[med-svn] [Git][med-team/spades][master] Lots of more python to python3 conversions
Andreas Tille
gitlab at salsa.debian.org
Mon Nov 18 13:21:56 GMT 2019
Andreas Tille pushed to branch master at Debian Med / spades
Commits:
2dd0d58b by Andreas Tille at 2019-11-18T13:21:18Z
Lots of more python to python3 conversions
- - - - -
2 changed files:
- debian/patches/python3.patch
- debian/patches/yaml_load.patch
Changes:
=====================================
debian/patches/python3.patch
=====================================
@@ -58,6 +58,18 @@ Description: Make sure Python3 interpreter is used in scripts
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
+@@ -52,9 +52,9 @@ def reads_line(libs):
+ def command_line(barcode, output_dir, params, continue_launch):
+ # logfile = os.path.join(output_dir, "logs", barcode.id + ".out")
+ if continue_launch and os.path.exists(os.path.join(output_dir, barcode.id, "params.txt")):
+- result = ["python " + os.path.join(spades_home, "spades.py"), "--truseq", "-o", os.path.join(output_dir, barcode.id), "--continue", params]
++ result = ["python3 " + os.path.join(spades_home, "spades.py"), "--truseq", "-o", os.path.join(output_dir, barcode.id), "--continue", params]
+ else:
+- result = ["python " + os.path.join(spades_home, "spades.py"), "--truseq", "-t", "1", "-o", os.path.join(output_dir, barcode.id), reads_line(barcode.libs), params]
++ result = ["python3 " + os.path.join(spades_home, "spades.py"), "--truseq", "-t", "1", "-o", os.path.join(output_dir, barcode.id), reads_line(barcode.libs), params]
+ # result = ["./truspades.py", "-o", os.path.join(output_dir, barcode.id), reads_line(barcode.libs), " ".join(params), "\n"]
+ return " ".join(result)
+
--- a/assembler/src/projects/mts/scripts/bin_profiles.py
+++ b/assembler/src/projects/mts/scripts/bin_profiles.py
@@ -1,4 +1,4 @@
@@ -212,6 +224,24 @@ Description: Make sure Python3 interpreter is used in scripts
'''
A simple Python wrapper for the bh_tsne binary that makes it easier to use it
+@@ -15,7 +15,7 @@ Example:
+
+ The output will not be normalised, maybe the below one-liner is of interest?:
+
+- python -c 'import numpy; from sys import stdin, stdout;
++ python3 -c 'import numpy; from sys import stdin, stdout;
+ d = numpy.loadtxt(stdin); d -= d.min(axis=0); d /= d.max(axis=0);
+ numpy.savetxt(stdout, d, fmt="%.8f", delimiter="\t")'
+
+@@ -207,7 +207,7 @@ def run_bh_tsne(data, no_dims=2, perplex
+ try:
+ os.waitpid(child_pid, 0)
+ except KeyboardInterrupt:
+- print("Please run this program directly from python and not from ipython or jupyter.")
++ print("Please run this program directly from python3 and not from ipython3 or jupyter.")
+ print("This is an issue due to asynchronous error handling.")
+
+ res = []
--- a/assembler/src/projects/mts/scripts/choose_bins.py
+++ b/assembler/src/projects/mts/scripts/choose_bins.py
@@ -1,5 +1,4 @@
@@ -354,3 +384,789 @@ Description: Make sure Python3 interpreter is used in scripts
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/spades_pipeline/corrector_logic.py
++++ b/assembler/src/spades_pipeline/corrector_logic.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python -O
++#!/usr/bin/python3 -O
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/contig_analysis/break_scaffolds_into_contigs.py
++++ b/assembler/src/tools/contig_analysis/break_scaffolds_into_contigs.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/contig_analysis/compare_gaps_pos.py
++++ b/assembler/src/tools/contig_analysis/compare_gaps_pos.py
+@@ -1,5 +1,4 @@
+-
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/contig_analysis/gap_finder.py
++++ b/assembler/src/tools/contig_analysis/gap_finder.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/contig_analysis/visualizer/mis_parser.py
++++ b/assembler/src/tools/contig_analysis/visualizer/mis_parser.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python -O
++#!/usr/bin/python3 -O
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/contig_analysis/visualizer/misassemblies.py
++++ b/assembler/src/tools/contig_analysis/visualizer/misassemblies.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python -O
++#!/usr/bin/python3 -O
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/contig_analysis/visualizer/misassemblies_old.py
++++ b/assembler/src/tools/contig_analysis/visualizer/misassemblies_old.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python -O
++#!/usr/bin/python3 -O
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/contig_analysis/visualizer/miss_nocov.py
++++ b/assembler/src/tools/contig_analysis/visualizer/miss_nocov.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python -O
++#!/usr/bin/python3 -O
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/contig_analysis/visualizer/run_viz.sh
++++ b/assembler/src/tools/contig_analysis/visualizer/run_viz.sh
+@@ -13,9 +13,9 @@ touch list.txt
+
+ for file in $(ls *.stdout)
+ do
+- python parser.py $file >> list.txt
++ python3 parser.py $file >> list.txt
+ done
+
+-python misassemblies.py -o plot -a list.txt --arcs
