +0,0 @@
-# Brian J. Haas
-
-SUBS = src
-
-all install depend clean:
- X=`pwd`; \
- for i in $(SUBS); \
- do echo '<<<' $$i '>>>'; cd $$X/$$i; make $@; done
-
-# DO NOT DELETE
diff --git a/util/abundance_estimates_to_matrix.pl b/util/abundance_estimates_to_matrix.pl
index c13b931..e5a031f 100755
--- a/util/abundance_estimates_to_matrix.pl
+++ b/util/abundance_estimates_to_matrix.pl
@@ -13,12 +13,11 @@ my $usage = <<__EOUSAGE__;
# Usage: $0 --est_method <method> sample1.results sample2.results ...
# Required:
#
-# --est_method <string> RSEM|eXpress (needs to know what format to expect)
-#
+# --est_method <string> RSEM|eXpress|kallisto (needs to know what format to expect)
#
# Options:
#
-# --cross_sample_fpkm_norm <string> TMM|UpperQuartile|none (default: TMM)
+# --cross_sample_norm <string> TMM|UpperQuartile|none (default: TMM)
#
# --name_sample_by_basedir name sample column by dirname instead of filename
# --basedir_index <int> default(-2)
@@ -35,7 +34,8 @@ __EOUSAGE__
my $help_flag;
my $est_method;
-my $cross_sample_fpkm_norm = "TMM";
+my $val_type;
+my $cross_sample_norm = "TMM";
my $name_sample_by_basedir = 0;
my $out_prefix = "matrix";
my $basedir_index = -2;
@@ -43,10 +43,9 @@ my $basedir_index = -2;
&GetOptions('help|h' => \$help_flag,
'est_method=s' => \$est_method,
- 'cross_sample_fpkm_norm=s' => \$cross_sample_fpkm_norm,
+ 'cross_sample_norm=s' => \$cross_sample_norm,
'name_sample_by_basedir' => \$name_sample_by_basedir,
'out_prefix=s' => \$out_prefix,
-
'basedir_index=i' => \$basedir_index,
);
@@ -56,11 +55,11 @@ unless ($est_method && @ARGV) {
die $usage;
}
-unless ($est_method =~ /^(RSEM|eXpress)$/i) {
+unless ($est_method =~ /^(RSEM|eXpress|kallisto)$/i) {
die "Error, dont recognize --est_method $est_method ";
}
-unless ($cross_sample_fpkm_norm =~ /^(TMM|UpperQuartile|none)$/i) {
- die "Error, dont recognize --cross_sample_fpkm_norm $cross_sample_fpkm_norm ";
+unless ($cross_sample_norm =~ /^(TMM|UpperQuartile|none)$/i) {
+ die "Error, dont recognize --cross_sample_norm $cross_sample_norm ";
}
my @files = @ARGV;
@@ -92,9 +91,8 @@ if (scalar @files == 1) {
7 IsoPct
-## eXpress:
+## eXpress v1.5:
-0 bundle_id
1 target_id
2 length
3 eff_length
@@ -108,22 +106,39 @@ if (scalar @files == 1) {
11 fpkm_conf_low
12 fpkm_conf_high
13 solvable
+14 tpm
+
+
+## kallisto:
+0 target_id
+1 length
+2 eff_length
+3 est_counts
+4 tpm
=cut
;
-my ($acc_field, $counts_field, $fpkm_field);
+my ($acc_field, $counts_field, $fpkm_field, $tpm_field);
if ($est_method =~ /^rsem$/i) {
$acc_field = 0;
- $counts_field = 4;
- $fpkm_field = 6;
+ $counts_field = "expected_count";
+ $fpkm_field = "FPKM";
+ $tpm_field = "TPM";
}
-elsif ($est_method =~ /^express$/i) {
- $acc_field = 1;
- $counts_field = 7;
- $fpkm_field = 10;
+elsif ($est_method =~ /^express$/i) { # as of v1.5
+ $acc_field = "target_id";
+ $counts_field = "eff_counts";
+ $fpkm_field = "fpkm";
+ $tpm_field = "tpm";
+}
+elsif ($est_method =~ /^kallisto$/i) {
+ $acc_field = "target_id";
+ $counts_field = "est_counts";
+ $fpkm_field = "tpm";
+ $tpm_field = "tpm";
}
else {
die "Error, dont recognize --est_method $est_method ";
@@ -136,17 +151,22 @@ main: {
foreach my $file (@files) {
print STDERR "-reading file: $file\n";
open (my $fh, $file) or die "Error, cannot open file $file";
- my $header = <$fh>; # ignore it
+ my $header = <$fh>;
+ chomp $header;
+ my %fields = &parse_field_positions($header);
+ #use Data::Dumper; print STDERR Dumper(\%fields);
while (<$fh>) {
chomp;
my @x = split(/\t/);
- my $acc = $x[$acc_field];
- my $count = $x[$counts_field];
- my $fpkm = $x[$fpkm_field];
-
+ my $acc = $x[ $fields{$acc_field} ];
+ my $count = $x[ $fields{$counts_field} ];
+ my $fpkm = $x[ $fields{$fpkm_field} ];
+ my $tpm = $x[ $fields{$tpm_field} ];
+
$data{$acc}->{$file}->{count} = $count;
- $data{$acc}->{$file}->{fpkm} = $fpkm;
+ $data{$acc}->{$file}->{FPKM} = $fpkm;
+ $data{$acc}->{$file}->{TPM} = $tpm;
}
close $fh;
}
@@ -164,9 +184,9 @@ main: {
print STDERR "\n\n* Outputting combined matrix.\n\n";
my $counts_matrix_file = "$out_prefix.counts.matrix";
- my $fpkm_matrix_file = "$out_prefix.not_cross_norm.fpkm.tmp";
+ my $TPM_matrix_file = "$out_prefix.TPM.not_cross_norm";
open (my $ofh_counts, ">$counts_matrix_file") or die "Error, cannot write file $counts_matrix_file";
- open (my $ofh_fpkm, ">$fpkm_matrix_file") or die "Error, cannot write file $fpkm_matrix_file";
+ open (my $ofh_TPM, ">$TPM_matrix_file") or die "Error, cannot write file $TPM_matrix_file";
{ # check to see if they're unique
my %filename_map = map { + $_ => 1 } @filenames;
@@ -184,12 +204,12 @@ main: {
print $ofh_counts join("\t", "", @filenames) . "\n";
- print $ofh_fpkm join("\t", "", @filenames) . "\n";
+ print $ofh_TPM join("\t", "", @filenames) . "\n";
foreach my $acc (keys %data) {
print $ofh_counts "$acc";
- print $ofh_fpkm "$acc";
+ print $ofh_TPM "$acc";
foreach my $file (@files) {
@@ -197,31 +217,34 @@ main: {
unless (defined $count) {
$count = "NA";
}
- my $fpkm = $data{$acc}->{$file}->{fpkm};
- unless (defined $fpkm) {
- $fpkm = "NA";
+ my $tpm = $data{$acc}->{$file}->{TPM};
+ if (defined $tpm) {
+ $tpm = $tpm/1;
+ }
+ else {
+ $tpm = "NA";
}
print $ofh_counts "\t$count";
- print $ofh_fpkm "\t$fpkm";
+ print $ofh_TPM "\t$tpm";
}
print $ofh_counts "\n";
- print $ofh_fpkm "\n";
+ print $ofh_TPM "\n";
}
close $ofh_counts;
- close $ofh_fpkm;
+ close $ofh_TPM;
- if ($cross_sample_fpkm_norm =~ /^TMM$/i) {
- my $cmd = "$FindBin::Bin/support_scripts/run_TMM_scale_matrix.pl --matrix $fpkm_matrix_file > $out_prefix.$cross_sample_fpkm_norm.fpkm.matrix";
+ if ($cross_sample_norm =~ /^TMM$/i) {
+ my $cmd = "$FindBin::Bin/support_scripts/run_TMM_scale_matrix.pl --matrix $TPM_matrix_file > $out_prefix.$cross_sample_norm.EXPR.matrix";
&process_cmd($cmd);
}
- elsif ($cross_sample_fpkm_norm =~ /^UpperQuartile$/) {
- my $cmd = "$FindBin::Bin/support_scripts/run_UpperQuartileNormalization_matrix.pl --matrix $fpkm_matrix_file > $out_prefix.$cross_sample_fpkm_norm.fpkm.matrix";
+ elsif ($cross_sample_norm =~ /^UpperQuartile$/) {
+ my $cmd = "$FindBin::Bin/support_scripts/run_UpperQuartileNormalization_matrix.pl --matrix $TPM_matrix_file > $out_prefix.$cross_sample_norm.EXPR.matrix";
&process_cmd($cmd);
}
- elsif ($cross_sample_fpkm_norm =~ /^none$/i) {
+ elsif ($cross_sample_norm =~ /^none$/i) {
print STDERR "-not performing cross-sample normalization.\n";
}
@@ -229,7 +252,7 @@ main: {
exit(0);
}
-
+
####
sub process_cmd {
my ($cmd) = @_;
@@ -243,3 +266,17 @@ sub process_cmd {
return;
}
+
+####
+sub parse_field_positions {
+ my ($header) = @_;
+
+ my %field_pos;
+ my @fields = split(/\s+/, $header);
+ for (my $i = 0; $i <= $#fields; $i++) {
+ $field_pos{$fields[$i]} = $i;
+ $field_pos{$i} = $i; # for fixed column assignment
+ }
+
+ return(%field_pos);
+}
diff --git a/util/align_and_estimate_abundance.pl b/util/align_and_estimate_abundance.pl
index 88e4f3a..182dc12 100755
--- a/util/align_and_estimate_abundance.pl
+++ b/util/align_and_estimate_abundance.pl
@@ -5,6 +5,7 @@ use warnings;
use FindBin;
use Cwd;
+use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
@@ -13,26 +14,49 @@ my $RSEM_DIR = "$FindBin::Bin/../trinity-plugins/rsem";
$ENV{PATH} = "$RSEM_DIR:$ENV{PATH}"; # be sure to use the included rsem package over other ones installed.
-my %aligner_params = ( 'bowtie_RSEM' => '--all --best --strata -m 300 --chunkmbs 512',
-
- 'bowtie2_RSEM' => '--no-mixed --no-discordant --gbar 1000 --end-to-end',
-
- 'bowtie_eXpress' => '--all --best --strata -m 300 --chunkmbs 512',
-
- 'bowtie2_eXpress' => '--end-to-end',
-
-
-
- 'bowtie_none' => '--all --best --strata -m 300 --chunkmbs 512',
-
- 'bowtie2_none' => '--no-mixed --no-discordant --gbar 1000 --end-to-end',
-
-
+my %aligner_params = (
+
+ ############
+ ## Bowtie-1
+ ############
+
+
+ 'bowtie_RSEM' => '--all --best --strata -m 300 --chunkmbs 512',
+ # params used by RSEM itself:
+ # -a -m 200
+
+
+ 'bowtie_eXpress' => '--all --best --strata -m 300 --chunkmbs 512',
+ # bowtie -aS -X 800 --offrate 1 (requires: bowtie-build --offrate 1)
+
+
+ #############
+ ## Bowtie-2
+ #############
+
+ 'bowtie2_RSEM' => '--no-mixed --no-discordant --gbar 1000 --end-to-end -k 200 ',
+
+ ## params used by RSEM itself:
+ # --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -k 200
+
+
+ 'bowtie2_eXpress' => '--no-mixed --no-discordant --gbar 1000 --end-to-end -k 200 ',
+
+
+ # recommended eXpress params: http://bio.math.berkeley.edu/eXpress/faq.html
+ # -a -X 600 --rdg 6,5 --rfg 6,5 --score-min L,-.6,-.4 --no-discordant --no-mixed
+
+
+ 'bowtie_none' => '--all --best --strata -m 300 --chunkmbs 512',
+
+ 'bowtie2_none' => '--no-mixed --no-discordant --gbar 1000 --end-to-end -k 200 ',
+
);
my $rsem_add_opts = "";
my $eXpress_add_opts = "";
+my $kallisto_add_opts = "";
my $usage = <<__EOUSAGE__;
@@ -51,9 +75,15 @@ my $usage = <<__EOUSAGE__;
#
# --single <string>
#
-# --est_method <string> RSEM|eXpress abundance estimation method.
+# --est_method <string> abundance estimation method.
+# alignment_based: RSEM|eXpress
+# alignment_free: kallisto
+#
+# --output_dir <string> write all files to output directory
+#
#
-# --aln_method <string> bowtie|bowtie2|(path to bam file) alignment method. (note: RSEM requires bowtie)
+# if alignment_based est_method:
+# --aln_method <string> bowtie|bowtie2|(path to bam file) alignment method. (note: RSEM requires bowtie)
# (if you already have a bam file, you can use it here instead of rerunning bowtie)
#
# Optional:
@@ -66,8 +96,6 @@ my $usage = <<__EOUSAGE__;
#
# --debug retain intermediate files
#
-# --output_dir <string> write all files to output directory
-#
#
# --gene_trans_map <string> file containing 'gene(tab)transcript' identifiers per line.
# or
@@ -79,7 +107,8 @@ my $usage = <<__EOUSAGE__;
# --output_prefix <string> prefix for output files. Defaults to --est_method setting.
#
#
-# --coordsort_bam provide coord-sorted bam in addition to the default (unsorted) bam.
+# if alignment_based method:
+# --coordsort_bam provide coord-sorted bam in addition to the default (unsorted) bam.
#
# --show_full_usage_info provide more detailed usage info for customizing the alignment or abundance estimation parameters.
#
@@ -107,6 +136,7 @@ my $usage = <<__EOUSAGE__;
#
#########################################################################
+
__EOUSAGE__
;
@@ -134,6 +164,8 @@ my $advanced_usage_info = <<__EOADVANCEDUSAGE__;
