[med-svn] [augustus] 02/02: add more man pages
Sascha Steinbiss
sascha at steinbiss.name
Thu Mar 24 11:26:47 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository augustus.
commit 301638349f73a696d3fa181efbe322e628d21b3d
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Thu Mar 24 11:26:32 2016 +0000
add more man pages
---
debian/mansrc/checkTargetSortedness.1.adoc | 23 ++++++++
debian/mansrc/curve2hints.1.adoc | 47 ++++++++++++++++
debian/mansrc/filterBam.1.adoc | 87 ++++++++++++++++++++++++++++++
debian/mansrc/homGeneMapping.1.adoc | 81 ++++++++++++++++++++++++++++
4 files changed, 238 insertions(+)
diff --git a/debian/mansrc/checkTargetSortedness.1.adoc b/debian/mansrc/checkTargetSortedness.1.adoc
new file mode 100644
index 0000000..5f83131
--- /dev/null
+++ b/debian/mansrc/checkTargetSortedness.1.adoc
@@ -0,0 +1,23 @@
+# checkTargetSortedness(1)
+
+## NAME
+
+checkTargetSortedness - check BAM file for sortedness
+
+## SYNOPSIS
+
+*checkTargetSortedness* infile.bam
+
+## OPTIONS
+
+'infile.bam' is the name of the BAM file to check for sortedness. The program will output a
+short messsage describing the sortedness status of the file.
+
+## AUTHORS
+
+AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
+
+## ADDITIONAL DOCUMENTATION
+
+An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.
+
diff --git a/debian/mansrc/curve2hints.1.adoc b/debian/mansrc/curve2hints.1.adoc
new file mode 100644
index 0000000..22bee26
--- /dev/null
+++ b/debian/mansrc/curve2hints.1.adoc
@@ -0,0 +1,47 @@
+# curve2hints(1)
+
+## NAME
+
+curve2hints - tool to make exon segmentation and grouping the exons together to form AUGUSTUS hints
+
+## SYNOPSIS
+
+*curve2hints* --in=file --outexons=out.gff --c=int --s=float
+
+## OPTIONS
+
+*--in=s*::
+ iput file is single file containing tracks in wig format
+
+*--outexons=s*::
+ file for the output segmentaion
+
+*--c*::
+ specify the threshold to distinguish between introns and exons in terms of coverage depths (default 4)
+
+*--s*::
+ specify the ratio *(1-lambda1)/(1-lambda2)* It should be >1 (default 1.12)
+
+*--z*::
+ specify the chunk size (default value 50000)
+
+*--r*::
+ To enable re-estimation of distribution from the output produced
+
+*--train_file*::
+ Specify the gff file to be used for training the distributions.It should contain the position of both introns and exons
+
+*--bed_file*::
+ Specify the output bedfile which contains the position of gene jumps (default: output.bed)
+
+*--augustus_hints*::
+ Specify the output augustus hint file(default: augustus_hints.gff)
+
+## AUTHORS
+
+AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
+
+## ADDITIONAL DOCUMENTATION
+
+An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.
+
diff --git a/debian/mansrc/filterBam.1.adoc b/debian/mansrc/filterBam.1.adoc
new file mode 100644
index 0000000..e3091c4
--- /dev/null
+++ b/debian/mansrc/filterBam.1.adoc
@@ -0,0 +1,87 @@
+# filterBam(1)
+
+## NAME
+
+filterBam - filter BAM file for use with AUGUSTUS tools
+
+## SYNOPSIS
+
+*filterBam* --in in.bam --out out.bam [options]
+
+## DESCRIPTION
+
+The input file must be sorted lexicographically by 'queryname', with e.g.
+
+ - *sort -k 1,1* [be aware: 'export LC_ALL=C' might be used because sort ignores characters like ':']
+ Also, please bear in mind that this will require converting your BAM file into SAM.
+
+ - *samtools* and *bamtools* provide facilities to do the sorting,
+ but they are not guaranteed to work because of the problem mentioned above.
+
+ - In the case of *samtools*, the command is: 'samtools sort [-n] file.bam'.
+ The option [-n] should sort by query name, just as 'sort -k 10,10' would do in a PSL file.
+ Without options, the sorting will be done by reference name and target coordinate, just as a 'sort -n -k 16,16 | sort -k 14,14' would do with PSL.
+ For more information check the man page included in samtools distribution.
+
+ - bamtools can also sort bam files: *bamtools sort -queryname -in file.bam*,
+ but only provides the option to do it by queryname.
+
+If the option 'paired' is used, then alignment names must include suffixes /1,/2 or /f,/r.