++python3 misassemblies.py -o plot -a list.txt --arcs
+
+ rm list.txt
+--- a/assembler/src/tools/reads_utils/reads_quality.py
++++ b/assembler/src/tools/reads_utils/reads_quality.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/cleancontigs/sort_contigs.py
++++ b/assembler/src/tools/cleancontigs/sort_contigs.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/contig_analysis/analyze_sinks.py
++++ b/assembler/src/tools/contig_analysis/analyze_sinks.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/contig_analysis/compare_fasta.py
++++ b/assembler/src/tools/contig_analysis/compare_fasta.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/contig_analysis/compare_gaps.py
++++ b/assembler/src/tools/contig_analysis/compare_gaps.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/contig_analysis/compare_runs.sh
++++ b/assembler/src/tools/contig_analysis/compare_runs.sh
+@@ -11,5 +11,5 @@
+ for file in $(ls $1/saves/*.sqn)
+ do
+ echo $(basename $file)
+- python compare_fasta.py $1/saves/$(basename $file) $2/saves/$(basename $file)
++ python3 compare_fasta.py $1/saves/$(basename $file) $2/saves/$(basename $file)
+ done
+--- a/assembler/src/tools/contig_analysis/compare_used_snps.py
++++ b/assembler/src/tools/contig_analysis/compare_used_snps.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/contig_analysis/visualizer/parser.py
++++ b/assembler/src/tools/contig_analysis/visualizer/parser.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python -O
++#!/usr/bin/python3 -O
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/contig_analysis/visualizer/run_parser.sh
++++ b/assembler/src/tools/contig_analysis/visualizer/run_parser.sh
+@@ -10,5 +10,5 @@
+
+ for file in $(ls *.stdout)
+ do
+- python parser.py $file >> list.txt
++ python3 parser.py $file >> list.txt
+ done
+--- a/assembler/src/tools/misc/sam_analyzer_2.py
++++ b/assembler/src/tools/misc/sam_analyzer_2.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.sh
++++ b/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.sh
+@@ -23,8 +23,8 @@ echo Building taxonomy index for $1 ...
+ echo Temporary file: $tempfile
+ echo Index prefix: $indxfile
+
+-python preprocessing.py < $1 > $tempfile
++python3 preprocessing.py < $1 > $tempfile
+
+ bowtie-build $tempfile $indxfile
+
+-rm $tempfile
+\ No newline at end of file
++rm $tempfile
+--- a/assembler/src/tools/clean_contaminations/16SrRNA/taxonomy.sh
++++ b/assembler/src/tools/clean_contaminations/16SrRNA/taxonomy.sh
+@@ -24,4 +24,4 @@ fi
+
+ echo Analyzing taxonomy for $1 ...
+
+-bowtie --threads $threads -k 10 --best --chunkmbs 1024 SSURef_108_NR_tax_silva_v2.fasta $1 | python parse_tax_from_bowtie.py
++bowtie --threads $threads -k 10 --best --chunkmbs 1024 SSURef_108_NR_tax_silva_v2.fasta $1 | python3 parse_tax_from_bowtie.py
+--- a/assembler/src/tools/clean_contaminations/clean_contam_by_index_id.sh
++++ b/assembler/src/tools/clean_contaminations/clean_contam_by_index_id.sh
+@@ -111,7 +111,7 @@ function clean_paired ()
+ bowtie -c -q -p 16 --suppress 6,7,8 $i $cleanedleft > "${output_folder}/paired_log1_${timestamp}.tmp" 2> /dev/null
+ bowtie -c -q -p 16 --suppress 6,7,8 $i $cleanedright > "${output_folder}/paired_log2_${timestamp}.tmp" 2> /dev/null
+ echo "running filter_reads.py"
+- python ${path_to_script}/../reads_utils/filter/filter_reads.py $cleanedleft $cleanedright "${output_folder}/paired_log1_${timestamp}.tmp" "${output_folder}/paired_log2_${timestamp}.tmp"
++ python3 ${path_to_script}/../reads_utils/filter/filter_reads.py $cleanedleft $cleanedright "${output_folder}/paired_log1_${timestamp}.tmp" "${output_folder}/paired_log2_${timestamp}.tmp"
+ mv $filteredleft $cleanedleft
+ mv $filteredright $cleanedright
+ done
+@@ -199,7 +199,7 @@ do
+ then
+ echo "building index for sequence $i"
+ mkdir -p "${path_to_db}/index/${i:0:2}"
+- python ${path_to_script}/read_fasta_using_index.py $i "${blast_database}.fasta" > "${i}.fasta.tmp"
++ python3 ${path_to_script}/read_fasta_using_index.py $i "${blast_database}.fasta" > "${i}.fasta.tmp"
+ bowtie-build "${i}.fasta.tmp" "${path_to_db}/index/${i:0:2}/${i}"
+ rm "${i}.fasta.tmp"
+ fi
+@@ -220,7 +220,7 @@ then
+ else
+ ln -s $all_reads "${output_folder}/${filename}"
+ fi
+- python ${path_to_script}/../reads_utils/conversion/split_any_fastq.py "${output_folder}/${filename}"
++ python3 ${path_to_script}/../reads_utils/conversion/split_any_fastq.py "${output_folder}/${filename}"
+ filename=${filename%.*}
+ left="${output_folder}/${filename}_left.${extension}"
+ right="${output_folder}/${filename}_right.${extension}"
+--- a/assembler/src/tools/cleancontigs/cleancontigs.py
++++ b/assembler/src/tools/cleancontigs/cleancontigs.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/contig_analysis/get_misassembled_contigs.py
++++ b/assembler/src/tools/contig_analysis/get_misassembled_contigs.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python -O
++#!/usr/bin/python3 -O
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/contig_analysis/texify_results.py