#
# --eXpress_add_opts <string> default: "$eXpress_add_opts"
#
+# --kallisto_add_opts <string> default: $kallisto_add_opts
+
# * note, options for handling strand-specific reads are already taken care of internally, so no need to
# pass on those parameters.
#
@@ -161,7 +193,7 @@ my $gene_trans_map_file;
my $max_ins_size = 800;
my $est_method;
-my $aln_method;
+my $aln_method = "";
my $retain_sorted_bam_file = 0;
@@ -178,7 +210,7 @@ my $trinity_mode;
my $include_rsem_bam;
my $coordsort_bam_flag = 0;
-&GetOptions ( 'h' => \$help_flag,
+&GetOptions ( 'help|h' => \$help_flag,
'transcripts=s' => \$transcripts,
'name_sorted_bam=s' => \$bam_file,
'debug' => \$DEBUG_flag,
@@ -222,7 +254,8 @@ my $coordsort_bam_flag = 0;
'rsem_add_opts=s' => \$rsem_add_opts,
'eXpress_add_opts=s' => \$eXpress_add_opts,
-
+ 'kallisto_add_opts=s' => \$kallisto_add_opts,
+
'coordsort_bam' => \$coordsort_bam_flag,
);
@@ -239,48 +272,62 @@ if ($help_flag) {
if ($show_full_usage_info) {
die "$usage\n\n$advanced_usage_info\n\n";
}
+unless ($est_method) {
+ die $usage;
+}
+
+my @EST_METHODS = qw(RSEM eXpress kallisto);
+my %ALIGNMENT_BASED_EST_METHODS = map { + $_ => 1 } qw (RSEM eXpress);
+my %ALIGNMENT_FREE_EST_METHODS = map { + $_ => 1 } qw (kallisto);
-unless (($est_method && $aln_method && $prep_reference && $transcripts) ## just prep reference
- || ($transcripts && $aln_method && $est_method && $seqType && ($single || ($left && $right))) # do alignment
+unless ($output_dir) {
+ die "Error, must specify output directory name via: --output_dir ";
+}
+
+unless (($est_method && $prep_reference && $transcripts) ## just prep reference
+ || ($transcripts && $est_method && $seqType && ($single || ($left && $right))) # do alignment
+
) {
die "Error, missing parameter. See example usage options below.\n" . $usage;
}
my $PROCESSING_EXISTING_BAM_FLAG = 0;
-if ($aln_method =~ /\.bam$/) {
- if (-s $aln_method) {
- # no problem, using the bam file
- $PROCESSING_EXISTING_BAM_FLAG = 1;
+
+if ($ALIGNMENT_FREE_EST_METHODS{$est_method}) {
+ $aln_method = "none";
+}
+else {
+ if ($aln_method =~ /\.bam$/) {
+ if (-s $aln_method) {
+ # no problem, using the bam file
+ $PROCESSING_EXISTING_BAM_FLAG = 1;
+ }
+ else {
+ die "Error, file $aln_method does not exist or is empty. ";
+ }
}
- else {
- die "Error, file $aln_method does not exist or is empty. ";
+ elsif ($aln_method !~ /bowtie2?/) {
+ die "Error, --aln_method must be either 'bowtie' or 'bowtie2' ";
}
}
-elsif ($aln_method !~ /bowtie2?/) {
- die "Error, --aln_method must be either 'bowtie' or 'bowtie2' ";
-}
-unless ($est_method =~ /^(RSEM|eXpress|none)$/) {
- die "Error, --est_method 'RSEM' or 'eXpress' only, and capitalization matters. :) \n";
+
+unless ($est_method =~ /^(RSEM|eXpress|kallisto|none)$/) {
+ die "Error, --est_method @EST_METHODS only, and capitalization matters. :) \n";
}
+$left = &create_full_path($left) if $left;
+$right = &create_full_path($right) if $right;
+$single = &create_full_path($single) if $single;
+$transcripts = &create_full_path($transcripts);
-if ($output_dir) {
- $left = &create_full_path($left) if $left;
- $right = &create_full_path($right) if $right;
- $single = &create_full_path($single) if $single;
-
- $transcripts = &create_full_path($transcripts);
+$gene_trans_map_file = &create_full_path($gene_trans_map_file) if $gene_trans_map_file;
- if ($gene_trans_map_file) {
- $gene_trans_map_file = &create_full_path($gene_trans_map_file);
- }
-}
if ($left && $left =~ /\.gz$/) {
@@ -326,8 +373,10 @@ if ( $thread_count !~ /^\d+$/ ) {
elsif ($est_method =~ /^eXpress$/i) {
push (@tools, 'express');
}
+ elsif ($est_method eq 'kallisto') {
+ push (@tools, 'kallisto');
+ }
-
foreach my $tool (@tools) {
my $p = `which $tool`;
unless ($p =~ /\w/) {
@@ -343,21 +392,50 @@ if ( $thread_count !~ /^\d+$/ ) {
main: {
- ###############################################
- ## Prepare transcript database for alignments
- ###############################################
-
- my $db_index_name = "$transcripts.${aln_method}";
-
if ($trinity_mode && ! $gene_trans_map_file) {
$gene_trans_map_file = "$transcripts.gene_trans_map";
my $cmd = "$FindBin::Bin/support_scripts/get_Trinity_gene_to_trans_map.pl $transcripts > $gene_trans_map_file";
&process_cmd($cmd) unless (-e $gene_trans_map_file);
}
+
+ if ($ALIGNMENT_BASED_EST_METHODS{$est_method}) {
+ &run_alignment_BASED_estimation();
+
+ }
+ else {
+ &run_alignment_FREE_estimation();
+ }
+
+ exit(0);
+}
+
+
+
+####
+sub run_alignment_FREE_estimation {
+
+ if ($est_method eq "kallisto") {
+ &run_kallisto();
+ }
+}
+
+
+
+####
+sub run_alignment_BASED_estimation {
+
+ my $db_index_name = "$transcripts.${aln_method}";
+
+
unless ($PROCESSING_EXISTING_BAM_FLAG) {
-
+
+ ###############################################
+ ## Prepare transcript database for alignments
+ ###############################################
+
+
if ($prep_reference) {
my $cmd = "${aln_method}-build $transcripts $db_index_name";
@@ -398,8 +476,6 @@ main: {
unless (-e "$rsem_prefix.rsem.prepped.ok") {
-
-
&process_cmd("touch $rsem_prefix.rsem.prepped.started");
my $cmd = "rsem-prepare-reference "; #--no-bowtie"; # update for RSEM-2.15
@@ -430,21 +506,16 @@ main: {
exit(0);
}
-
+
#####################
## Run alignments
#####################
-
-
- if ($output_dir) {
-
- my $init_dir = cwd();
-
- system("mkdir -p $output_dir");
- chdir $output_dir or die "Error, cannot cd to output directory $output_dir";
+ unless (-d $output_dir) {
+ system("mkdir -p $output_dir");
}
-
+ chdir $output_dir or die "Error, cannot cd to output directory $output_dir";
+
my $prefix = $output_prefix;
if ($prefix) {
$prefix .= "."; # add separator in filename
@@ -511,12 +582,11 @@ main: {
}
- exit(0);
+ return;
}
-
####
sub sort_bam_file {
my ($bam_file) = @_;
@@ -560,26 +630,17 @@ sub run_eXpress {
## run eXpress
my $express_cmd = "express $SS_opt $eXpress_add_opts $transcripts";
-
+
my $cmd = "$express_cmd $bam_file";
&process_cmd($cmd);
if ($gene_trans_map_file) {
- &make_eXpress_genes_file("results.xprs", $gene_trans_map_file);
+
+ my $cmd = "$FindBin::Bin/support_scripts/eXpress_trans_to_gene_results.pl results.xprs $gene_trans_map_file > results.xprs.genes";
+ &process_cmd($cmd);
}
return;
-
-}
-
-####
-sub make_eXpress_genes_file {
- my ($results_xprs_file, $gene_to_trans_map_file) = @_;
-
- my $cmd = "$FindBin::Bin/support_scripts/eXpress_trans_to_gene_results.pl $results_xprs_file $gene_to_trans_map_file > $results_xprs_file.genes";
- &process_cmd($cmd);
-
- return;
}
@@ -691,7 +752,7 @@ sub add_zcat_gz {
if ($file =~ /\.gz$/) {
- $file = "<(zcat $file)";
+ $file = "<(gunzip -c $file)"; # used to be zcat
}
@@ -702,3 +763,40 @@ sub add_zcat_gz {
return($file_listing);
}
+
+
+####
+sub run_kallisto {
+
+ my $kallisto_index = "$transcripts.kallisto_idx";
+
+ if ( (! $prep_reference) && (! -e $kallisto_index)) {
+ confess "Error, no kallisto index file: $kallisto_index, and --prep_reference not set. Re-run with --prep_reference";
+ }
+ if ($prep_reference && ! -e $kallisto_index) {
+
+ my $cmd = "kallisto index -i $kallisto_index $transcripts";
+ &process_cmd($cmd);
+ }
+
+ if ($left && $right) {
+
+ my $cmd = "kallisto quant -i $kallisto_index $kallisto_add_opts -o $output_dir $left $right";
+ &process_cmd($cmd);
+ }
+ elsif ($single) {
+ my $cmd = "kallisto quant -l $fragment_length -i $kallisto_index -o $output_dir $kallisto_add_opts $single";
+ &process_cmd($cmd);
+ }
+
+
+ if ($gene_trans_map_file) {
+
+ my $cmd = "$FindBin::Bin/support_scripts/kallisto_trans_to_gene_results.pl $output_dir/abundance.tsv $gene_trans_map_file > $output_dir/abundance.tsv.genes";
+ &process_cmd($cmd);
+ }
+
+
+ return;
+}
+
diff --git a/util/filter_fasta_by_rsem_values.pl b/util/filter_fasta_by_rsem_values.pl
index e2bceec..ed6ca22 100755
--- a/util/filter_fasta_by_rsem_values.pl
+++ b/util/filter_fasta_by_rsem_values.pl
@@ -11,9 +11,9 @@ USAGE: filter_fasta_by_rsem_values.pl
--rsem_output=/path/to/RSEM.isoforms.results[,...]
--fasta=/path/to/Trinity.fasta
--output=/path/to/output.fasta
- [ --tpm_cutoff=10000
- --fpkm_cutoff=1200
- --isopct_cutoff=1.00
+ [ --tpm_cutoff=1.0
+ --fpkm_cutoff=0.5
+ --isopct_cutoff=0.05
]
=head1 OPTIONS
diff --git a/util/insilico_read_normalization.pl b/util/insilico_read_normalization.pl
index 4b78886..16ba3ac 100755
--- a/util/insilico_read_normalization.pl
+++ b/util/insilico_read_normalization.pl
@@ -467,6 +467,12 @@ sub build_selected_index {
chomp $line;
next unless $line =~ /\S/;
+ ## want core, .... just in case.
+ $line =~ s|/\w$||;
+
+ #print STDERR "-want $line\n";
+
+
$index{$line} = 0;
}
diff --git a/util/misc/blast_outfmt6_group_segments.pl b/util/misc/blast_outfmt6_group_segments.pl
new file mode 100755
index 0000000..604b6c2
--- /dev/null
+++ b/util/misc/blast_outfmt6_group_segments.pl
@@ -0,0 +1,165 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use FindBin;
+use lib "$FindBin::Bin/../../PerlLib";
+use Fasta_reader;
+use List::Util qw(min max);
+use Overlap_piler;
+
+my $usage = "\n\n\tusage: $0 blast.outfmt6 query_fasta target_fasta\n\n\n";
+
+my $blast_file = $ARGV[0] or die $usage;
+my $query_fasta = $ARGV[1] or die $usage;
+my $target_fasta = $ARGV[2] or die $usage;
+
+
+my %query_seq_lens = &get_seq_lengths($query_fasta);
+
+my %target_seq_lens;
+if ($query_fasta eq $target_fasta) {
+ %target_seq_lens = %query_seq_lens;
+}
+else {
+ %target_seq_lens = &get_seq_lengths($target_fasta);
+}
+
+main: {
+
+ # header
+ print join("\t", "#query_acc", "target_acc", "avg_per_id", "min_Evalue",
+ "query_match_range", "target_match_range", "pct_query_len", "pct_target_len", "max_pct_len") . "\n";
+
+
+ my @hits;
+ my $prev_query_target_pair = "";
+
+ open (my $fh, $blast_file) or die "Error, cannot open file $blast_file";
+ while (<$fh>) {
+ chomp;
+ my @x = split(/\t/);
+ my $query_acc = $x[0];
+ my $target_acc = $x[1];
+
+ my $query_target_pair = join("$;", $query_acc, $target_acc);
+ if ($query_target_pair ne $prev_query_target_pair) {
+ &process_hits(@hits) if @hits;
+ @hits = ();
+ }
+ push (@hits, [@x]);
+ $prev_query_target_pair = $query_target_pair;
+ }
+
+ # get last one
+ &process_hits(@hits);
+
+ exit(0);
+}
+
+####
+sub process_hits {
+ my @hits = @_;
+
+ #use Data::Dumper; print Dumper(\@hits);
+
+
+ my @query_coords;
+ my @target_coords;
+
+ my $query_acc = "";
+ my $target_acc = "";
+
+ my $sum_pct_id_len = 0;
+ my $sum_len = 0;
+
+ my $min_evalue = 1;
+
+ foreach my $hit (@hits) {
+ my @fields = @$hit;
+
+ unless ($query_acc) {
+ $query_acc = $fields[0];
+ $target_acc = $fields[1];
+ }
+
+ my ($query_lend, $query_rend) = sort {$a<=>$b} ($fields[6], $fields[7]);
+ my ($target_lend, $target_rend) = sort {$a<=>$b} ($fields[8], $fields[9]);
+
+ my $per_id = $fields[2];
+ my $query_seg_len = $query_rend - $query_lend + 1;
+ $sum_pct_id_len += $query_seg_len * $per_id;
+ $sum_len += $query_seg_len;
+
+ my $evalue = $fields[10];
+ if ($evalue < $min_evalue) {
+ $min_evalue = $evalue;
+ }
+
+ push (@query_coords, [$query_lend, $query_rend]);
+ push (@target_coords, [$target_lend, $target_rend]);
+
+ }
+
+ my $avg_per_id = sprintf("%.2f", $sum_pct_id_len / $sum_len);
+
+
+ my $query_match_len = 0;
+ my @query_match_regions;
+ {
+
+ my @query_piles = &Overlap_piler::simple_coordsets_collapser(@query_coords);
+ foreach my $pile (@query_piles) {
+ my ($pile_lend, $pile_rend) = @$pile;
+ $query_match_len += $pile_rend - $pile_lend + 1;
+ push (@query_match_regions, "$pile_lend-$pile_rend");
+ }
+ }
+
+ my $target_match_len = 0;
+ my @target_match_regions;
+ {
+ my @target_piles = &Overlap_piler::simple_coordsets_collapser(@target_coords);
+ foreach my $pile (@target_piles) {
+ my ($pile_lend, $pile_rend) = @$pile;
+ $target_match_len += $pile_rend - $pile_lend + 1;
+ push (@target_match_regions, "$pile_lend-$pile_rend");
+ }
+ }
+
+ my $query_len = $query_seq_lens{$query_acc} or die "Error, cannot find seq length for query: $query_acc";
+ my $target_len = $target_seq_lens{$target_acc} or die "Error, cannot find seq length for target: $target_acc";
+
+ my $pct_query_len = sprintf("%.2f", $query_match_len / $query_len * 100);
+ my $pct_target_len = sprintf("%.2f", $target_match_len / $target_len * 100);
+
+
+ print join("\t", $query_acc, $target_acc, $avg_per_id, $min_evalue,
+ join(",", @query_match_regions), join(",", @target_match_regions),
+ $pct_query_len, $pct_target_len, max($pct_query_len, $pct_target_len) ) . "\n";
+
+
+ return;
+}
+
+
+####
+sub get_seq_lengths {
+ my ($fasta_file) = @_;
+
+ my %seq_lens;
+
+ my $fasta_reader = new Fasta_reader($fasta_file);
+ while (my $seq_obj = $fasta_reader->next()) {
+
+ my $acc = $seq_obj->get_accession();
+ my $seq_len = length($seq_obj->get_sequence());
+
+ # print STDERR "$acc => $seq_len\n";
+
+ $seq_lens{$acc} = $seq_len;
+ }
+
+ return(%seq_lens);
+}
+
diff --git a/util/misc/blast_outfmt6_group_segments.to_Markov_Clustering.pl b/util/misc/blast_outfmt6_group_segments.to_Markov_Clustering.pl
new file mode 100755
index 0000000..be3c82f
--- /dev/null
+++ b/util/misc/blast_outfmt6_group_segments.to_Markov_Clustering.pl
@@ -0,0 +1,167 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use Carp;
+use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
+use FindBin;
+use lib "$FindBin::Bin/../../PerlLib";
+use Pipeliner;
+use File::Basename;
+
+
+my $usage = <<__EOUSAGE__;
+
+#######################################################################################
+#
+# --outfmt6_grouped <string> outfmt6 grouped output
+#
+# --min_pct_len <int> minimum percent length covered by pairwise matches
+#
+# --min_per_id <int> minimum percent identity
+#
+# --inflation_factor <float> inflation factor for MCL clustering
+#
+#######################################################################################
+
+
+__EOUSAGE__
+
+ ;
+
+
+
+my $help_flag;
+my $outfmt6_grouped_file;
+my $inflation_factor;
+my $min_pct_len;
+my $min_per_id;
+
+&GetOptions ( 'h' => \$help_flag,
+
+ 'outfmt6_grouped=s' => \$outfmt6_grouped_file,
+
+ 'min_pct_len=i' => \$min_pct_len,
+
+ 'min_per_id=i' => \$min_per_id,
+
+ 'inflation_factor=f' => \$inflation_factor,
+
+ );
+
+if ($help_flag) {
+ die $usage;
+}
+
+if (@ARGV) {
+ die "Error, dont understand parameters @ARGV";
+}
+
+
+unless ($outfmt6_grouped_file && $inflation_factor && $min_pct_len && $min_per_id) {
+ die $usage;
+}
+
+
+# add MCL to PATH setting
+$ENV{PATH} = "/seq/regev_genome_portal/SOFTWARE/MCL/bin/:$ENV{PATH}";
+
+
+
+main: {
+
+
+ my $filtered_hits = basename($outfmt6_grouped_file . ".minLEN_${min_pct_len}_pct_len.minPID_${min_per_id}.abc");
+ my $checkpoint = ".$filtered_hits.ok";
+ if (! -e $checkpoint) {
+
+ my %best_hits;
+
+
+
+ open (my $fh, $outfmt6_grouped_file) or die "Error, cannot open file $outfmt6_grouped_file";
+ while (<$fh>) {
+ if (/^\#/) { next; }
+ chomp;
+ my @x = split(/\t/);
+ my ($transA, $transB, $per_id, $E_value, @rest) = split(/\t/);
+ my $per_len_match = pop @rest;
+
+ if ($per_len_match >= $min_pct_len && $per_id >= $min_per_id) {
+ my $geneA = &parse_gene_name($transA);
+ my $geneB = &parse_gene_name($transB);
+
+ if ($geneA eq $geneB) { next; }
+
+ ($geneA, $geneB) = sort ($geneA, $geneB);
+ my $gene_pair_token = join("$;", $geneA, $geneB);
+
+
+ my $lowest_evalue = $best_hits{$gene_pair_token};
+ if ( (! defined $lowest_evalue) || $lowest_evalue > $E_value) {
+ $best_hits{$gene_pair_token} = $E_value;
+ }
+
+
+ }
+ }
+
+ # write best hits file
+ open (my $ofh, ">$filtered_hits") or die "Error, cannot write to $filtered_hits";
+ foreach my $gene_pair_token (keys %best_hits) {
+ my ($geneA, $geneB) = split(/$;/, $gene_pair_token);
+ my $E_value = $best_hits{$gene_pair_token};
+ print $ofh join("\t", $geneA, $geneB, $E_value) . "\n";
+ }
+ close $ofh;
+
+ `touch $checkpoint`;
+ }
+
+ my $pipeliner = new Pipeliner(-verbose => 1);
+ my $cmd = "mcxload -abc $filtered_hits --stream-mirror --stream-neg-log10 "
+ . " -stream-tf 'ceil(200)' -o $filtered_hits.mci -write-tab $filtered_hits.tab";
+
+ $pipeliner->add_commands( new Command($cmd, ".$filtered_hits.tab.ok") );
+
+ $inflation_factor = sprintf("%.1f", $inflation_factor);
+ my $inflation_factor_dec_removed = $inflation_factor;
+ $inflation_factor_dec_removed =~ s/\.//;
+
+ $cmd = "mcl $filtered_hits.mci -I $inflation_factor";
+ my $mcl_outfile = "out.$filtered_hits.mci.I$inflation_factor_dec_removed";
+ $pipeliner->add_commands( new Command($cmd, ".$mcl_outfile.ok"));
+
+
+ $cmd = "mcxdump -icl $mcl_outfile -tabr $filtered_hits.tab -o dump.$mcl_outfile";
+ $pipeliner->add_commands( new Command($cmd, ".dump.$mcl_outfile.ok"));
+
+
+ $pipeliner->run();
+
+
+ exit(0);
+
+}
+
+####
+sub parse_gene_name {
+ my ($trans_info) = @_;
+
+ my ($gene_symbol, $trans_id);
+ if (/;/) {
+ ($trans_id, $gene_symbol) = split(/;/, $trans_info);
+ }
+ elsif (/\|/) {
+ ($gene_symbol, $trans_id) = split(/\|/, $trans_info);
+ }
+
+
+ if ($gene_symbol) {
+ return($gene_symbol);
+ }
+ else {
+ return($trans_info);
+ }
+}
diff --git a/util/misc/blast_outfmt6_group_segments.tophit_coverage.pl b/util/misc/blast_outfmt6_group_segments.tophit_coverage.pl
new file mode 100755
index 0000000..90f3d32
--- /dev/null
+++ b/util/misc/blast_outfmt6_group_segments.tophit_coverage.pl
@@ -0,0 +1,110 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+my $usage = "usage: $0 blast.grouped\n\n";
+
+my $blast_out = $ARGV[0] or die $usage;
+
+main: {
+
+
+ my $counter = 0;
+
+ my %query_to_top_hit; # only storing the hit with the greatest blast score.