+
+## OPTIONS
+
+*--best*::
+ output all best matches that satisfy minId and minCover (default 0)
+
+*--noIntrons*::
+ do not allow longer gaps -for RNA-RNA alignments- (default 0)
+
+*--paired*::
+ require that paired reads are on opposite strands of same target
+ (default 0). NOTE: see prerequisite section above.
+
+*--uniq*::
+ take only best match, iff, second best is much worse (default 0)
+
+*--verbose*::
+ output debugging info (default 0)
+
+*--insertLimit n*::
+ maximum assumed size of inserts (default 10)
+
+*--maxIntronLen n*::
+ maximal separation of paired reads (default 500000)
+
+*--maxSortesTest n*::
+ maximal sortedness (default 100000)
+
+*--minCover n*::
+ minimal percentage of coverage of the query read (default 80)
+
+*--minId n*::
+ minimal percentage of identity (default 92)
+
+*--minIntronLen n*::
+ minimal intron length (default 35)
+
+*--uniqThresh n*::
+ threshold % for uniq, second best must be at most this fraction of best (default 0.96)
+
+*--commonGeneFile s*::
+ file name in which to write cases where one read maps several different genes
+
+*--pairBedFile s*::
+ file name of pairedness coverage: a BED format file in which for each position the number of
+ filtered read pairs is reported that contain the position in
+ or between the reads
+
+*--pairwiseAlignments*::
+ use in case alignments were done in pairwise fashion (default: 0)
+
+## AUTHORS
+
+AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
+
+## ADDITIONAL DOCUMENTATION
+
+An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.
diff --git a/debian/mansrc/homGeneMapping.1.adoc b/debian/mansrc/homGeneMapping.1.adoc
new file mode 100644
index 0000000..15a5669
--- /dev/null
+++ b/debian/mansrc/homGeneMapping.1.adoc
@@ -0,0 +1,81 @@
+# homGeneMapping(1)
+
+## NAME
+
+homGeneMapping - create summary of gene homology
+
+## SYNOPSIS
+
+*homGeneMapping* [options] --gtfs=gffilenames.tbl --halfile=aln.hal
+
+## DESCRIPTION
+
+*homGeneMapping* takes a set of gene predictions of different genomes and a hal
+alignment of the genomes and prints a summary for each gene, e.g.
+
+ - how many of its exons/introns are in agreement with genes of other genomes
+ - how many of its exons/introns are supported by extrinsic evidence from any of the genomes
+ - a list of geneids of homologous genes
+
+## OPTIONS
+
+### Mandatory parameters
+
+*--halfile=aln.hal*::
+ input hal file
+
+*--gtfs=gtffilenames.tbl*::
+ a text file containing the locations of the input gene files
+ and optionally the hints files (both in GTF format).
+ The file is formatted as follows:
+
+ name_of_genome_1 path/to/genefile/of/genome_1 path/to/hintsfile/of/genome_1
+ name_of_genome_2 path/to/genefile/of/genome_2 path/to/hintsfile/of/genome_2
+ ...
+ name_of_genome_N path/to/genefile/of/genome_N path/to/hintsfile/of/genome_N
+
+### Additional options
+
+*--cpus=N*::
+ N is the number of CPUs to use (default: 1)
+
+*--noDupes*::
+ do not map between duplications in hal graph. (default: off)
+
+*--halLiftover_exec_dir=DIR*::
+ Directory that contains the executable halLiftover
+ If not specified it must be in $PATH environment variable.
+
+*--tmpdir=DIR*::
+ a temporary file directory that stores lifted over files. (default 'tmp/' in current directory)
+
+*--outdir=DIR*::
+ file direcory that stores output gene files. (default: current directory)
+
+*--printHomologs=FILE*::
+ prints disjunct sets of homologous transcripts to FILE, e.g.
+
+ # 0 dana
+ # 1 dere
+ # 2 dgri
+ # 3 dmel
+ # 4 dmoj
+ # 5 dper
+ (0, jg4139.t1) (0, jg4140.t1) (1, jg7797.t1) (2, jg3247.t1) (4, jg6720.t1) (5, jg313.t1)
+ (1, jg14269.t1) (3, jg89.t1) (5, jg290.t1)
+ ...
+ Two transcripts are in the same set, if all their exons/introns are homologs and their are
+ no additional exons/introns.
+ This option requires the Boost C++ Library
+
+## EXAMPLE
+
+homGeneMapping --noDupes --halLiftover_exec_dir=~/tools/progressiveCactus/submodules/hal/bin --gtfs=gtffilenames.tbl --halfile=msca.hal
+
+## AUTHORS
+
+AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
+
+## ADDITIONAL DOCUMENTATION
+
+An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.
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