++++ b/assembler/src/tools/contig_analysis/texify_results.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/contig_analysis/visualizer/main.py
++++ b/assembler/src/tools/contig_analysis/visualizer/main.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python -O
++#!/usr/bin/python3 -O
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/dataset_tar
++++ b/assembler/src/tools/dataset_tar
+@@ -3,4 +3,4 @@
+ DIR="$( cd "$( dirname "$0" )" && pwd )"
+ BASE="$( cd "$( dirname "$0" )" && cd ../.. && pwd )"
+ pushd $BASE/data/input > /dev/null
+-python $BASE/src/tools/dataset.py tar $BASE/configs/debruijn/datasets.info $1
++python3 $BASE/src/tools/dataset.py tar $BASE/configs/debruijn/datasets.info $1
+--- a/assembler/src/tools/loc_pic.py
++++ b/assembler/src/tools/loc_pic.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/misc/gcc_version_check.py
++++ b/assembler/src/tools/misc/gcc_version_check.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/misc/sam_analysis_sorter.py
++++ b/assembler/src/tools/misc/sam_analysis_sorter.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/reads_utils/crop/crop_genome.py
++++ b/assembler/src/tools/reads_utils/crop/crop_genome.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python -O
++#!/usr/bin/python3 -O
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/reads_utils/crop/paired_crop.py
++++ b/assembler/src/tools/reads_utils/crop/paired_crop.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python -O
++#!/usr/bin/python3 -O
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/reads_utils/paired_reads_quality.py
++++ b/assembler/src/tools/reads_utils/paired_reads_quality.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/reads_utils/stat/coverage.py
++++ b/assembler/src/tools/reads_utils/stat/coverage.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python -O
++#!/usr/bin/python3 -O
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/reads_utils/stat/coverage_hist.py
++++ b/assembler/src/tools/reads_utils/stat/coverage_hist.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python -O
++#!/usr/bin/python3 -O
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/reads_utils/stat/is.py
++++ b/assembler/src/tools/reads_utils/stat/is.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python -O
++#!/usr/bin/python3 -O
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/reads_utils/stat/raw.py
++++ b/assembler/src/tools/reads_utils/stat/raw.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python -O
++#!/usr/bin/python3 -O
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/reads_utils/stat/raws_w_orientation.py
++++ b/assembler/src/tools/reads_utils/stat/raws_w_orientation.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python -O
++#!/usr/bin/python3 -O
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/reads_utils/stat/shift.py
++++ b/assembler/src/tools/reads_utils/stat/shift.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python -O
++#!/usr/bin/python3 -O
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/reads_utils/stat/single_log_to_paired.py
++++ b/assembler/src/tools/reads_utils/stat/single_log_to_paired.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/reads_utils/stat/trim.py
++++ b/assembler/src/tools/reads_utils/stat/trim.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python -O
++#!/usr/bin/python3 -O
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/spades_download_stats/filter.py
++++ b/assembler/src/tools/spades_download_stats/filter.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ #***************************************************************************
+ ##* Copyright (c) 2011-2014 Saint-Petersburg Academic University
+--- a/assembler/src/test/teamcity/deprecated/spades_mc_is220_1k.sh
++++ b/assembler/src/test/teamcity/deprecated/spades_mc_is220_1k.sh
+@@ -12,6 +12,6 @@ pushd ../../../
+ rm -rf spades_output/ECOLI_IS220_QUAKE_1K
+ ./spades.py --only-assembler --generate-sam-file -k 21,55 -1 ./data/input/E.coli/is220/cropped/s_6.first1000_1.fastq.gz -2 ./data/input/E.coli/is220/cropped/s_6.first1000_2.fastq.gz -o spades_output/ECOLI_IS220_QUAKE_1K
+ rm -rf ~/quast-1.3/ECOLI_IS220_QUAKE_1K/
+-python ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS220_QUAKE_1K/ spades_output/ECOLI_IS220_QUAKE_1K/contigs.fasta
+-python src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS220_QUAKE_1K/transposed_report.tsv 1000 0
++python3 ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS220_QUAKE_1K/ spades_output/ECOLI_IS220_QUAKE_1K/contigs.fasta
++python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS220_QUAKE_1K/transposed_report.tsv 1000 0
+ popd
+--- a/assembler/src/tools/estimation_deprecated/Nx_plot.py
++++ b/assembler/src/tools/estimation_deprecated/Nx_plot.py
+@@ -1,3 +1,4 @@
++#!/usr/bin/python3
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+ # Copyright (c) 2011-2014 Saint Petersburg Academic University
+@@ -18,9 +19,9 @@ import fastaparser
+ if len(sys.argv) < 2:
+ print "Draws Nx plot (from N00 through N50 to N100)"
+ print
+- print "Usage: python", sys.argv[0], "FASTA1 [FASTA2 [FASTA3 ..."