+
+ # outfmt6:
+ # qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore
+
+ open (my $fh, $blast_out) or die "Error, cannot open file $blast_out";
+ while (<$fh>) {
+ if (/^\#/) { next; }
+ chomp;
+ my $line = $_;
+ my @x = split(/\t/);
+ my $query_id = $x[0];
+ my $db_id = $x[1];
+ my $percent_id = $x[2];
+ my $Evalue = $x[3];
+
+ my $pct_target_len = $x[7];
+
+
+ if ( (! exists $query_to_top_hit{$query_id}) || ($Evalue < $query_to_top_hit{$query_id}->{Evalue})
+ ||
+ ($Evalue == $query_to_top_hit{$query_id}->{Evalue}
+ &&
+ $pct_target_len > $query_to_top_hit{$query_id}->{pct_target_len} )
+ ) {
+
+ $query_to_top_hit{$query_id} = { query_id => $query_id,
+ db_id => $db_id,
+ percent_id => $percent_id,
+ Evalue => $Evalue,
+ pct_target_len => $pct_target_len,
+ };
+
+ }
+ }
+ close $fh;
+
+
+ ## get the best transcript hit per db ID
+
+ my %db_id_to_trans_hits;
+
+ foreach my $hit_struct (values %query_to_top_hit) {
+
+ my $db_id = $hit_struct->{db_id};
+
+ push (@{$db_id_to_trans_hits{$db_id}}, $hit_struct);
+ }
+
+
+ ## histogram summary
+
+ my @bins = qw(10 20 30 40 50 60 70 80 90 100);
+ my %bin_counts;
+
+
+ foreach my $db_id (keys %db_id_to_trans_hits) {
+
+ my @hit_structs = @{$db_id_to_trans_hits{$db_id}};
+
+ @hit_structs = sort {$a->{Evalue} <=> $b->{Evalue}
+ ||
+ $b->{pct_target_len} <=> $a->{pct_target_len} } @hit_structs;
+
+
+ my $entry = shift @hit_structs; # take the lowest E-value w/ longest pct_target_len
+
+ my $pct_cov = $entry->{pct_target_len};
+
+ my $prev_bin = 0;
+ foreach my $bin (@bins) {
+ if ($pct_cov > $prev_bin && $pct_cov <= $bin) {
+ $bin_counts{$bin}++;
+ }
+ $prev_bin = $bin;
+ }
+
+ }
+
+
+ ## Report counts per bin
+ print "#hit_pct_cov_bin\tcount_in_bin\t>bin_below\n";
+
+ my $cumul = 0;
+ foreach my $bin (reverse(@bins)) {
+ my $count = $bin_counts{$bin} || 0;
+ $cumul += $count;
+ print join("\t", $bin, $count, $cumul) . "\n";
+ }
+
+
+
+ exit(0);
+
+
+}
diff --git a/util/misc/contig_E_statistic.pl b/util/misc/contig_ExN50_statistic.pl
similarity index 54%
rename from util/misc/contig_E_statistic.pl
rename to util/misc/contig_ExN50_statistic.pl
index e6bb148..ade42b5 100755
--- a/util/misc/contig_E_statistic.pl
+++ b/util/misc/contig_ExN50_statistic.pl
@@ -3,47 +3,51 @@
use strict;
use warnings;
-my $usage = "usage: $0 TMM.fpkm.matrix trans_lengths\n\n";
+use FindBin;
+use lib ("$FindBin::Bin/../../PerlLib");
+use Fasta_reader;
+
+my $usage = "usage: $0 EXPR.matrix Trinity.fasta\n\n";
my $matrix_file = $ARGV[0] or die $usage;
-my $trans_lengths_file = $ARGV[1] or die $usage;
+my $fasta_file = $ARGV[1] or die $usage;
my %trans_lengths;
{
- open (my $fh, $trans_lengths_file) or die $!;
- while (<$fh>) {
- chomp;
- my ($trans_acc, $seq_len) = split(/\s+/);
- $trans_lengths{$trans_acc} = $seq_len;
+ my $fasta_reader = new Fasta_reader($fasta_file);
+ while (my $seq_obj = $fasta_reader->next()) {
+
+ my $acc = $seq_obj->get_accession();
+ my $sequence = $seq_obj->get_sequence();
+
+ my $seq_len = length($sequence);
+
+ $trans_lengths{$acc} = $seq_len;
}
- close $fh;
}
-
-
-
open (my $fh, $matrix_file) or die $!;
my $header = <$fh>;
my @trans;
-my $sum_fpkm = 0;
+my $sum_expr = 0;
while (<$fh>) {
chomp;
my @x = split(/\t/);
my $acc = shift @x; # gene accession
- my $max_fpkm = 0;
- my $trans_sum_fpkm = 0;
+ my $max_expr = 0;
+ my $trans_sum_expr = 0;
while (@x) {
- my $fpkm = shift @x;
+ my $expr = shift @x;
- $trans_sum_fpkm += $fpkm;
- $sum_fpkm += $fpkm;
+ $trans_sum_expr += $expr;
+ $sum_expr += $expr;
- if ($fpkm > $max_fpkm) {
- $max_fpkm = $fpkm;
+ if ($expr > $max_expr) {
+ $max_expr = $expr;
}
}
@@ -51,13 +55,13 @@ while (<$fh>) {
push (@trans, { acc => $acc,
len => $seq_len,
- sum_fpkm => $trans_sum_fpkm,
- max_fpkm => $max_fpkm,
+ sum_expr => $trans_sum_expr,
+ max_expr => $max_expr,
});
}
- at trans = reverse sort { $a->{sum_fpkm} <=> $b->{sum_fpkm}
+ at trans = reverse sort { $a->{sum_expr} <=> $b->{sum_expr}
||
$a->{len} <=> $b->{len} } @trans;
@@ -65,9 +69,9 @@ while (<$fh>) {
## write output table
{
open (my $ofh, ">$matrix_file.E-inputs") or die $!;
- print $ofh join("\t", "#acc", "length", "max_fpkm_over_samples", "sum_fpkm_over_samples") . "\n";
+ print $ofh join("\t", "#acc", "length", "max_expr_over_samples", "sum_expr_over_samples") . "\n";
foreach my $t (@trans) {
- print $ofh join("\t", $t->{acc}, $t->{len}, $t->{max_fpkm}, $t->{sum_fpkm}) . "\n";
+ print $ofh join("\t", $t->{acc}, $t->{len}, $t->{max_expr}, $t->{sum_expr}) . "\n";
}
close $ofh;
}
@@ -77,7 +81,7 @@ my %Estats_wanted = map { $_ => 1 } (1..100);
-print "#E\tmin_fpkm\tE-N50\tnum_transcripts\n";
+print "#E\tmin_expr\tE-N50\tnum_transcripts\n";
my $sum = 0;
my @captured;
@@ -86,31 +90,31 @@ while (@trans) {
my $t = shift @trans;
push (@captured, $t);
- $sum += $t->{sum_fpkm};
+ $sum += $t->{sum_expr};
- my $pct = int($sum/$sum_fpkm * 100);
+ my $pct = int($sum/$sum_expr * 100);
if ($Estats_wanted{$pct}) {
- my $min_max_fpkm = &get_min_max(@captured);
+ my $min_max_expr = &get_min_max(@captured);
delete($Estats_wanted{$pct});
my $N50 = &calc_N50(@captured);
my $num_trans = scalar(@captured);
- print "E$pct\t$min_max_fpkm\t$N50\t$num_trans\n";
+ print "E$pct\t$min_max_expr\t$N50\t$num_trans\n";
}
}
# ensure that we do E100
if (%Estats_wanted) {
- my $min_max_fpkm = &get_min_max(@captured);
+ my $min_max_expr = &get_min_max(@captured);
my $N50 = &calc_N50(@captured);
my $num_trans = scalar(@captured);
- print "E100\t$min_max_fpkm\t$N50\t$num_trans\n";
+ print "E100\t$min_max_expr\t$N50\t$num_trans\n";
}
@@ -121,10 +125,10 @@ exit(0);
sub get_min_max {
my @entries = @_;
- my $min = $entries[0]->{max_fpkm};
+ my $min = $entries[0]->{max_expr};
foreach my $entry (@entries) {
- if ($entry->{max_fpkm} < $min) {
- $min = $entry->{max_fpkm};
+ if ($entry->{max_expr} < $min) {
+ $min = $entry->{max_expr};
}
}
diff --git a/util/misc/count_features_given_MIN_FPKM_threshold.pl b/util/misc/count_features_given_MIN_FPKM_threshold.pl
index 00e2ab9..6a7b968 100755
--- a/util/misc/count_features_given_MIN_FPKM_threshold.pl
+++ b/util/misc/count_features_given_MIN_FPKM_threshold.pl
@@ -39,6 +39,6 @@ while (@fpkms) {
$num_features++;
}
-print "$min_fpkm_thresh\t$num_features\n";
+print "" . (-1*$min_fpkm_thresh) . "\t$num_features\n";
exit(0);
diff --git a/util/misc/count_matrix_features_given_MIN_FPKM_threshold.pl b/util/misc/count_matrix_features_given_MIN_FPKM_threshold.pl
deleted file mode 100755
index 5abae98..0000000
--- a/util/misc/count_matrix_features_given_MIN_FPKM_threshold.pl
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/usr/bin/env perl
-
-use strict;
-use warnings;
-
-my $usage = "usage: $0 fpkm.matrix\n\n";
-
-
-my $matrix_file = $ARGV[0] or die $usage;
-
-open (my $fh, $matrix_file) or die $!;
-my $header = <$fh>;
-
-my @fpkms;
-while (<$fh>) {
- chomp;
- my @x = split(/\t/);
- shift @x; # gene accession
- my $max_fpkm = shift @x;
- while (@x) {
- my $fpkm = shift @x;
- if ($fpkm > $max_fpkm) {
- $max_fpkm = $fpkm;
- }
- }
- push (@fpkms, $max_fpkm);
-}
-
- at fpkms = reverse sort {$a<=>$b} @fpkms;
-
-my $min_fpkm_thresh = int($fpkms[0] + 0.5);
-my $num_features = 1;
-
-print "neg_min_fpkm\tnum_features\n";
-
-shift @fpkms;
-while (@fpkms) {
-
- my $fpkm = shift @fpkms;
- $fpkm = int($fpkm+0.5);
-
- if ($fpkm < $min_fpkm_thresh) {
- print "" . (-1*$min_fpkm_thresh) . "\t$num_features\n";
- $min_fpkm_thresh = $fpkm;
-
- }
- $num_features++;
-}
-
-print "$min_fpkm_thresh\t$num_features\n";
-
-exit(0);
diff --git a/util/misc/count_matrix_features_given_MIN_TPM_threshold.pl b/util/misc/count_matrix_features_given_MIN_TPM_threshold.pl
new file mode 100755
index 0000000..41711e9
--- /dev/null
+++ b/util/misc/count_matrix_features_given_MIN_TPM_threshold.pl
@@ -0,0 +1,52 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+my $usage = "usage: $0 tpm.matrix\n\n";
+
+
+my $matrix_file = $ARGV[0] or die $usage;
+
+open (my $fh, $matrix_file) or die $!;
+my $header = <$fh>;
+
+my @tpms;
+while (<$fh>) {
+ chomp;
+ my @x = split(/\t/);
+ shift @x; # gene accession
+ my $max_tpm = shift @x;
+ while (@x) {
+ my $tpm = shift @x;
+ if ($tpm > $max_tpm) {
+ $max_tpm = $tpm;
+ }
+ }
+ push (@tpms, $max_tpm);
+}
+
+ at tpms = reverse sort {$a<=>$b} @tpms;
+
+my $min_tpm_thresh = int($tpms[0] + 0.5);
+my $num_features = 1;
+
+print "neg_min_tpm\tnum_features\n";
+
+shift @tpms;
+while (@tpms) {
+
+ my $tpm = shift @tpms;
+ $tpm = int($tpm+0.5);
+
+ if ($tpm < $min_tpm_thresh) {
+ print "" . (-1*$min_tpm_thresh) . "\t$num_features\n";
+ $min_tpm_thresh = $tpm;
+
+ }
+ $num_features++;
+}
+
+print "$min_tpm_thresh\t$num_features\n";
+
+exit(0);
diff --git a/util/misc/get_longest_isoform_seq_per_trinity_gene.pl b/util/misc/get_longest_isoform_seq_per_trinity_gene.pl
new file mode 100755
index 0000000..2ce55ee
--- /dev/null
+++ b/util/misc/get_longest_isoform_seq_per_trinity_gene.pl
@@ -0,0 +1,62 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use FindBin;
+use lib ("$FindBin::Bin/../../PerlLib");
+use Fasta_reader;
+
+print STDERR "\n\n\tNOTE - longest transcript isn't always the best transcript!... consider filtering based on relative expression support ... \n\n";
+
+my $usage = "usage: $0 Trinity.fasta\n\n";
+
+my $trin_fasta = $ARGV[0] or die $usage;
+
+main: {
+ my %gene_to_longest_transcript;
+
+ my $fasta_reader = new Fasta_reader($trin_fasta);
+ while (my $seq_obj = $fasta_reader->next()) {
+
+ my $acc = $seq_obj->get_accession();
+ my $header = $seq_obj->get_header();
+
+ my $gene_id;
+
+ if ($acc =~ /^(.*comp\d+_c\d+)_seq/) {
+ $gene_id = $1;
+ }
+ elsif ($acc =~ /^(.*c\d+_g\d+)_i/) {
+ $gene_id = $1;
+ }
+
+ unless ($gene_id) {
+ die "Error, cannot parse gene identifier from acc: $acc";
+ }
+
+ my $sequence = $seq_obj->get_sequence();
+
+ if ( (! exists $gene_to_longest_transcript{$gene_id})
+ ||
+ $gene_to_longest_transcript{$gene_id}->{length} < length($sequence)) {
+
+ $gene_to_longest_transcript{$gene_id} = { length => length($sequence),
+ acc => $acc,
+ sequence => $sequence,
+ header => $header,
+ };
+ }
+
+
+ }
+
+ foreach my $longest_seq ( reverse sort {$a->{length}<=>$b->{length}} values %gene_to_longest_transcript) {
+
+ print ">" . $longest_seq->{header} . "\n" . $longest_seq->{sequence} . "\n";
+
+ }
+
+ print STDERR "\n\nok. Done.\n\n";
+
+ exit(0);
+}
diff --git a/util/misc/gmap_gff3_to_percent_length_stats.pl b/util/misc/gmap_gff3_to_percent_length_stats.pl
index cd8dbf1..cceb585 100755
--- a/util/misc/gmap_gff3_to_percent_length_stats.pl
+++ b/util/misc/gmap_gff3_to_percent_length_stats.pl
@@ -19,6 +19,7 @@ main: {
open (my $fh, $gmap_gff3) or die $!;
while (<$fh>) {
+ if (/^\#/) { next; }
chomp;
my @x = split(/\t/);
my $info = $x[8];
diff --git a/util/misc/merge_RSEM_output_to_matrix.pl b/util/misc/merge_RSEM_output_to_matrix.pl
new file mode 100755
index 0000000..1122d92
--- /dev/null
+++ b/util/misc/merge_RSEM_output_to_matrix.pl
@@ -0,0 +1,142 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use Getopt::Long qw(:config no_ignore_case bundling pass_through);
+
+use File::Basename;
+
+my $usage = <<__EOUSAGE__;
+
+
+############################################################################################
+#
+# Required:
+#
+# --rsem_files <string> file containing a list of RSEM output files.
+# (note, should be isoform or gene.results files, dont mix)
+#
+# --mode <string> counts|fpkm|tpm
+#
+# Optional:
+#
+# --trans_mode_bundle_gene_id specify the transcript identifier as 'gene|trans'
+#
+############################################################################################
+
+__EOUSAGE__
+
+ ;
+
+
+
+my $rsem_files_list_file;
+my $mode;
+my $trans_mode_bundle_gene_id = 0;
+my $help_flag;
+
+&GetOptions( 'help|h' => \$help_flag,
+
+ 'rsem_files=s' => \$rsem_files_list_file,
+ 'mode=s' => \$mode,
+ 'trans_mode_bundle_gene_id' => \$trans_mode_bundle_gene_id,
+ );
+
+if ($help_flag) {
+ die $usage;
+}
+unless ($rsem_files_list_file && $mode) {
+
+ die $usage;
+}
+
+unless ($mode =~ /^(counts|fpkm|tpm)$/i) {
+ die "Error, mode $mode not recognized";
+}
+
+
+=header_format
+
+0 transcript_id
+1 gene_id
+2 length
+3 effective_length
+4 expected_count
+5 TPM
+6 FPKM
+7 IsoPct
+
+=cut
+
+
+main: {
+
+
+ unless (-f $rsem_files_list_file) { die "$usage\nError: cannot open file $rsem_files_list_file"; }
+ my @rsem_files = `cat $rsem_files_list_file`;
+ chomp @rsem_files;
+
+ my %data;
+
+ foreach my $file (@rsem_files) {
+
+ print STDERR "-capturing $mode from file: $file\n";
+
+ open (my $fh, $file) or die "Error, cannot open file $file";
+ my $header = <$fh>; # ignore it
+ while (<$fh>) {
+ chomp;
+ my @x = split(/\t/);
+ my $acc = $x[0];
+
+ if ($trans_mode_bundle_gene_id) {
+ my $gene = $x[1];
+ $acc = "$gene|$acc";
+ }
+
+ my $count = $x[4];
+ my $tpm = $x[5];
+ my $fpkm = $x[6];
+
+
+ $data{$acc}->{$file} = ($mode =~ /counts/i) ? $count : ($mode =~ /fpkm/) ? $fpkm : $tpm;
+ }
+ close $fh;
+ }
+
+
+ print STDERR "\n\n* done parsing files. Now outputting matrix.\n\n";
+
+ my @filenames = @rsem_files;
+ foreach my $file (@filenames) {
+ $file = basename($file);
+ $file =~ s/-/_/g; # R doesn't like '-' in column headers
+ $file =~ s/\.(genes|isoforms)\.results//;
+ }
+
+
+ print join("\t", "", @filenames) . "\n";
+ foreach my $acc (keys %data) {
+
+ print "$acc";
+
+ foreach my $file (@rsem_files) {
+
+ my $count = $data{$acc}->{$file};
+ unless (defined $count) {
+ $count = "NA";
+ }
+
+ print "\t$count";
+
+ }
+
+ print "\n";
+
+ }
+
+
+ exit(0);
+}
+
+
diff --git a/util/misc/pair_up_fastq_files_1_2.pl b/util/misc/pair_up_fastq_files_1_2.pl
new file mode 100755
index 0000000..0391585
--- /dev/null
+++ b/util/misc/pair_up_fastq_files_1_2.pl
@@ -0,0 +1,30 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use Cwd;
+
+my $curr_dir = cwd();
+
+foreach my $file (<*_1.*fastq*>, <*_1*.fq*>) {
+
+ $file =~ /^(\S+)_1\.*/ or die "Error, cannot decipher filename $file";
+ my $core = $1;
+
+ my $right_fq = $file;
+ $right_fq =~ s/_1\./_2\./;
+
+ unless (-s $right_fq) {
+ die "Error, cannot find Right.fq file corresponding to $file";
+ }
+
+ print join("\t", $core, "$curr_dir/$file", "$curr_dir/$right_fq") . "\n";
+
+}
+
+
+exit(0);
+
+
+
diff --git a/util/misc/pair_up_fastq_files_LeftRight.pl b/util/misc/pair_up_fastq_files_LeftRight.pl
new file mode 100755
index 0000000..bf1ee0b
--- /dev/null
+++ b/util/misc/pair_up_fastq_files_LeftRight.pl
@@ -0,0 +1,32 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use Cwd;
+
+my $curr_dir = cwd();
+
+foreach my $file (<*.Left.fq*>, <*.left.fq*>, <*_Left.fq*>, <*_left.fq*>) {
+
+ $file =~ /^(\S+)[\._]Left.fq/i or die "Error, cannot decipher filename $file";
+ my $core = $1;
+
+ my $right_fq = $file;
+ $right_fq =~ s/([\._])Left/${1}Right/;
+ $right_fq =~ s/([\._])left/${1}right/;
+
+
+ unless (-s $right_fq) {
+ die "Error, cannot find Right.fq file corresponding to $file";
+ }
+
+ print join("\t", $core, "$curr_dir/$file", "$curr_dir/$right_fq") . "\n";
+
+}
+
+
+exit(0);
+
+
+
diff --git a/util/misc/pair_up_fastq_files_R1_R2.pl b/util/misc/pair_up_fastq_files_R1_R2.pl
new file mode 100755
index 0000000..03815fa
--- /dev/null
+++ b/util/misc/pair_up_fastq_files_R1_R2.pl
@@ -0,0 +1,30 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use Cwd;
+
+my $curr_dir = cwd();
+
+foreach my $file (<*_R1*.fastq*>, <*_R1*.fq*>, <*.R1*.fastq*>, <*.R1*.fq*>) {
+
+ $file =~ /^(\S+)[\._]R1[\._].*f(ast)?q/ or die "Error, cannot decipher filename $file";
+ my $core = $1;
+
+ my $right_fq = $file;
+ $right_fq =~ s/([\._])R1([\._])/$1R2$2/ or die "Error, cannot convert R1 to R2 in $right_fq";
+
+ unless (-s $right_fq) {
+ die "Error, cannot find Right.fq file corresponding to $file";
+ }
+
+ print join("\t", $core, "$curr_dir/$file", "$curr_dir/$right_fq") . "\n";
+
+}
+
+
+exit(0);
+
+
+
diff --git a/util/misc/run_GSNAP.pl b/util/misc/run_GSNAP.pl
index fdaea5a..2ad4337 100755
--- a/util/misc/run_GSNAP.pl
+++ b/util/misc/run_GSNAP.pl
@@ -116,7 +116,7 @@ main: {
$require_proper_pairs = " -f 2 ";
}
- my $cmd = "bash -c \"set -o pipefail && gsnap -D $genomeBaseDir -d $genomeDir -A sam -N 1 -w $max_intron $gsnap_use_sarray -n $num_top_hits -t $CPU $reads $splice_param | samtools view -bS -F 4 $require_proper_pairs - | samtools sort -@ $CPU - $out_prefix.cSorted \"";
+ my $cmd = "bash -c \"set -o pipefail && gsnap -D $genomeBaseDir -d $genomeDir -A sam -N 1 -w $max_intron $gsnap_use_sarray -n $num_top_hits -t $CPU $reads $splice_param @ARGV | samtools view -bS -F 4 $require_proper_pairs - | samtools sort -@ $CPU - $out_prefix.cSorted \"";
&process_cmd($cmd);
if (-s "$out_prefix.cSorted.bam") {
diff --git a/util/misc/run_HISAT.pl b/util/misc/run_HISAT.pl
index 5e6a69b..3a7252d 100755
--- a/util/misc/run_HISAT.pl
+++ b/util/misc/run_HISAT.pl
@@ -4,6 +4,8 @@ use strict;
use warnings;
use FindBin;
+use lib("$FindBin::Bin/../../PerlLib");
+use Pipeliner;
use File::Basename;
use Cwd;
@@ -74,10 +76,12 @@ main: {
&process_cmd($cmd);
}
- my $gtf_splice = "$gtf_file.hisat.splice";
+
my $splice_incl = "";
if ($gtf_file) {
+
+ my $gtf_splice = "$gtf_file.hisat.splice";
unless (-s $gtf_splice) {
my $cmd = "$HISAT_HOME/extract_splice_sites.py $gtf_file > $gtf_file.hisat.splice";
@@ -96,15 +100,34 @@ main: {
$top_hits_count = " -k $num_top_hits ";
}
- my $cmd = "bash -c \"set -o pipefail && $HISAT_HOME/hisat -x $hisat_index -q $reads $splice_incl -p $CPU $top_hits_count @ARGV | samtools view -@ $CPU -F 4 -Sb - | samtools sort -@ $CPU -o - - > $out_prefix.cSorted.bam \"";
+ my @tmpfiles;
+
+ my $pipeliner = new Pipeliner(-verbose => 1);
+
+ my $cmd = "bash -c \"set -o pipefail && $HISAT_HOME/hisat -x $hisat_index -q $reads $splice_incl -p $CPU $top_hits_count @ARGV | gzip -c > $out_prefix.sam.gz\" ";
+
+ $pipeliner->add_commands( new Command($cmd, "$out_prefix.sam.gz.ok") );
+ push (@tmpfiles, "$out_prefix.sam.gz");
+
+ $cmd = "bash -c \"set -o pipefail && gunzip -c $out_prefix.sam.gz | samtools view -@ $CPU -F 4 -Sb - > $out_prefix.bam \"";
+ $pipeliner->add_commands( new Command($cmd, "$out_prefix.bam.ok") );
+ push (@tmpfiles, "$out_prefix.bam");
+
+
+ $cmd = "samtools sort -@ $CPU $out_prefix.bam $out_prefix.cSorted";
+ $pipeliner->add_commands( new Command($cmd, "$out_prefix.cSorted.bam.ok") );
+
+
+ $pipeliner->run();
- &process_cmd($cmd);
if (-s "$out_prefix.cSorted.bam") {
$cmd = "samtools index $out_prefix.cSorted.bam";
&process_cmd($cmd);
}
+ unlink(@tmpfiles);
+
exit(0);
}
diff --git a/util/misc/run_STAR.pl b/util/misc/run_STAR.pl
new file mode 100755
index 0000000..fa8c269
--- /dev/null
+++ b/util/misc/run_STAR.pl
@@ -0,0 +1,186 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+use lib("$FindBin::RealBin/../../PerlLib");
+use Pipeliner;
+use File::Basename;
+use Cwd;
+
+use Carp;
+use Getopt::Long qw(:config no_ignore_case bundling pass_through);
+
+
+my $usage = <<__EOUSAGE__;
+
+######################################################################
+#
+# Required:
+# --genome <string> target genome to align to
+# --reads <string> fastq files. If pairs, indicate both in quotes, ie. "left.fq right.fq"
+#
+# Optional:
+# -G <string> GTF file for incorporating reference splice site info.