++ print "Usage: python3", sys.argv[0], "FASTA1 [FASTA2 [FASTA3 ..."
+ print
+- print "Example: python", sys.argv[0], "../../data/debruijn/we_contigs.fasta ../../data/debruijn/velvet_contigs.fa"
++ print "Example: python3", sys.argv[0], "../../data/debruijn/we_contigs.fasta ../../data/debruijn/velvet_contigs.fa"
+ exit(0)
+
+ for filename in sys.argv[1:]:
+--- a/assembler/src/tools/truseq/quast_all.sh
++++ b/assembler/src/tools/truseq/quast_all.sh
+@@ -14,7 +14,7 @@ mkdir $3/tmp
+ mkdir $3/all_reports
+ ls $1 | xargs -P $4 -I {} -t quast --min-contig 1000 --contig-thresholds 5000,8000,12000 -e -R $2/{}.fasta $1/{}/scaffolds.fasta -o $3/tmp/{}
+ ls $1 | xargs -P $4 -I {} -t cp $3/tmp/{}/report.tsv $3/all_reports/{}.tsv
+-python quast_all.py $3/all_reports $3
++python3 quast_all.py $3/all_reports $3
+ grep "( inversion )" $3/tmp/*/contigs_reports/contigs_report_*.stdout > $3/inversions.txt
+ grep "( translocation )" $3/tmp/*/contigs_reports/contigs_report_*.stdout > $3/translocations.txt
+ grep "( relocation," $3/tmp/*/contigs_reports/contigs_report_*.stdout > $3/relocations.txt
+--- a/assembler/src/test/teamcity/deprecated/spades_mc_is220_1k_ant.sh
++++ b/assembler/src/test/teamcity/deprecated/spades_mc_is220_1k_ant.sh
+@@ -12,6 +12,6 @@ pushd ../../../
+ rm -rf spades_output/ECOLI_IS220_QUAKE_1K
+ ./spades.py -k 21,55 --only-assembler -1 /tmp/data/input/E.coli/is220/cropped/s_6.first1000_1.fastq.gz -2 /tmp/data/input/E.coli/is220/cropped/s_6.first1000_2.fastq.gz -o spades_output/ECOLI_IS220_QUAKE_1K
+ rm -rf ~/quast-1.3/ECOLI_IS220_QUAKE_1K/
+-python ~/quast-1.3/quast.py -R /tmp/data/input/E.coli/MG1655-K12.fasta.gz -G /tmp/data/input/E.coli/genes/genes.gff -O /tmp/data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS220_QUAKE_1K/ spades_output/ECOLI_IS220_QUAKE_1K/contigs.fasta
+-python src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS220_QUAKE_1K/transposed_report.tsv 1000 0
++python3 ~/quast-1.3/quast.py -R /tmp/data/input/E.coli/MG1655-K12.fasta.gz -G /tmp/data/input/E.coli/genes/genes.gff -O /tmp/data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS220_QUAKE_1K/ spades_output/ECOLI_IS220_QUAKE_1K/contigs.fasta
++python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS220_QUAKE_1K/transposed_report.tsv 1000 0
+ popd
+--- a/assembler/src/test/teamcity/deprecated/spades_sc_mruber_pre.sh
++++ b/assembler/src/test/teamcity/deprecated/spades_sc_mruber_pre.sh
+@@ -17,9 +17,9 @@ rm -rf /tmp/data/output/spades_output/MR
+
+ rm -rf ~/quast-1.3/MRUBER_PRENORM/
+
+-python ~/quast-1.3/quast.py -R data/input/M.ruber/ref.fasta -G data/input/M.ruber/MRU_genes.txt -o ~/quast-1.3/MRUBER_PRENORM/ /tmp/data/output/spades_output/MRUBER_PRENORM/contigs.fasta
++python3 ~/quast-1.3/quast.py -R data/input/M.ruber/ref.fasta -G data/input/M.ruber/MRU_genes.txt -o ~/quast-1.3/MRUBER_PRENORM/ /tmp/data/output/spades_output/MRUBER_PRENORM/contigs.fasta
+
+-python src/test/teamcity/assess.py ~/quast-1.3/MRUBER_PRENORM/transposed_report.tsv 49100 16 2152 75.6 65 21
++python3 src/test/teamcity/assess.py ~/quast-1.3/MRUBER_PRENORM/transposed_report.tsv 49100 16 2152 75.6 65 21
+ exitlvl=$?