+# --CPU <int> number of threads (default: 2)
+# --out_prefix <string> output prefix (default: star)
+# --out_dir <string> output directory (default: current working directory)
+#
+#######################################################################
+
+
+__EOUSAGE__
+
+ ;
+
+
+my ($genome, $reads);
+
+my $CPU = 2;
+
+my $help_flag;
+
+my $out_prefix = "star";
+my $gtf_file;
+my $out_dir;
+my $ADV = 0;
+
+&GetOptions( 'h' => \$help_flag,
+ 'genome=s' => \$genome,
+ 'reads=s' => \$reads,
+ 'CPU=i' => \$CPU,
+ 'out_prefix=s' => \$out_prefix,
+ 'G=s' => \$gtf_file,
+ 'out_dir=s' => \$out_dir,
+ 'ADV' => \$ADV,
+
+ );
+
+
+unless ($genome && $reads) {
+ die $usage;
+}
+
+if ($help_flag) {
+ die $usage;
+}
+
+
+my $star_prog = `which STAR`;
+chomp $star_prog;
+unless ($star_prog =~ /\w/) {
+ die "Error, cannot locate STAR program. Be sure it's in your PATH setting. ";
+}
+
+
+main: {
+
+ ## ensure all full paths
+ $genome = &Pipeliner::ensure_full_path($genome);
+ $gtf_file = &Pipeliner::ensure_full_path($gtf_file) if $gtf_file;
+
+ my @read_files = split(/\s+/, $reads);
+ foreach my $read_file (@read_files) {
+ if ($read_file) {
+ $read_file = &Pipeliner::ensure_full_path($read_file);
+ }
+ }
+ $reads = join(" ", @read_files);
+
+ if ($out_dir) {
+ unless (-d $out_dir) {
+ mkdir $out_dir or die "Error, cannot mkdir $out_dir";
+ }
+ chdir $out_dir or die "Error, cannot cd to $out_dir";
+ }
+
+
+ my $star_index = "$genome.star.idx";
+ if (! -e "$star_index/build.ok") {
+ ## build star index
+ unless (-d $star_index) {
+ mkdir($star_index) or die "Error, cannot mkdir $star_index";
+ }
+
+
+ my $cmd = "$star_prog --runThreadN $CPU --runMode genomeGenerate --genomeDir $star_index "
+ . " --twopassMode Basic "
+ . " --genomeFastaFiles $genome "
+ . " --limitGenomeGenerateRAM 40419136213 ";
+ if ($gtf_file) {
+ $cmd .= " --sjdbGTFfile $gtf_file "
+ . " --sjdbOverhang 100 ";
+
+ }
+
+ &process_cmd($cmd);
+
+ &process_cmd("touch $star_index/build.ok");
+
+ }
+
+
+ ## run STAR
+
+ my @tmpfiles;
+
+ my $pipeliner = new Pipeliner(-verbose => 1);
+
+ my $cmd = "$star_prog "
+ . " --runThreadN $CPU "
+ . " --genomeDir $star_index "
+ . " --outSAMtype BAM SortedByCoordinate "
+ . " --readFilesIn $reads "
+ . " --chimJunctionOverhangMin 12 "
+ . " --chimSegmentMin 12 "
+ . " --twopassMode Basic "
+ . " --alignSJDBoverhangMin 10 "
+ . " --chimSegmentReadGapMax parameter 3 "
+ . " --limitBAMsortRAM 20000000000";
+
+ #if ($ADV) {
+ $cmd .= " --alignSJstitchMismatchNmax 5 -1 5 5 "; #which allows for up to 5 mismatches for non-canonical GC/AG, and AT/AC junctions, and any number of mismatches for canonical junctions (the default values 0 -1 0 0 replicate the old behavior (from AlexD)
+ #}
+
+ if ($reads =~ /\.gz$/) {
+ $cmd .= " --readFilesCommand 'gunzip -c' ";
+ }
+
+ $pipeliner->add_commands( new Command($cmd, "star_align.ok") );
+
+
+
+ my $bam_outfile = "Aligned.sortedByCoord.out.bam";
+ my $renamed_bam_outfile = "$out_prefix.sortedByCoord.out.bam";
+ $pipeliner->add_commands( new Command("mv $bam_outfile $renamed_bam_outfile", "$renamed_bam_outfile.ok") );
+
+
+ $pipeliner->add_commands( new Command("samtools index $renamed_bam_outfile", "$renamed_bam_outfile.bai.ok") );
+
+
+ $pipeliner->run();
+
+
+ exit(0);
+}
+
+
+
+####
+sub process_cmd {
+ my ($cmd) = @_;
+
+ print STDERR "CMD: $cmd\n";
+ #return;
+
+ my $ret = system($cmd);
+ if ($ret) {
+ die "Error, cmd: $cmd died with ret ($ret)";
+ }
+
+ return;
+}
+
+
+
diff --git a/util/misc/run_trimmomatic_qual_trimming.pl b/util/misc/run_trimmomatic_qual_trimming.pl
index 4306f1c..81c11d9 100755
--- a/util/misc/run_trimmomatic_qual_trimming.pl
+++ b/util/misc/run_trimmomatic_qual_trimming.pl
@@ -22,10 +22,7 @@ my $usage = <<__EOUSAGE__;
#
# --CPU <int> default: 4
#
-# --LEADING <int> default: 15
-# --TRAILING <int> default: 15
-#
-# --MINLEN <int> default: 36
+# --trim_params <string> "SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25"
#
###############################################################
@@ -40,19 +37,16 @@ my $right;
my $single;
my $threads = 4;
-my $LEADING = 15;
-my $TRAILING = 15;
-my $MINLEN = 36;
+my $trim_params = "SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25";
&GetOptions( 'left=s' => \$left,
'right=s' => \$right,
'single=s' => \$single,
'CPU=i' => \$threads,
-
- 'LEADING=i' => \$LEADING,
- 'TRAILING=i' => \$TRAILING,
- 'MINLEN=i' => \$MINLEN,
+
+ 'trim_params=s' => \$trim_params,
+
);
@@ -78,18 +72,18 @@ main: {
if ($left && $right) {
- $cmd = "java -jar $FindBin::Bin/../trinity-plugins/Trimmomatic/trimmomatic.jar PE -threads $threads -phred33 "
+ $cmd = "java -jar $FindBin::Bin/../../trinity-plugins/Trimmomatic/trimmomatic.jar PE -threads $threads -phred33 "
. " $left $right "
. " $left.P.qtrim.fq $left.U.qtrim.fq "
. " $right.P.qtrim.fq $right.U.qtrim.fq "
- . " LEADING:$LEADING TRAILING:$TRAILING MINLEN:$MINLEN ";
+ . " $trim_params ";
}
else {
- $cmd = "java -jar $FindBin::Bin/../trinity-plugins/Trimmomatic/trimmomatic.jar SE -threads $threads -phred33 "
+ $cmd = "java -jar $FindBin::Bin/../../trinity-plugins/Trimmomatic/trimmomatic.jar SE -threads $threads -phred33 "
. " $single "
. " $single.qtrim.fq "
- . " LEADING:$LEADING TRAILING:$TRAILING MINLEN:$MINLEN ";
+ . " $trim_params ";
}
diff --git a/util/misc/simulate_illuminaPE_from_transcripts.pl b/util/misc/simulate_illuminaPE_from_transcripts.pl
index ecaa1e8..400d09f 100755
--- a/util/misc/simulate_illuminaPE_from_transcripts.pl
+++ b/util/misc/simulate_illuminaPE_from_transcripts.pl
@@ -38,6 +38,8 @@ my $usage = <<__EOUSAGE__;
#
# :: note, generates left.fa and right.fa in FR stranded format
#
+# --make_fastq generate fastq instead of fasta (note, uses 'C' for all the qual scores)
+#
#################################################################
__EOUSAGE__
@@ -58,6 +60,8 @@ my $include_volcano_spread = 0;
my $error_rate = 0;
my $MAX_DEPTH = 1;
+my $make_fastq_flag = 0;
+
&GetOptions ( 'h' => \$help_flag,
'transcripts=s' => \$transcripts,
'read_length=i' => \$read_length,
@@ -67,10 +71,12 @@ my $MAX_DEPTH = 1;
'require_proper_pairs' => \$require_proper_pairs_flag,
'include_volcano_spread' => \$include_volcano_spread,
'error_rate=f' => \$error_rate,
- 'max_depth=i' => \$MAX_DEPTH,
-
+ 'max_depth=i' => \$MAX_DEPTH,
+ 'make_fastq' => \$make_fastq_flag,
+
);
+
if ($help_flag) {
die $usage;
}
@@ -85,7 +91,7 @@ if ($error_rate > 0.25) {
main: {
-
+
my $fasta_reader = new Fasta_reader($transcripts);
print STDERR "-parsing incoming $transcripts...";
my %read_seqs = $fasta_reader->retrieve_all_seqs_hash();
@@ -94,114 +100,113 @@ main: {
my $num_trans = scalar (keys %read_seqs);
my $counter = 0;
- open (my $left_ofh, ">$out_prefix.left.simPE.fa") or die $!;
- open (my $right_ofh, ">$out_prefix.right.simPE.fa") or die $!;
-
+ my $ext = ($make_fastq_flag) ? "fq" : "fa";
+ open (my $left_ofh, ">$out_prefix.left.simPE.$ext") or die $!;
+ open (my $right_ofh, ">$out_prefix.right.simPE.$ext") or die $!;
+
foreach my $read_acc (keys %read_seqs) {
-
- for my $depth (1..$MAX_DEPTH) {
-
-
- $counter++;
- print STDERR "\r[" . sprintf("%.2f%% = $counter/$num_trans] ", $counter/$num_trans*100);
-
- my $seq = uc $read_seqs{$read_acc};
-
-
- ## uniform dist
- for (my $i = 0; $i <= length($seq); $i+=$spacing) {
-
- my $left_read_seq = "";
- my $right_read_seq = "";
- my $ill_acc = $read_acc . "_Ap$i-$counter";
-
- my $left_start = $i - $read_length - $pair_gap;
- if ($left_start >= 0) {
- $left_read_seq = substr($seq, $left_start, $read_length);
- }
-
- my $right_start = $i;
- if ($right_start + $read_length <= length($seq)) {
- $right_read_seq = substr($seq, $right_start, $read_length);
- }
-
- if ($require_proper_pairs_flag && ! ($left_read_seq && $right_read_seq)) { next; }
-
-
- if ($left_read_seq) {
- if ($error_rate > 0) {
- $left_read_seq = &introduce_errors($left_read_seq, $error_rate);
- }
-
- print $left_ofh ">$ill_acc/1\n"
- . "$left_read_seq\n";
- }
- if ($right_read_seq) {
- $right_read_seq = &reverse_complement($right_read_seq);
-
- if ($error_rate > 0) {
- $right_read_seq = &introduce_errors($right_read_seq, $error_rate);
- }
-
- print $right_ofh ">$ill_acc/2\n"
- . "$right_read_seq\n";
- }
- }
-
-
- volcano_spread:
- if ($include_volcano_spread) {
-
- ## volcano spread
- for (my $i = 0; $i <= length($seq)/2; $i+=$spacing) {
-
- my $left_read_seq = "";
- my $right_read_seq = "";
- my $ill_acc = $read_acc . "_Bp$i";
-
-
- my $left_start = $i;
- if ($left_start >= 0) {
- $left_read_seq = substr($seq, $left_start, $read_length);
- }
-
- my $right_start = length($seq)-$read_length -$i + 1;
-
- if ($left_start + $read_length >= $right_start) { next; } ## don't overlap them.
-
- if ($right_start + $read_length <= length($seq)) {
- $right_read_seq = substr($seq, $right_start, $read_length);
- }
-
-
- if ($require_proper_pairs_flag && ! ($left_read_seq && $right_read_seq)) { next; }
-
- if ($left_read_seq) {
-
- if ($error_rate > 0) {
- $left_read_seq = &introduce_errors($left_read_seq, $error_rate);
- }
-
- print $left_ofh ">$ill_acc/1\n"
- . "$left_read_seq\n";
- }
- if ($right_read_seq) {
-
- $right_read_seq = &reverse_complement($right_read_seq);
-
- if ($error_rate > 0) {
- $right_read_seq = &introduce_errors($right_read_seq, $error_rate);
- }
-
- print $right_ofh ">$ill_acc/2\n"
- . "$right_read_seq\n";
- }
- }
-
- }
- }
-
+
+ for my $depth (1..$MAX_DEPTH) {
+
+
+ $counter++;
+ print STDERR "\r[" . sprintf("%.2f%% = $counter/$num_trans] ", $counter/$num_trans*100);
+
+ my $seq = uc $read_seqs{$read_acc};
+
+
+ ## uniform dist
+ for (my $i = 0; $i <= length($seq); $i+=$spacing) {
+
+ my $left_read_seq = "";
+ my $right_read_seq = "";
+ my $ill_acc = $read_acc . "_Ap$i-$counter";
+
+ my $left_start = $i - $read_length - $pair_gap;
+ if ($left_start >= 0) {
+ $left_read_seq = substr($seq, $left_start, $read_length);
+ }
+
+ my $right_start = $i;
+ if ($right_start + $read_length <= length($seq)) {
+ $right_read_seq = substr($seq, $right_start, $read_length);
+ }
+
+ if ($require_proper_pairs_flag && ! ($left_read_seq && $right_read_seq)) { next; }
+
+
+ if ($left_read_seq) {
+ if ($error_rate > 0) {
+ $left_read_seq = &introduce_errors($left_read_seq, $error_rate);
+ }
+
+ &write_seq($left_ofh, "$ill_acc/1", $left_read_seq);
+ }
+ if ($right_read_seq) {
+ $right_read_seq = &reverse_complement($right_read_seq);
+
+ if ($error_rate > 0) {
+ $right_read_seq = &introduce_errors($right_read_seq, $error_rate);
+ }
+
+ &write_seq($right_ofh, "$ill_acc/2", $right_read_seq);
+ }
+ }
+
+
+ volcano_spread:
+ if ($include_volcano_spread) {
+
+ ## volcano spread
+ for (my $i = 0; $i <= length($seq)/2; $i+=$spacing) {
+
+ my $left_read_seq = "";
+ my $right_read_seq = "";
+ my $ill_acc = $read_acc . "_Bp$i";
+
+
+ my $left_start = $i;
+ if ($left_start >= 0) {
+ $left_read_seq = substr($seq, $left_start, $read_length);
+ }
+
+ my $right_start = length($seq)-$read_length -$i + 1;
+
+ if ($left_start + $read_length >= $right_start) { next; } ## don't overlap them.
+
+ if ($right_start + $read_length <= length($seq)) {
+ $right_read_seq = substr($seq, $right_start, $read_length);
+ }
+
+
+ if ($require_proper_pairs_flag && ! ($left_read_seq && $right_read_seq)) { next; }
+
+ if ($left_read_seq) {
+
+ if ($error_rate > 0) {
+ $left_read_seq = &introduce_errors($left_read_seq, $error_rate);
+ }
+
+ &write_seq($left_ofh, "$ill_acc/1", $left_read_seq);
+
+ }
+ if ($right_read_seq) {
+
+ $right_read_seq = &reverse_complement($right_read_seq);
+
+ if ($error_rate > 0) {
+ $right_read_seq = &introduce_errors($right_read_seq, $error_rate);
+ }
+
+ &write_seq($right_ofh, "$ill_acc/2", $right_read_seq);
+
+ }
+ }
+
+ }
+ }
+
}
close $left_ofh;
@@ -213,6 +218,22 @@ main: {
}
+
+
+####
+sub write_seq {
+ my ($ofh, $acc, $seq) = @_;
+
+ if ($make_fastq_flag) {
+ print $ofh join("\n", "\@$acc", $seq, "+", 'C' x length($seq)) . "\n";
+ }
+ else {
+ # fasta
+ print $ofh join("\n", ">$acc", $seq) . "\n";
+ }
+ return;
+}
+
####
sub process_cmd {
my ($cmd) = @_;
diff --git a/util/misc/sixFrameTranslation.pl b/util/misc/sixFrameTranslation.pl
new file mode 100755
index 0000000..3d93a2d
--- /dev/null
+++ b/util/misc/sixFrameTranslation.pl
@@ -0,0 +1,38 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+use lib ("$FindBin::Bin/../../PerlLib");
+use Fasta_reader;
+use Nuc_translator;
+
+
+my $usage = "\nn\\tusage: $0 nucFasta \n\n";
+
+my $fasta_file = $ARGV[0] or die $usage;
+
+main: {
+ my $fasta_reader = new Fasta_reader($fasta_file);
+ while (my $seq_obj = $fasta_reader->next()) {
+
+ my $accession = $seq_obj->get_accession();
+ my $sequence = $seq_obj->get_sequence();
+ my $header = $seq_obj->get_header();
+
+ for my $frame (1..6) {
+ my $translation = &translate_sequence($sequence, $frame);
+
+ $translation =~ s/(\S{60})/$1\n/g;
+ chomp $translation;
+
+ print ">$accession.F${frame}_trans $header\n$translation\n";
+ }
+ }
+
+ exit(0);
+}
+
+
+
diff --git a/util/run_Trinity_edgeR_pipeline.pl b/util/run_DE_analysis_from_samples_file.pl
similarity index 51%
copy from util/run_Trinity_edgeR_pipeline.pl
copy to util/run_DE_analysis_from_samples_file.pl
index 895c743..4cbd356 100755
--- a/util/run_Trinity_edgeR_pipeline.pl
+++ b/util/run_DE_analysis_from_samples_file.pl
@@ -18,6 +18,8 @@ my $usage = <<__EOUSAGE__;
#
# Required:
#
+# --DE_method <string> DE method (options: edgeR, DESeq2)
+#
# --samples_file <string> tab-delimited text file indicating biological replicate relationships.
# ex.
# cond_A cond_A_rep1 A_rep1_left.fq A_rep1_right.fq
@@ -49,19 +51,28 @@ __EOUSAGE__
my $help_flag;
my $read_samples_descr_file;
my $PAUSE_EACH_STEP = 0;
-my $GENES_TOO = 0;
+my $DE_method;
&GetOptions ( 'h' => \$help_flag,
'samples_file=s' => \$read_samples_descr_file,
'I' => \$PAUSE_EACH_STEP,
- 'genes_too' => \$GENES_TOO,
+ 'DE_method=s' => \$DE_method,
);
-if ($help_flag || ! $read_samples_descr_file) {
+if ($help_flag) {
die $usage;
}
+unless ($read_samples_descr_file && $DE_method) {
+ die $usage;
+}
+
+unless ($read_samples_descr_file =~ /^\//) {
+ $read_samples_descr_file = cwd() . "/$read_samples_descr_file";
+}
+
+
{
## Check for required software
my @needed_tools = qw (R bowtie bowtie-build); # Trinity.pl, RSEM, and samtools are set by relative paths.
@@ -86,186 +97,18 @@ my %conditions_to_read_info = &parse_sample_descriptions($read_samples_descr_fil
my @conditions = sort keys %conditions_to_read_info;
-## first, gunzip the inputs as needed.