+ popd
+
+--- a/assembler/src/projects/mts/binners/gattaca.snake
++++ b/assembler/src/projects/mts/binners/gattaca.snake
+@@ -32,8 +32,8 @@ rule gattaca:
+ threads: THREADS
+ log: "binning/gattaca.log"
+ message: "Running GATTACA clustering"
+- shell: "set +u; source activate py27; set -u\n"
+- "python {SOFT}/gattaca/src/python/gattaca.py cluster --contigs {input.contigs}"
++ shell: "set +u; source activate py37; set -u\n"
++ "python3 {SOFT}/gattaca/src/python/gattaca.py cluster --contigs {input.contigs}"
+ " --coverage {input.profiles} --algorithm dirichlet --clusters {output} >{log} 2>&1\n"
+ "rm -f assembly/splits/all_filtered.fasta.fai"
+
+--- a/assembler/src/test/teamcity/deprecated/spades_sc_lane1_full.sh
++++ b/assembler/src/test/teamcity/deprecated/spades_sc_lane1_full.sh
+@@ -17,9 +17,9 @@ rm -rf /tmp/data/output/spades_output/EC
+
+ rm -rf ~/quast-1.3/ECOLI_SC_LANE_1/
+
+-python ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_SC_LANE_1/ /tmp/data/output/spades_output/ECOLI_SC_LANE_1/contigs.fasta
++python3 ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_SC_LANE_1/ /tmp/data/output/spades_output/ECOLI_SC_LANE_1/contigs.fasta
+
+-python src/test/teamcity/assess.py ~/quast-1.3/ECOLI_SC_LANE_1/transposed_report.tsv 108000 2 4080 96.4 4 0.7
++python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_SC_LANE_1/transposed_report.tsv 108000 2 4080 96.4 4 0.7
+ exitlvl=$?
+ popd
+
+--- a/assembler/src/tools/estimation_deprecated/README
++++ b/assembler/src/tools/estimation_deprecated/README
+@@ -1,3 +1,3 @@
+ Prerequisites:
+
+- sudo apt-get install python python-matplotlib python-numpy
++ sudo apt-get install python3 python3-matplotlib python3-numpy
+--- a/assembler/src/test/teamcity/deprecated/bh_ecoli_1k.sh
++++ b/assembler/src/test/teamcity/deprecated/bh_ecoli_1k.sh
+@@ -11,6 +11,6 @@ set -e
+ pushd ../../../
+ rm -rf spades_output/ECOLI_1K_TEAMCITY_BH
+ ./spades.py --only-error-correction -1 ./data/input/E.coli/is220/cropped/s_6.first1000_1.fastq.gz -2 ./data/input/E.coli/is220/cropped/s_6.first1000_2.fastq.gz -o spades_output/ECOLI_1K_TEAMCITY_BH
+-python src/tools/reads_utils/reads_quality.py -r test_dataset/reference_1K.fa.gz -o spades_output/ECOLI_1K_TEAMCITY_BH/reads_quality_results spades_output/ECOLI_1K_TEAMCITY_BH/corrected/dataset.info
+-python src/test/teamcity/assess_reads.py spades_output/ECOLI_1K_TEAMCITY_BH/reads_quality_results/report.horizontal.tsv 100 100
++python3 src/tools/reads_utils/reads_quality.py -r test_dataset/reference_1K.fa.gz -o spades_output/ECOLI_1K_TEAMCITY_BH/reads_quality_results spades_output/ECOLI_1K_TEAMCITY_BH/corrected/dataset.info
++python3 src/test/teamcity/assess_reads.py spades_output/ECOLI_1K_TEAMCITY_BH/reads_quality_results/report.horizontal.tsv 100 100
+ popd
+--- a/assembler/src/test/teamcity/deprecated/spades_sc_lane1.sh
++++ b/assembler/src/test/teamcity/deprecated/spades_sc_lane1.sh
+@@ -17,9 +17,9 @@ rm -rf /tmp/data/output/spades_output/EC
+
+ rm -rf ~/quast-1.3/ECOLI_SC_LANE_1_BH_woHUMAN/
+
+-python ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_SC_LANE_1_BH_woHUMAN/ /tmp/data/output/spades_output/ECOLI_SC_LANE_1_BH_woHUMAN/contigs.fasta
++python3 ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_SC_LANE_1_BH_woHUMAN/ /tmp/data/output/spades_output/ECOLI_SC_LANE_1_BH_woHUMAN/contigs.fasta
+
+-python src/test/teamcity/assess.py ~/quast-1.3/ECOLI_SC_LANE_1_BH_woHUMAN/transposed_report.tsv 85000 7
++python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_SC_LANE_1_BH_woHUMAN/transposed_report.tsv 85000 7
+ exitlvl=$?