-
-my $reads_ALL_left_fq = "reads.ALL.left.fq";
-my $reads_ALL_right_fq = "reads.ALL.right.fq";
-
-my $REGENERATE_ALL_FQ = 1;
-if (-s $reads_ALL_left_fq && -s $reads_ALL_right_fq) {
- $REGENERATE_ALL_FQ = 0;
-}
-
-
-## concatenate all entries before running Trinity
-
-
-foreach my $condition (@conditions) {
-
- my $replicates_href = $conditions_to_read_info{$condition};
-
- my @replicates = keys %$replicates_href;
- foreach my $replicate (@replicates) {
- my ($left_fq_file, $right_fq_file) = @{$replicates_href->{$replicate}};
-
-
- if (-s "$left_fq_file.gz" && ! -s $left_fq_file) {
- &process_cmd("gunzip -c $left_fq_file.gz > $left_fq_file",
- "Uncompressing $left_fq_file.gz"
- );
- }
-
- if ($right_fq_file && -s "$right_fq_file.gz" && ! -s $right_fq_file) {
- &process_cmd("gunzip -c $right_fq_file.gz > $right_fq_file",
- "Uncompressiong $right_fq_file.gz");
- }
-
- if ($REGENERATE_ALL_FQ) {
-
- &process_cmd("cat $left_fq_file >> $reads_ALL_left_fq",
- "Concatenating left.fq files");
-
- &process_cmd("cat $right_fq_file >> $reads_ALL_right_fq",
- "Concatenating right.fq files"
- ) if $right_fq_file; ## only left if 'single'
-
- }
-
- }
-
-}
-
-unless (-s "trinity_out_dir/Trinity.fasta") {
-
- my $cmd;
-
- if (-s $reads_ALL_right_fq) {
- ## got pairs
-
- ## Run Trinity:
- $cmd = "$BASEDIR/Trinity --left $reads_ALL_left_fq --right $reads_ALL_right_fq ";
-
- }
- else {
- # run left as single
- $cmd = "$BASEDIR/Trinity --single $reads_ALL_left_fq ";
-
- }
-
- my @trinity_params = qw ( --seqType --max_memory --CPU --SS_lib_type --monitoring --no_reduce );
-
- my %trin_params = map { + $_ => 1 } @trinity_params;
-
- foreach my $param (keys %PARAMS) {
- if ($trin_params{$param}) {
- my $val = $PARAMS{$param};
- if (defined $val) {
- $cmd .= " $param $val ";
- }
- else {
- $cmd .= " $param ";
- }
- }
- }
-
- &process_cmd($cmd, "Running Trinity de novo transcriptome assembly");
-
-}
-
-#############################################################
-## Run RSEM, compute abundance estimates for each replicate.
-#############################################################
-
-
-
-my @trans_rsem_files;
-my @genes_rsem_files;
-
-foreach my $condition (@conditions) {
-
- my $replicates_href = $conditions_to_read_info{$condition};
-
- my @replicates = keys %$replicates_href;
- foreach my $replicate (@replicates) {
- my ($left_fq_file, $right_fq_file) = @{$replicates_href->{$replicate}};
-
- ## run RSEM
- my $seqType = $PARAMS{"--seqType"} or die "Error, --seqType not specified";
- my $cmd = "$BASEDIR/util/align_and_estimate_abundance.pl "
- . " --transcripts trinity_out_dir/Trinity.fasta "
- . " --seqType $seqType "
- . " --prep_reference "
- . " --output_prefix $replicate "
- . " --aln_method bowtie --est_method RSEM "
- . " --trinity_mode "
-
- ;
-
- if ($left_fq_file && $right_fq_file) {
- $cmd .= " --left $left_fq_file --right $right_fq_file ";
- }
- elsif ($left_fq_file) {
- $cmd .= " --single $left_fq_file ";
- }
- else {
- die "Error, no left or right read files";
- }
- if (my $SS_lib_type = $PARAMS{'--SS_lib_type'}) {
- $cmd .= " --SS_lib_type $SS_lib_type ";
- }
- if (my $cpu = $PARAMS{'--CPU'}) {
- $cmd .= " --thread_count $cpu ";
- }
-
- &process_cmd($cmd,
- "Running RSEM to perform abundance estimation on sample $replicate"
- ) unless (-s "$replicate.isoforms.results");
-
-
- push (@trans_rsem_files, "$replicate.isoforms.results");
- push (@genes_rsem_files, "$replicate.genes.results");
- }
-
-}
-
-if ($PARAMS{NO_RUN_DE}) {
- print STDERR "Stopping at abundance estimation.\n";
- exit(0);
-}
-
-
-######################################
-# Make count matrices for DE analysis
-######################################
-
-# make iso matrix
-my $cmd = "$BASEDIR/util/abundance_estimates_to_matrix.pl --est_method RSEM --out_prefix Trinity_trans " . join (" " , @trans_rsem_files);
-
-&process_cmd($cmd,
- "Generating transcript (isoform) count matrix file."
- ) unless (-s "Trinity_trans.counts.matrix");
-
-
-# make the 'gene' matrix
-$cmd = "$BASEDIR/util/abundance_estimates_to_matrix.pl --est_method RSEM --out_prefix Trinity_genes " . join (" " , @genes_rsem_files);
-
-&process_cmd($cmd,
- "Generating Trinity component (gene) count matrix file"
- ) unless (-s "Trinity_genes.counts.matrix");
-
-
-################
-## run EdgeR
-################
+##################
+## run DE analysis
+##################
foreach my $target_type ("trans", "genes") {
- my $edgeR_dir = "edgeR_${target_type}";
+ my $edgeR_dir = "${DE_method}_${target_type}";
my $cmd = "$BASEDIR/Analysis/DifferentialExpression/run_DE_analysis.pl "
. " --matrix Trinity_${target_type}.counts.matrix "
- . " --method edgeR "
+ . " --method $DE_method "
. " --samples_file $read_samples_descr_file "
. " --output $edgeR_dir ";
diff --git a/util/run_Trinity_edgeR_pipeline.pl b/util/run_RSEM_from_samples_file.pl
similarity index 64%
copy from util/run_Trinity_edgeR_pipeline.pl
copy to util/run_RSEM_from_samples_file.pl
index 895c743..67d0ccd 100755
--- a/util/run_Trinity_edgeR_pipeline.pl
+++ b/util/run_RSEM_from_samples_file.pl
@@ -18,6 +18,8 @@ my $usage = <<__EOUSAGE__;
#
# Required:
#
+# --trinity_fasta <string> Trinity fasta file
+#
# --samples_file <string> tab-delimited text file indicating biological replicate relationships.
# ex.
# cond_A cond_A_rep1 A_rep1_left.fq A_rep1_right.fq
@@ -33,8 +35,6 @@ my $usage = <<__EOUSAGE__;
# --SS_lib_type=RF
#
#
-#
-#
# Optional:
#
# -I Interactive mode, waits between commands.
@@ -49,16 +49,21 @@ __EOUSAGE__
my $help_flag;
my $read_samples_descr_file;
my $PAUSE_EACH_STEP = 0;
-my $GENES_TOO = 0;
+my $trinity_fasta_file;
&GetOptions ( 'h' => \$help_flag,
+ 'trinity_fasta=s' => \$trinity_fasta_file,
'samples_file=s' => \$read_samples_descr_file,
'I' => \$PAUSE_EACH_STEP,
- 'genes_too' => \$GENES_TOO,
-
+
);
-if ($help_flag || ! $read_samples_descr_file) {
+
+if ($help_flag) {
+ die $usage;
+}
+
+unless ($trinity_fasta_file && $read_samples_descr_file) {
die $usage;
}
@@ -86,92 +91,6 @@ my %conditions_to_read_info = &parse_sample_descriptions($read_samples_descr_fil
my @conditions = sort keys %conditions_to_read_info;
-## first, gunzip the inputs as needed.
-
-my $reads_ALL_left_fq = "reads.ALL.left.fq";
-my $reads_ALL_right_fq = "reads.ALL.right.fq";
-
-my $REGENERATE_ALL_FQ = 1;
-if (-s $reads_ALL_left_fq && -s $reads_ALL_right_fq) {
- $REGENERATE_ALL_FQ = 0;
-}
-
-
-## concatenate all entries before running Trinity
-
-
-foreach my $condition (@conditions) {
-
- my $replicates_href = $conditions_to_read_info{$condition};
-
- my @replicates = keys %$replicates_href;
- foreach my $replicate (@replicates) {
- my ($left_fq_file, $right_fq_file) = @{$replicates_href->{$replicate}};
-
-
- if (-s "$left_fq_file.gz" && ! -s $left_fq_file) {
- &process_cmd("gunzip -c $left_fq_file.gz > $left_fq_file",
- "Uncompressing $left_fq_file.gz"
- );
- }
-
- if ($right_fq_file && -s "$right_fq_file.gz" && ! -s $right_fq_file) {
- &process_cmd("gunzip -c $right_fq_file.gz > $right_fq_file",
- "Uncompressiong $right_fq_file.gz");
- }
-
- if ($REGENERATE_ALL_FQ) {
-
- &process_cmd("cat $left_fq_file >> $reads_ALL_left_fq",
- "Concatenating left.fq files");
-
- &process_cmd("cat $right_fq_file >> $reads_ALL_right_fq",
- "Concatenating right.fq files"
- ) if $right_fq_file; ## only left if 'single'
-
- }
-
- }
-
-}
-
-unless (-s "trinity_out_dir/Trinity.fasta") {
-
- my $cmd;
-
- if (-s $reads_ALL_right_fq) {
- ## got pairs
-
- ## Run Trinity:
- $cmd = "$BASEDIR/Trinity --left $reads_ALL_left_fq --right $reads_ALL_right_fq ";
-
- }
- else {
- # run left as single
- $cmd = "$BASEDIR/Trinity --single $reads_ALL_left_fq ";
-
- }
-
- my @trinity_params = qw ( --seqType --max_memory --CPU --SS_lib_type --monitoring --no_reduce );
-
- my %trin_params = map { + $_ => 1 } @trinity_params;
-
- foreach my $param (keys %PARAMS) {
- if ($trin_params{$param}) {
- my $val = $PARAMS{$param};
- if (defined $val) {
- $cmd .= " $param $val ";
- }
- else {
- $cmd .= " $param ";
- }
- }
- }
-
- &process_cmd($cmd, "Running Trinity de novo transcriptome assembly");
-
-}
-
#############################################################
## Run RSEM, compute abundance estimates for each replicate.
#############################################################
@@ -192,7 +111,7 @@ foreach my $condition (@conditions) {
## run RSEM
my $seqType = $PARAMS{"--seqType"} or die "Error, --seqType not specified";
my $cmd = "$BASEDIR/util/align_and_estimate_abundance.pl "
- . " --transcripts trinity_out_dir/Trinity.fasta "
+ . " --transcripts $trinity_fasta_file "
. " --seqType $seqType "
. " --prep_reference "
. " --output_prefix $replicate "
@@ -228,11 +147,6 @@ foreach my $condition (@conditions) {
}
-if ($PARAMS{NO_RUN_DE}) {
- print STDERR "Stopping at abundance estimation.\n";
- exit(0);
-}
-
######################################
# Make count matrices for DE analysis
@@ -255,47 +169,6 @@ $cmd = "$BASEDIR/util/abundance_estimates_to_matrix.pl --est_method RSEM --out_p
-################
-## run EdgeR
-################
-
-foreach my $target_type ("trans", "genes") {
-
- my $edgeR_dir = "edgeR_${target_type}";
-
- my $cmd = "$BASEDIR/Analysis/DifferentialExpression/run_DE_analysis.pl "
- . " --matrix Trinity_${target_type}.counts.matrix "
- . " --method edgeR "
- . " --samples_file $read_samples_descr_file "
- . " --output $edgeR_dir ";
-
- &process_cmd($cmd, "Running edgeR for $target_type") unless (-d $edgeR_dir);
-
-
- chdir $edgeR_dir or die "Error, cannot cd to $edgeR_dir";
-
- ## extract the diff. expressed transcripts.
- $cmd = "$BASEDIR/Analysis/DifferentialExpression/analyze_diff_expr.pl "
- . " --matrix ../Trinity_${target_type}.TMM.fpkm.matrix --samples $read_samples_descr_file ";
-
-
- if (exists $PARAMS{"-P"}) {
- $cmd .= " -P " . $PARAMS{"-P"};
- }
- if (exists $PARAMS{"-C"}) {
- $cmd .= " -C " . $PARAMS{"-C"};
- }
-
- &process_cmd($cmd, "Running analysis of DE $target_type, hierarchically clustering transcripts and samples");
-
- chdir $workdir or die "Error, cannot cd back to $workdir";
-}
-
-
-print "Done.\n";
-
-
-
exit(0);
diff --git a/util/run_Trinity_edgeR_pipeline.pl b/util/run_Trinity_edgeR_pipeline.pl
index 895c743..b7a30de 100755
--- a/util/run_Trinity_edgeR_pipeline.pl
+++ b/util/run_Trinity_edgeR_pipeline.pl
@@ -196,6 +196,7 @@ foreach my $condition (@conditions) {
. " --seqType $seqType "
. " --prep_reference "
. " --output_prefix $replicate "
+ . " --output_dir . "
. " --aln_method bowtie --est_method RSEM "
. " --trinity_mode "
@@ -267,7 +268,8 @@ foreach my $target_type ("trans", "genes") {
. " --matrix Trinity_${target_type}.counts.matrix "
. " --method edgeR "
. " --samples_file $read_samples_descr_file "
- . " --output $edgeR_dir ";
+ . " --output $edgeR_dir "
+ . " --dispersion 0.1 "; # fixed dispersion only used when no bio reps exist
&process_cmd($cmd, "Running edgeR for $target_type") unless (-d $edgeR_dir);
@@ -276,7 +278,7 @@ foreach my $target_type ("trans", "genes") {
## extract the diff. expressed transcripts.
$cmd = "$BASEDIR/Analysis/DifferentialExpression/analyze_diff_expr.pl "
- . " --matrix ../Trinity_${target_type}.TMM.fpkm.matrix --samples $read_samples_descr_file ";
+ . " --matrix ../Trinity_${target_type}.TMM.EXPR.matrix --samples $read_samples_descr_file ";
if (exists $PARAMS{"-P"}) {
diff --git a/util/run_Trinity_edgeR_pipeline.pl b/util/run_Trinity_from_samples_file.pl
similarity index 63%
copy from util/run_Trinity_edgeR_pipeline.pl
copy to util/run_Trinity_from_samples_file.pl
index 895c743..3e048d2 100755
--- a/util/run_Trinity_edgeR_pipeline.pl
+++ b/util/run_Trinity_from_samples_file.pl
@@ -152,7 +152,20 @@ unless (-s "trinity_out_dir/Trinity.fasta") {
}
- my @trinity_params = qw ( --seqType --max_memory --CPU --SS_lib_type --monitoring --no_reduce );
+ my @trinity_params = qw (
+--seqType
+--max_memory
+--CPU
+--SS_lib_type
+--monitoring
+--trimmomatic
+--normalize_reads
+--jaccard_clip
+--full_cleanup
+--quality_trimming_params
+--grid_conf
+
+ );
my %trin_params = map { + $_ => 1 } @trinity_params;
@@ -171,135 +184,13 @@ unless (-s "trinity_out_dir/Trinity.fasta") {
&process_cmd($cmd, "Running Trinity de novo transcriptome assembly");
}
-
-#############################################################
-## Run RSEM, compute abundance estimates for each replicate.
-#############################################################
-
-
-
-my @trans_rsem_files;
-my @genes_rsem_files;
-
-foreach my $condition (@conditions) {
-
- my $replicates_href = $conditions_to_read_info{$condition};
-
- my @replicates = keys %$replicates_href;
- foreach my $replicate (@replicates) {
- my ($left_fq_file, $right_fq_file) = @{$replicates_href->{$replicate}};
-
- ## run RSEM
- my $seqType = $PARAMS{"--seqType"} or die "Error, --seqType not specified";
- my $cmd = "$BASEDIR/util/align_and_estimate_abundance.pl "
- . " --transcripts trinity_out_dir/Trinity.fasta "
- . " --seqType $seqType "
- . " --prep_reference "
- . " --output_prefix $replicate "
- . " --aln_method bowtie --est_method RSEM "
- . " --trinity_mode "
-
- ;
-
- if ($left_fq_file && $right_fq_file) {
- $cmd .= " --left $left_fq_file --right $right_fq_file ";
- }
- elsif ($left_fq_file) {
- $cmd .= " --single $left_fq_file ";
- }
- else {
- die "Error, no left or right read files";
- }
- if (my $SS_lib_type = $PARAMS{'--SS_lib_type'}) {
- $cmd .= " --SS_lib_type $SS_lib_type ";
- }
- if (my $cpu = $PARAMS{'--CPU'}) {
- $cmd .= " --thread_count $cpu ";
- }
-
- &process_cmd($cmd,
- "Running RSEM to perform abundance estimation on sample $replicate"
- ) unless (-s "$replicate.isoforms.results");
-
-
- push (@trans_rsem_files, "$replicate.isoforms.results");
- push (@genes_rsem_files, "$replicate.genes.results");
- }
-
-}
-
-if ($PARAMS{NO_RUN_DE}) {
- print STDERR "Stopping at abundance estimation.\n";
- exit(0);
-}
-
-
-######################################
-# Make count matrices for DE analysis
-######################################
-
-# make iso matrix
-my $cmd = "$BASEDIR/util/abundance_estimates_to_matrix.pl --est_method RSEM --out_prefix Trinity_trans " . join (" " , @trans_rsem_files);
-
-&process_cmd($cmd,
- "Generating transcript (isoform) count matrix file."