+ popd
+
+--- a/assembler/src/test/teamcity/deprecated/spades_sc_mruber.sh
++++ b/assembler/src/test/teamcity/deprecated/spades_sc_mruber.sh
+@@ -17,9 +17,9 @@ rm -rf /tmp/data/output/spades_output/MR
+
+ rm -rf ~/quast-1.3/MRUBER/
+
+-python ~/quast-1.3/quast.py -R data/input/M.ruber/ref.fasta -G data/input/M.ruber/MRU_genes.txt -o ~/quast-1.3/MRUBER/ /tmp/data/output/spades_output/MRUBER/contigs.fasta
++python3 ~/quast-1.3/quast.py -R data/input/M.ruber/ref.fasta -G data/input/M.ruber/MRU_genes.txt -o ~/quast-1.3/MRUBER/ /tmp/data/output/spades_output/MRUBER/contigs.fasta
+
+-python src/test/teamcity/assess.py ~/quast-1.3/MRUBER/transposed_report.tsv 20000 20 1500 50.0 30 10
++python3 src/test/teamcity/assess.py ~/quast-1.3/MRUBER/transposed_report.tsv 20000 20 1500 50.0 30 10
+ exitlvl=$?
+ popd
+
+--- a/assembler/src/test/teamcity/deprecated/spades_sc_pmarinus.sh
++++ b/assembler/src/test/teamcity/deprecated/spades_sc_pmarinus.sh
+@@ -17,9 +17,9 @@ rm -rf /tmp/data/output/spades_output/PM
+
+ rm -rf ~/quast-1.3/PMARINUS/
+
+-python ~/quast-1.3/quast.py -R data/input/P.marinus/ref.fasta -o ~/quast-1.3/PMARINUS/ /tmp/data/output/spades_output/PMARINUS/contigs.fasta
++python3 ~/quast-1.3/quast.py -R data/input/P.marinus/ref.fasta -o ~/quast-1.3/PMARINUS/ /tmp/data/output/spades_output/PMARINUS/contigs.fasta
+
+-python src/test/teamcity/assess.py ~/quast-1.3/PMARINUS/transposed_report.tsv 292000 0 1612 95.3 3.4 1.5
++python3 src/test/teamcity/assess.py ~/quast-1.3/PMARINUS/transposed_report.tsv 292000 0 1612 95.3 3.4 1.5
+ exitlvl=$?
+ popd
+
+--- a/assembler/src/test/teamcity/deprecated/spades_sc_saureus_lane7.sh
++++ b/assembler/src/test/teamcity/deprecated/spades_sc_saureus_lane7.sh
+@@ -17,9 +17,9 @@ rm -rf /tmp/data/output/spades_output/SA
+
+ rm -rf ~/quast-1.3/SAUREUS_LANE_7/
+
+-python ~/quast-1.3/quast.py -R data/input/S.aureus/USA300_FPR3757.fasta -G data/input/S.aureus/genes/bacteria_genes.txt -o ~/quast-1.3/SAUREUS_LANE_7/ /tmp/data/output/spades_output/SAUREUS_LANE_7/contigs.fasta
++python3 ~/quast-1.3/quast.py -R data/input/S.aureus/USA300_FPR3757.fasta -G data/input/S.aureus/genes/bacteria_genes.txt -o ~/quast-1.3/SAUREUS_LANE_7/ /tmp/data/output/spades_output/SAUREUS_LANE_7/contigs.fasta
+
+-python src/test/teamcity/assess.py ~/quast-1.3/SAUREUS_LANE_7/transposed_report.tsv 85000 7 2500 99.8 6 6
++python3 src/test/teamcity/assess.py ~/quast-1.3/SAUREUS_LANE_7/transposed_report.tsv 85000 7 2500 99.8 6 6
+ exitlvl=$?