- ) unless (-s "Trinity_trans.counts.matrix");
-
-
-# make the 'gene' matrix
-$cmd = "$BASEDIR/util/abundance_estimates_to_matrix.pl --est_method RSEM --out_prefix Trinity_genes " . join (" " , @genes_rsem_files);
-
-&process_cmd($cmd,
- "Generating Trinity component (gene) count matrix file"
- ) unless (-s "Trinity_genes.counts.matrix");
-
-
-
-################
-## run EdgeR
-################
-
-foreach my $target_type ("trans", "genes") {
-
- my $edgeR_dir = "edgeR_${target_type}";
-
- my $cmd = "$BASEDIR/Analysis/DifferentialExpression/run_DE_analysis.pl "
- . " --matrix Trinity_${target_type}.counts.matrix "
- . " --method edgeR "
- . " --samples_file $read_samples_descr_file "
- . " --output $edgeR_dir ";
-
- &process_cmd($cmd, "Running edgeR for $target_type") unless (-d $edgeR_dir);
-
-
- chdir $edgeR_dir or die "Error, cannot cd to $edgeR_dir";
-
- ## extract the diff. expressed transcripts.
- $cmd = "$BASEDIR/Analysis/DifferentialExpression/analyze_diff_expr.pl "
- . " --matrix ../Trinity_${target_type}.TMM.fpkm.matrix --samples $read_samples_descr_file ";
-
-
- if (exists $PARAMS{"-P"}) {
- $cmd .= " -P " . $PARAMS{"-P"};
- }
- if (exists $PARAMS{"-C"}) {
- $cmd .= " -C " . $PARAMS{"-C"};
- }
-
- &process_cmd($cmd, "Running analysis of DE $target_type, hierarchically clustering transcripts and samples");
-
- chdir $workdir or die "Error, cannot cd back to $workdir";
-}
-
-
-print "Done.\n";
-
exit(0);
+
####
sub process_cmd {
my ($cmd, $msg) = @_;
diff --git a/util/support_scripts/partitioned_trinity_aggregator.pl b/util/support_scripts/GG_partitioned_trinity_aggregator.pl
similarity index 93%
copy from util/support_scripts/partitioned_trinity_aggregator.pl
copy to util/support_scripts/GG_partitioned_trinity_aggregator.pl
index 0fe7884..c0fccff 100755
--- a/util/support_scripts/partitioned_trinity_aggregator.pl
+++ b/util/support_scripts/GG_partitioned_trinity_aggregator.pl
@@ -23,7 +23,7 @@ while (<STDIN>) {
open (my $fh, $filename) or die "Error, cannot open file $filename";
while (<$fh>) {
if (/>/) {
- s/>/>$token$counter\|/;
+ s/>/>{$token}${counter}\_/;
}
print;
}
diff --git a/util/support_scripts/eXpress_trans_to_gene_results.pl b/util/support_scripts/eXpress_trans_to_gene_results.pl
index 607a115..5b250c1 100755
--- a/util/support_scripts/eXpress_trans_to_gene_results.pl
+++ b/util/support_scripts/eXpress_trans_to_gene_results.pl
@@ -52,7 +52,8 @@ main: {
my $length = $x[ $field_index{length} ];
my $eff_length = $x[ $field_index{eff_length} ];
my $eff_counts = $x[ $field_index{eff_counts} ];
-
+ my $tpm = $x[ $field_index{tpm} ];
+
my $gene = $trans_to_gene_info{$trans_id} or die "Error, cannot find gene identifier for transcript [$trans_id] ";
push (@{$gene_data{$gene}}, { trans_id => $trans_id,
@@ -60,7 +61,8 @@ main: {
length => $length,
eff_length => $eff_length,
eff_counts => $eff_counts,
- });
+ tpm => $tpm,
+ });
}
@@ -77,7 +79,8 @@ main: {
my @trans_ids;
my $sum_counts = 0;
my $sum_fpkm = 0;
-
+ my $sum_tpm = 0;
+
my $counts_per_len_sum = 0;
my $counts_per_eff_len_sum = 0;
@@ -85,16 +88,17 @@ main: {
my $sum_eff_lengths = 0;
my $num_trans = scalar(@trans_structs);
-
-
+
foreach my $struct (@trans_structs) {
#print Dumper($struct);
my $trans_id = $struct->{trans_id};
my $fpkm = $struct->{fpkm};
+ my $tpm = $struct->{tpm};
my $length = $struct->{length};
+
my $eff_length = $struct->{eff_length};
my $eff_counts = $struct->{eff_counts};
@@ -115,6 +119,8 @@ main: {
$sum_counts += $eff_counts;
$sum_fpkm += $fpkm;
+
+ $sum_tpm += $tpm;
}
my $gene_length = $sum_lengths / $num_trans;
@@ -136,7 +142,7 @@ main: {
length => sprintf("%.2f", $gene_length),
eff_length => sprintf("%.2f", $gene_eff_length),
eff_counts => sprintf("%.2f", $sum_counts),
-
+ tpm => $sum_tpm,
);
my @vals;
diff --git a/util/support_scripts/fastQ_to_tab.pl b/util/support_scripts/fastQ_to_tab.pl
index e28dd2d..6376cdd 100755
--- a/util/support_scripts/fastQ_to_tab.pl
+++ b/util/support_scripts/fastQ_to_tab.pl
@@ -43,8 +43,13 @@ unless ($inputFile) {
}
-
-open (my $fh, $inputFile) or die "Error, cannot open $inputFile";
+my $fh;
+if ($inputFile =~ /\.gz$/) {
+ open ($fh, "gunzip -c $inputFile | ") or die $!;
+}
+else {
+ open ($fh, $inputFile) or die "Error, cannot open $inputFile";
+}
my $counter = 0;
my $num_clean = 0;
@@ -81,6 +86,12 @@ while ($line) {
chomp $qual_header if $qual_header;
chomp $qual_line if $qual_line;
+
+ my @header_pts = split(/\s+/, $header);
+ if (scalar @header_pts > 1) {
+ $header = shift @header_pts;
+ }
+
if ($header && $seq && $qual_header && $qual_line &&
$qual_header =~ /^\+/ && length($seq) == length($qual_line)) {
diff --git a/util/support_scripts/eXpress_trans_to_gene_results.pl b/util/support_scripts/kallisto_trans_to_gene_results.pl
similarity index 78%
copy from util/support_scripts/eXpress_trans_to_gene_results.pl
copy to util/support_scripts/kallisto_trans_to_gene_results.pl
index 607a115..594bc06 100755
--- a/util/support_scripts/eXpress_trans_to_gene_results.pl
+++ b/util/support_scripts/kallisto_trans_to_gene_results.pl
@@ -4,9 +4,9 @@ use strict;
use warnings;
use Data::Dumper;
-my $usage = "\n\nusage: $0 results.xprs gene_to_trans_map_file.txt\n\n\n";
+my $usage = "\n\nusage: $0 abundance.tsv gene_to_trans_map_file.txt\n\n\n";
-my $results_xprs = $ARGV[0] or die $usage;
+my $abundance_tsv = $ARGV[0] or die $usage;
my $gene_to_trans_map_file = $ARGV[1] or die $usage;
@@ -28,14 +28,14 @@ main: {
}
- open (my $fh, $results_xprs) or die "Error, cannot open file $results_xprs";
+ open (my $fh, $abundance_tsv) or die "Error, cannot open file $abundance_tsv";
my $header = <$fh>;
chomp $header;
my %field_index;
my @fields = split(/\t/, $header);
{
- for (my $i = 1; $i <= $#fields; $i++) {
+ for (my $i = 0; $i <= $#fields; $i++) {
my $field = $fields[$i];
$field_index{$field} = $i;
}
@@ -48,18 +48,18 @@ main: {
my @x = split(/\t/);
my $trans_id = $x[ $field_index{target_id} ];
- my $fpkm = $x[ $field_index{fpkm} ];
+ my $tpm = $x[ $field_index{tpm} ];
my $length = $x[ $field_index{length} ];
my $eff_length = $x[ $field_index{eff_length} ];
- my $eff_counts = $x[ $field_index{eff_counts} ];
+ my $est_counts = $x[ $field_index{est_counts} ];
my $gene = $trans_to_gene_info{$trans_id} or die "Error, cannot find gene identifier for transcript [$trans_id] ";
push (@{$gene_data{$gene}}, { trans_id => $trans_id,
- fpkm => $fpkm,
+ tpm => $tpm,
length => $length,
eff_length => $eff_length,
- eff_counts => $eff_counts,
+ est_counts => $est_counts,
});
@@ -76,7 +76,7 @@ main: {
my @trans_ids;
my $sum_counts = 0;
- my $sum_fpkm = 0;
+ my $sum_tpm = 0;
my $counts_per_len_sum = 0;
my $counts_per_eff_len_sum = 0;
@@ -92,11 +92,11 @@ main: {
#print Dumper($struct);
my $trans_id = $struct->{trans_id};
- my $fpkm = $struct->{fpkm};
+ my $tpm = $struct->{tpm};
my $length = $struct->{length};
my $eff_length = $struct->{eff_length};
- my $eff_counts = $struct->{eff_counts};
+ my $est_counts = $struct->{est_counts};
unless ($eff_length > 0) {
$eff_length = 1; # cannot have zero length feature!
@@ -109,18 +109,18 @@ main: {
$sum_lengths += $length;
$sum_eff_lengths += $eff_length;
- $counts_per_len_sum += $eff_counts/$length;
+ $counts_per_len_sum += $est_counts/$length;
- $counts_per_eff_len_sum += $eff_counts/$eff_length;
+ $counts_per_eff_len_sum += $est_counts/$eff_length;
- $sum_counts += $eff_counts;
- $sum_fpkm += $fpkm;
+ $sum_counts += $est_counts;
+ $sum_tpm += $tpm;
}
my $gene_length = $sum_lengths / $num_trans;
my $gene_eff_length = $sum_eff_lengths / $num_trans;
if ($sum_counts) {
- # compute it based on the formula: FPKM_gene = FPKM_isoA + FPKM_IsoB + ...
+ # set lengths as weighted by expression of isoforms.
eval {
$gene_length = $sum_counts / $counts_per_len_sum;
$gene_eff_length = $sum_counts / $counts_per_eff_len_sum;
@@ -132,10 +132,10 @@ main: {
}
my %gene_info = ( target_id => $gene,
- fpkm => sprintf("%.2f", $sum_fpkm),
+ tpm => sprintf("%.2f", $sum_tpm),
length => sprintf("%.2f", $gene_length),
eff_length => sprintf("%.2f", $gene_eff_length),
- eff_counts => sprintf("%.2f", $sum_counts),
+ est_counts => sprintf("%.2f", $sum_counts),
);
diff --git a/util/support_scripts/merge_left_right_nameSorted_SAMs.pl b/util/support_scripts/merge_left_right_nameSorted_SAMs.pl
index d9a996e..1dda428 100755
--- a/util/support_scripts/merge_left_right_nameSorted_SAMs.pl
+++ b/util/support_scripts/merge_left_right_nameSorted_SAMs.pl
@@ -305,7 +305,7 @@ sub identify_mapped_pairs_single_scaffold {
&&
- abs ($left_entry->get_aligned_position() - $right_entry->get_aligned_position()) <= $max_dist_between_pairs
+ abs ($left_entry->get_aligned_start_position() - $right_entry->get_aligned_start_position()) <= $max_dist_between_pairs
) {
@@ -313,14 +313,14 @@ sub identify_mapped_pairs_single_scaffold {
if ( ($left_entry->get_query_strand eq '+'
&&
- $left_entry->get_aligned_position() < $right_entry->get_aligned_position()
+ $left_entry->get_aligned_start_position() < $right_entry->get_aligned_start_position()
)
||
($left_entry->get_query_strand eq '-'
&&
- $left_entry->get_aligned_position() > $right_entry->get_aligned_position() )
+ $left_entry->get_aligned_start_position() > $right_entry->get_aligned_start_position() )
)
{
diff --git a/util/support_scripts/partitioned_trinity_aggregator.pl b/util/support_scripts/partitioned_trinity_aggregator.pl
index 0fe7884..215fb5a 100755
--- a/util/support_scripts/partitioned_trinity_aggregator.pl
+++ b/util/support_scripts/partitioned_trinity_aggregator.pl
@@ -8,9 +8,6 @@ my $usage = "usage: $0 token < trinity_fasta_files_listing\n\n";
my $token = $ARGV[0] or die $usage;
-
-my $counter = 0;
-
while (<STDIN>) {
my $filename = $_;
chomp $filename;
@@ -19,11 +16,16 @@ while (<STDIN>) {
next;
}
if (-s $filename) {
- $counter++;
+
+ # ie. read_partitions/Fb_0/CBin_161/c16167.trinity.reads.fa
+
+ $filename =~ m|c(\d+)\.trinity\.reads| or die "Error, cannot parse Trinity component value from filename: $filename";
+ my $component = $1;
+
open (my $fh, $filename) or die "Error, cannot open file $filename";
while (<$fh>) {
if (/>/) {
- s/>/>$token$counter\|/;
+ s/>/>${token}${component}\_/;
}
print;
}
diff --git a/util/support_scripts/plugin_install_tests.sh b/util/support_scripts/plugin_install_tests.sh
index 0b650ac..990f7a5 100644
--- a/util/support_scripts/plugin_install_tests.sh
+++ b/util/support_scripts/plugin_install_tests.sh
@@ -15,10 +15,3 @@ then
else
echo "collectl Installation appears to have FAILED"
fi
-if [ -e "trinity-plugins/rsem/rsem-calculate-expression" ]
-then
- echo "rsem: has been Installed Properly"
-else
- echo "rsem: Installation appears to have FAILED"
-fi
-
diff --git a/util/support_scripts/run_TMM_scale_matrix.pl b/util/support_scripts/run_TMM_scale_matrix.pl
index 0de4694..58103ab 100755
--- a/util/support_scripts/run_TMM_scale_matrix.pl
+++ b/util/support_scripts/run_TMM_scale_matrix.pl
@@ -72,6 +72,7 @@ sub run_TMM {
print $ofh "library(edgeR)\n\n";
print $ofh "rnaseqMatrix = read.table(\"$counts_matrix_file\", header=T, row.names=1, com='', check.names=F)\n";
+ print $ofh "rnaseqMatrix = as.matrix(rnaseqMatrix)\n";
print $ofh "rnaseqMatrix = round(rnaseqMatrix)\n";
print $ofh "exp_study = DGEList(counts=rnaseqMatrix, group=factor(colnames(rnaseqMatrix)))\n";
print $ofh "exp_study = calcNormFactors(exp_study)\n";
diff --git a/util/support_scripts/tests.py b/util/support_scripts/tests/test.py
old mode 100644
new mode 100755
similarity index 80%
copy from util/support_scripts/tests.py
copy to util/support_scripts/tests/test.py
index 8bb17d3..06fbb6b
--- a/util/support_scripts/tests.py
+++ b/util/support_scripts/tests/test.py
@@ -4,7 +4,7 @@ import unittest
import shutil
import os
import time
-
+# dfsfd
# Prereqs:
# module load bowtie/0.12.8
# module load java
@@ -13,7 +13,7 @@ import time
# Copy the .gz files in sample_data/test_Trinity_Assembly to current directory
# Run using nosetests
MEM_FLAG = "--max_memory 2G"
-TEMP_FILES = ['both.fa', 'inchworm.K25.L25.fa', 'jellyfish.kmers.fa', 'scaffolding_entries.sam']
+TEMP_FILES = ['both.fa', 'inchworm.K25.L25.fa', 'jellyfish.kmers.fa']
class TestTrinity(unittest.TestCase):
@@ -34,7 +34,7 @@ class TestTrinity(unittest.TestCase):
handle = open("trinity_out_dir/Trinity.fasta", "rU")
seq_count = len([x for x in SeqIO.parse(handle, "fasta")])
handle.close()
- self.assertTrue(75 <= seq_count <= 90, msg='Found %s sequences' % seq_count)
+ self.assertTrue(75 <= seq_count <= 100, msg='Found %s sequences' % seq_count)
def test_sample_data_trimmed_and_normalized(self):
self.trinity(
@@ -87,7 +87,7 @@ class TestTrinity(unittest.TestCase):
self.trinity("Trinity %s --seqType fq --single reads.left.fq --SS_lib_type F --no_distributed_trinity_exec" % MEM_FLAG)
self.assertTrue(os.path.isfile("trinity_out_dir/inchworm.K25.L25.fa.finished"),
msg="Inchworm did not appear to run with no_distributed_trinity_exec flag")
- self.assertTrue(os.path.isfile("trinity_out_dir/jellyfish.1.finished"),
+ self.assertTrue(os.path.isfile("trinity_out_dir/jellyfish.kmers.fa.histo"),
msg="Jellyfish did not appear to run with no_distributed_trinity_exec flag")
self.assertFalse(os.path.isfile("trinity_out_dir/Trinity.fasta"),
msg="Trinity.fasta created with no_distributed_trinity_exec")
@@ -102,6 +102,33 @@ class TestTrinity(unittest.TestCase):
self.assertTrue(os.path.exists("trinity_test"), msg="Changed output directory but it was not created")
shutil.rmtree('trinity_test', True)
+ def test_scaffold_iworm_contigs(self):
+ os.environ['LD_LIBRARY_PATH'] = os.environ['LD_LIBRARY_PATH'] + ':../src/trinity-plugins/htslib'
+ exe = "../src/trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs"
+ bamfile = "iworm.bowtie.nameSorted.bam"
+ ifile = "inchworm.K25.L25.fa"
+ f = subprocess.check_output([exe, bamfile, ifile]).split('\n')
+ expected_result = [['a340;25', '339', 'a9;40', '8', '41'],
+ ['a719;8', '718', 'a832;15', '831', '33'],
+ ['a1;43', '0', 'a346;23', '345', '31'],
+ ['a346;23', '345', 'a9;40', '8', '26'],
+ ['a339;142', '338', 'a37;14', '36', '25'],
+ ['a3;61', '2', 'a432;9', '431', '23'],
+ ['a345;34', '344', 'a40;12', '39', '21'],
+ ['a354;96', '353', 'a368;13', '367', '18'],
+ ['a689;4', '688', 'a774;6', '773', '13']]
+
+ actual_result = [line.split('\t') for line in f if line]
+ self.assertEquals(expected_result, actual_result[0:9])
+ actual_lengths = [int(s[4].strip()) for s in actual_result]
+ expected_order = list(reversed(sorted(actual_lengths)))
+ self.assertEquals(expected_order, actual_lengths)
+
+ def test_Inchworm_handles_compressed_files(self):
+ self.trinity('Trinity %s --seqType fq --single reads.left.fq.gz --SS_lib_type F --no_run_chrysalis' % MEM_FLAG);
+ num_lines = sum(1 for line in open('trinity_out_dir/inchworm.K25.L25.fa'))
+ self.assertTrue(2875 <= num_lines <= 3100, msg='Found %s lines' % num_lines)
+
### information tests
def test_cite(self):
expected = '\n\n* Trinity:\nFull-length transcriptome assembly from RNA-Seq data without a reference genome.\nGrabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L,\nRaychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F,\nBirren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A.\nNature Biotechnology 29, 644\xe2\x80\x93652 (2011)\nPaper: http://www.nature.com/nbt/journal/v29/n7/full/nbt.1883.html\nCode: http://trinityrna [...]
@@ -113,9 +140,8 @@ class TestTrinity(unittest.TestCase):
subprocess.check_output(["Trinity", "--version"])
self.fail("Version returned 0 errorcode!")
except subprocess.CalledProcessError as e:
- #self.assertEqual('Trinity version: BLEEDING_EDGE\n', e.output)
- #self.assertEqual('Trinity version: trinityrnaseq_r20140717\n', e.output)
- self.assertEqual('Trinity version: Trinity_v2.0.2\n', e.output)
+ self.assertTrue('Trinity version: __TRINITY_VERSION_TAG__' in e.output)
+ self.assertTrue('using Trinity devel version. Note, latest production release is: v2.0.6' in e.output)
def test_show_full_usage_info(self):
@@ -135,7 +161,7 @@ class TestTrinity(unittest.TestCase):
def test_invalid_option_error(self):
error = self.get_error("Trinity --squidward")
- self.assertTrue("Error, do not understand options: --squidward" in error)
+ self.assertTrue("ERROR, don't recognize parameter: --squidward" in error)
def test_set_no_cleanup_and_full_cleanup_error(self):
error = self.get_error("Trinity --no_cleanup --full_cleanup")
diff --git a/util/support_scripts/tests/test_prep.py b/util/support_scripts/tests/test_prep.py
new file mode 100644
index 0000000..261ca09
--- /dev/null
+++ b/util/support_scripts/tests/test_prep.py
@@ -0,0 +1,122 @@
+import unittest
+import shutil
+import os
+import subprocess
+from Bio import SeqIO
+
+# single, leftright
+# fasta, fastq
+# one file, two files
+# forward, reverse
+# clear, gzip, bzip
+
+
+class TestTrinity(unittest.TestCase):
+
+ @classmethod
+ def setUpClass(cls):
+ try:
+ os.remove('coverage.log')
+ except:
+ pass
+
+ def tearDown(self):
+ shutil.rmtree('trinity_out_dir', True)
+ #pass
+
+ def test_fastq(self):
+ self.trinity("left1.fq", "fq")
+ self.assertEquals(30575, self.count_seqs())
+
+ def test_fastq_gz(self):
+ self.trinity("left1.fq.gz", "fq")
+ self.assertEquals(30575, self.count_seqs())
+
+ def test_fastq_bz2(self):
+ self.trinity("left1.fq.bz2", "fq")
+ self.assertEquals(30575, self.count_seqs())
+
+ def test_fastq_multiple_files_single(self):
+ self.trinity("left1.fq,left1.fq.gz", "fq")
+ self.assertEquals(61150, self.count_seqs())
+
+ def test_fastq_multiple_files_single_bz2(self):
+ self.trinity("left1.fq.bz2,left1.fq.gz", "fq")
+ self.assertEquals(61150, self.count_seqs())
+
+ def test_fastq_multiple_files_single_reverse(self):
+ self.trinity("left1.fq,left1.fq.gz", "fq", True)
+ self.assertEquals(61150, self.count_seqs())
+
+ def test_fasta(self):
+ self.trinity("left1.fa")
+ self.assertEquals(30575, self.count_seqs())
+
+ def test_fasta_gz(self):
+ self.trinity("left1.fa.gz")
+ self.assertEquals(30575, self.count_seqs())
+
+ def test_fasta_multiple_files_single(self):
+ self.trinity("left1.fa,left1.fa.gz")
+ self.assertEquals(61150, self.count_seqs())
+
+ def test_fasta_multiple_files_single_reverse(self):
+ self.trinity("left1.fa,left1.fa.gz", reverse=True)
+ self.assertEquals(61150, self.count_seqs())
+
+ def test_paired_fastq(self):
+ self.trinity("left1.fq", "fq", morefiles="right1.fq")
+ self.assertEquals(61150, self.count_seqs())
+
+ def test_paired_fastq_gz(self):
+ self.trinity("left1.fq.gz", "fq", morefiles="right1.fq.gz")
+ self.assertEquals(61150, self.count_seqs())
+
+ def test_fastq_multiple_files_paired(self):
+ self.trinity("left1.fq,left1.fq.gz", "fq", morefiles="right1.fq,right1.fq.gz")
+ self.assertEquals(122300, self.count_seqs())
+
+ def test_fastq_multiple_files_paired_reverse(self):
+ self.trinity("left1.fq,left1.fq.gz", "fq", reverse=True, morefiles="right1.fq,right1.fq.gz")
+ self.assertEquals(122300, self.count_seqs())
+
+ def test_fasta_paired(self):
+ self.trinity("left1.fa", morefiles="right1.fa")
+ self.assertEquals(61150, self.count_seqs())
+
+ def test_fasta_gz_paired(self):
+ self.trinity("left1.fa.gz", morefiles="right1.fa.gz")
+ self.assertEquals(61150, self.count_seqs())
+
+ def test_fasta_multiple_files_paired(self):
+ self.trinity("left1.fa,left1.fa.gz", morefiles="right1.fa,right1.fa.gz")
+ self.assertEquals(61150, self.count_seqs())
+
+ def test_fasta_multiple_files_paired(self):
+ self.trinity("left1.fa,left1.fa.gz", morefiles="right1.fa,right1.fa.gz", reverse=True)
+ self.assertEquals(122300, self.count_seqs())
+
+ def trinity(self, files, seqtype='fa', reverse=False, morefiles=None):
+ if morefiles:
+ tpl = "Trinity --left %s --right %s --prep --seqType %s --max_memory 2G --no_version_check"
+ cmdline = tpl % (files, morefiles, seqtype)
+ else:
+ tpl = "Trinity --single %s --prep --seqType %s --max_memory 2G --no_version_check"
+ cmdline = tpl % (files, seqtype)
+ if reverse:
+ cmdline += " --SS_lib_type " + ('RF' if morefiles else 'R')
+ print cmdline
+ with open("coverage.log", 'a') as file_out:
+ subprocess.call(cmdline,shell=True, stdout=file_out)
+
+ def count_seqs(self):
+ f = "trinity_out_dir/single.fa"
+ if os.path.isfile(f):
+ handle = open(f, "rU")
+ else:
+ handle = open("trinity_out_dir/both.fa", "rU")
+
+ seq_count = len([x for x in SeqIO.parse(handle, "fasta")])
+ handle.close()
+ return seq_count
+
diff --git a/util/support_scripts/tests.py b/util/support_scripts/tests/tests.py
similarity index 81%
rename from util/support_scripts/tests.py
rename to util/support_scripts/tests/tests.py
index 8bb17d3..2137524 100644
--- a/util/support_scripts/tests.py
+++ b/util/support_scripts/tests/tests.py
@@ -13,7 +13,7 @@ import time
# Copy the .gz files in sample_data/test_Trinity_Assembly to current directory
# Run using nosetests
MEM_FLAG = "--max_memory 2G"
-TEMP_FILES = ['both.fa', 'inchworm.K25.L25.fa', 'jellyfish.kmers.fa', 'scaffolding_entries.sam']
+TEMP_FILES = ['both.fa', 'inchworm.K25.L25.fa', 'jellyfish.kmers.fa']
class TestTrinity(unittest.TestCase):
@@ -34,7 +34,7 @@ class TestTrinity(unittest.TestCase):
handle = open("trinity_out_dir/Trinity.fasta", "rU")
seq_count = len([x for x in SeqIO.parse(handle, "fasta")])
handle.close()
- self.assertTrue(75 <= seq_count <= 90, msg='Found %s sequences' % seq_count)
+ self.assertTrue(75 <= seq_count <= 100, msg='Found %s sequences' % seq_count)
def test_sample_data_trimmed_and_normalized(self):
self.trinity(
@@ -87,7 +87,7 @@ class TestTrinity(unittest.TestCase):
self.trinity("Trinity %s --seqType fq --single reads.left.fq --SS_lib_type F --no_distributed_trinity_exec" % MEM_FLAG)
self.assertTrue(os.path.isfile("trinity_out_dir/inchworm.K25.L25.fa.finished"),
msg="Inchworm did not appear to run with no_distributed_trinity_exec flag")
- self.assertTrue(os.path.isfile("trinity_out_dir/jellyfish.1.finished"),
+ self.assertTrue(os.path.isfile("trinity_out_dir/jellyfish.kmers.fa.histo"),
msg="Jellyfish did not appear to run with no_distributed_trinity_exec flag")
self.assertFalse(os.path.isfile("trinity_out_dir/Trinity.fasta"),
msg="Trinity.fasta created with no_distributed_trinity_exec")
@@ -102,6 +102,33 @@ class TestTrinity(unittest.TestCase):
self.assertTrue(os.path.exists("trinity_test"), msg="Changed output directory but it was not created")
shutil.rmtree('trinity_test', True)
+ def test_scaffold_iworm_contigs(self):
+ os.environ['LD_LIBRARY_PATH'] = os.environ['LD_LIBRARY_PATH'] + ':../src/trinity-plugins/htslib'
+ exe = "../src/trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs"
+ bamfile = "iworm.bowtie.nameSorted.bam"
+ ifile = "inchworm.K25.L25.fa"
+ f = subprocess.check_output([exe, bamfile, ifile]).split('\n')
+ expected_result = [['a340;25', '339', 'a9;40', '8', '41'],
+ ['a719;8', '718', 'a832;15', '831', '33'],
+ ['a1;43', '0', 'a346;23', '345', '31'],
+ ['a346;23', '345', 'a9;40', '8', '26'],
+ ['a339;142', '338', 'a37;14', '36', '25'],
+ ['a3;61', '2', 'a432;9', '431', '23'],
+ ['a345;34', '344', 'a40;12', '39', '21'],
+ ['a354;96', '353', 'a368;13', '367', '18'],
+ ['a689;4', '688', 'a774;6', '773', '13']]
+
+ actual_result = [line.split('\t') for line in f if line]
+ self.assertEquals(expected_result, actual_result[0:9])
+ actual_lengths = [int(s[4].strip()) for s in actual_result]
+ expected_order = list(reversed(sorted(actual_lengths)))
+ self.assertEquals(expected_order, actual_lengths)
+
+ def test_Inchworm_handles_compressed_files(self):
+ self.trinity('Trinity %s --seqType fq --single reads.left.fq.gz --SS_lib_type F --no_run_chrysalis' % MEM_FLAG);
+ num_lines = sum(1 for line in open('trinity_out_dir/inchworm.K25.L25.fa'))
+ self.assertTrue(2900 <= num_lines <= 3100, msg='Found %s lines' % num_lines)
+
### information tests
def test_cite(self):
expected = '\n\n* Trinity:\nFull-length transcriptome assembly from RNA-Seq data without a reference genome.\nGrabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L,\nRaychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F,\nBirren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A.\nNature Biotechnology 29, 644\xe2\x80\x93652 (2011)\nPaper: http://www.nature.com/nbt/journal/v29/n7/full/nbt.1883.html\nCode: http://trinityrna [...]
@@ -113,9 +140,8 @@ class TestTrinity(unittest.TestCase):
subprocess.check_output(["Trinity", "--version"])
self.fail("Version returned 0 errorcode!")
except subprocess.CalledProcessError as e:
- #self.assertEqual('Trinity version: BLEEDING_EDGE\n', e.output)
- #self.assertEqual('Trinity version: trinityrnaseq_r20140717\n', e.output)
- self.assertEqual('Trinity version: Trinity_v2.0.2\n', e.output)
+ self.assertTrue('Trinity version: __TRINITY_VERSION_TAG__' in e.output)
+ self.assertTrue('using Trinity devel version. Note, latest production release is: v2.0.6' in e.output)
def test_show_full_usage_info(self):
diff --git a/util/support_scripts/trinity_install_tests.sh b/util/support_scripts/trinity_install_tests.sh
index 9c2de48..7d4e6a8 100644
--- a/util/support_scripts/trinity_install_tests.sh
+++ b/util/support_scripts/trinity_install_tests.sh
@@ -59,3 +59,9 @@ else
echo "parafly Installation appears to have FAILED"
fi
+if [ -e "trinity-plugins/BIN/samtools" ]
+then
+ echo "samtools-0.1.19 has been Installed Properly"
+else
+ echo "samtools-0.1.19 Installation appears to have FAILED"
+fi
diff --git a/util/support_scripts/GG_write_trinity_cmds.pl b/util/support_scripts/write_partitioned_trinity_cmds.pl
similarity index 100%
rename from util/support_scripts/GG_write_trinity_cmds.pl
rename to util/support_scripts/write_partitioned_trinity_cmds.pl
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