+ popd
+
+--- a/assembler/src/test/teamcity/deprecated/spades_mc_is480.sh
++++ b/assembler/src/test/teamcity/deprecated/spades_mc_is480.sh
+@@ -1,4 +1,3 @@
+-
+ #!/bin/bash
+
+ ############################################################################
+@@ -13,6 +12,6 @@ pushd ../../../
+ rm -rf /tmp/data/output/spades_output/ECOLI_IS480_QUAKE
+ ./spades.py --only-assembler -k 21,33,55 -m 12 -1 data/input/E.coli/is480/ERR022075_1.cor.fastq.gz -2 data/input/E.coli/is480/ERR022075_2.cor.fastq.gz -s data/input/E.coli/is480/ERR022075_1.cor_single.fastq.gz -s data/input/E.coli/is480/ERR022075_2.cor_single.fastq.gz -o /tmp/data/output/spades_output/ECOLI_IS480_QUAKE
+ rm -rf ~/quast-1.3/ECOLI_IS480_QUAKE/
+-python ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS480_QUAKE/ /tmp/data/output/spades_output/ECOLI_IS480_QUAKE/contigs.fasta
+-python src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS480_QUAKE/transposed_report.tsv 133000 4
++python3 ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS480_QUAKE/ /tmp/data/output/spades_output/ECOLI_IS480_QUAKE/contigs.fasta
++python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS480_QUAKE/transposed_report.tsv 133000 4
+ popd
+--- a/assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7_pre.sh
++++ b/assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7_pre.sh
+@@ -17,9 +17,9 @@ rm -rf /tmp/data/output/spades_output/EC
+
+ rm -rf ~/quast-1.3/ECOLI_SC_JGI_LANE_7_PRENORM/
+
+-python ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_SC_JGI_LANE_7_PRENORM/ /tmp/data/output/spades_output/ECOLI_SC_JGI_LANE_7_PRENORM/contigs.fasta
++python3 ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_SC_JGI_LANE_7_PRENORM/ /tmp/data/output/spades_output/ECOLI_SC_JGI_LANE_7_PRENORM/contigs.fasta
+
+-python src/test/teamcity/assess.py ~/quast-1.3/ECOLI_SC_JGI_LANE_7_PRENORM/transposed_report.tsv 115000 4 4240 99.8 4 0.8
++python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_SC_JGI_LANE_7_PRENORM/transposed_report.tsv 115000 4 4240 99.8 4 0.8
+ exitlvl=$?
+ popd
+
+--- a/assembler/src/test/teamcity/teamcity.py
++++ b/assembler/src/test/teamcity/teamcity.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ ############################################################################
+ # Copyright (c) 2015-2017 Saint Petersburg State University
+@@ -30,7 +30,7 @@ from teamcity_support import *
+ ### main ###
+ try:
+ if len(sys.argv) == 1:
+- command = 'python {} -h'.format(sys.argv[0])
++ command = 'python3 {} -h'.format(sys.argv[0])
+ subprocess.call(command, shell=True)
+ sys.exit(1)
+
+--- a/assembler/src/test/teamcity/deprecated/spades_mc_is220.sh
++++ b/assembler/src/test/teamcity/deprecated/spades_mc_is220.sh
+@@ -1,4 +1,3 @@
+-
+ #!/bin/bash
+
+ ############################################################################
+@@ -13,6 +12,6 @@ pushd ../../../
+ rm -rf /tmp/data/output/spades_output/ECOLI_IS220_QUAKE
+ ./spades.py --generate-sam-file --only-assembler -m 12 -k 21,33,55 -1 data/input/E.coli/is220/s_6_1.cor.fastq.gz -2 data/input/E.coli/is220/s_6_2.cor.fastq.gz -s data/input/E.coli/is220/s_6_1.cor_single.fastq.gz -s data/input/E.coli/is220/s_6_2.cor_single.fastq.gz -o /tmp/data/output/spades_output/ECOLI_IS220_QUAKE
+ rm -rf ~/quast-1.3/ECOLI_IS220_QUAKE/
+-python ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS220_QUAKE/ /tmp/data/output/spades_output/ECOLI_IS220_QUAKE/contigs.fasta
+-python src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS220_QUAKE/transposed_report.tsv 80000 3
++python3 ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS220_QUAKE/ /tmp/data/output/spades_output/ECOLI_IS220_QUAKE/contigs.fasta
++python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS220_QUAKE/transposed_report.tsv 80000 3
+ popd
+--- a/assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7.sh
++++ b/assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7.sh
+@@ -17,9 +17,9 @@ rm -rf /tmp/data/output/spades_output/EC
+
+ rm -rf ~/quast-1.3/ECOLI_SC_JGI_LANE_7/
+
+-python ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_SC_JGI_LANE_7/ /tmp/data/output/spades_output/ECOLI_SC_JGI_LANE_7/contigs.fasta
++python3 ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_SC_JGI_LANE_7/ /tmp/data/output/spades_output/ECOLI_SC_JGI_LANE_7/contigs.fasta
+
+-python src/test/teamcity/assess.py ~/quast-1.3/ECOLI_SC_JGI_LANE_7/transposed_report.tsv 115000 4 4260 99.8 3.2 0.7
++python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_SC_JGI_LANE_7/transposed_report.tsv 115000 4 4260 99.8 3.2 0.7
+ exitlvl=$?
+ popd
+
+--- a/assembler/src/test/teamcity/deprecated/spades_sc_phepa_pre.sh
++++ b/assembler/src/test/teamcity/deprecated/spades_sc_phepa_pre.sh
+@@ -17,9 +17,9 @@ rm -rf /tmp/data/output/spades_output/PH
+
+ rm -rf ~/quast-1.3/PHEPARINUS_PRENORM/
+
+-python ~/quast-1.3/quast.py -R data/input/P.heparinus/ref.fasta -G data/input/P.heparinus/PHE_genes.txt -o ~/quast-1.3/PHEPARINUS_PRENORM/ /tmp/data/output/spades_output/PHEPARINUS_PRENORM/contigs.fasta
++python3 ~/quast-1.3/quast.py -R data/input/P.heparinus/ref.fasta -G data/input/P.heparinus/PHE_genes.txt -o ~/quast-1.3/PHEPARINUS_PRENORM/ /tmp/data/output/spades_output/PHEPARINUS_PRENORM/contigs.fasta
+
+-python src/test/teamcity/assess.py ~/quast-1.3/PHEPARINUS_PRENORM/transposed_report.tsv 160000 9 3900 95.5 10.0 1.0
++python3 src/test/teamcity/assess.py ~/quast-1.3/PHEPARINUS_PRENORM/transposed_report.tsv 160000 9 3900 95.5 10.0 1.0
+ exitlvl=$?
+ popd
+
+--- a/assembler/src/tools/estimation/run_real.sh
++++ b/assembler/src/tools/estimation/run_real.sh
+@@ -1,3 +1,4 @@
++#!/bin/sh
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+ # Copyright (c) 2011-2014 Saint Petersburg Academic University
+@@ -5,4 +6,4 @@
+ # See file LICENSE for details.
+ ############################################################################
+
+-python real_cumulative.py ~/algorithmic-biology/assembler/data/debruijn/latest/contigs_before_enlarge.fasta 0.5 ~/algorithmic-biology/assembler/data/debruijn/latest/contigs_final.fasta 0.5 ../quality/velvet_paired55.fa 1 ../quality/velvet_unpaired55.fa
++python3 real_cumulative.py ~/algorithmic-biology/assembler/data/debruijn/latest/contigs_before_enlarge.fasta 0.5 ~/algorithmic-biology/assembler/data/debruijn/latest/contigs_final.fasta 0.5 ../quality/velvet_paired55.fa 1 ../quality/velvet_unpaired55.fa
+--- a/assembler/src/tools/res_counter/run.pl
++++ b/assembler/src/tools/res_counter/run.pl
+@@ -14,7 +14,7 @@ print "started...\n";
+
+ my $stat_proc = fork;
+ if ($stat_proc == 0) {
+- exec "python $script_dir/stats_counter.py $child 1>>rc_stats.txt 2>>rc_stats.txt";
++ exec "python3 $script_dir/stats_counter.py $child 1>>rc_stats.txt 2>>rc_stats.txt";
+ }
+
+ waitpid($child, 0);
+--- a/assembler/src/test/teamcity/deprecated/bh_ecoli_mda_lane1.sh
++++ b/assembler/src/test/teamcity/deprecated/bh_ecoli_mda_lane1.sh
+@@ -11,6 +11,6 @@ set -e
+ pushd ../../../
+ rm -rf /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH
+ ./spades.py --sc --only-error-correction --12 ./data/input/E.coli/sc_lane_1/ecoli_mda_lane1.fastq.gz -m 160 -o /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH
+-python src/tools/reads_utils/reads_quality.py -r data/input/E.coli/MG1655-K12.fasta.gz -o /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH/reads_quality_results /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH/corrected/dataset.info
+-python src/test/teamcity/assess_reads.py /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH/reads_quality_results/report.horizontal.tsv 90 97 # 97 97
++python3 src/tools/reads_utils/reads_quality.py -r data/input/E.coli/MG1655-K12.fasta.gz -o /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH/reads_quality_results /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH/corrected/dataset.info
++python3 src/test/teamcity/assess_reads.py /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH/reads_quality_results/report.horizontal.tsv 90 97 # 97 97
+ popd
+--- a/assembler/src/test/teamcity/update_threshold.py
++++ b/assembler/src/test/teamcity/update_threshold.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+@@ -264,7 +264,7 @@ def check_args(args):
+ ### main ###
+ try:
+ if len(sys.argv) == 1:
+- command = 'python {} -h'.format(sys.argv[0])
++ command = 'python3 {} -h'.format(sys.argv[0])
+ subprocess.call(command, shell=True)
+ sys.exit(1)
+
+--- a/assembler/src/test/teamcity/deprecated/full_run.sh
++++ b/assembler/src/test/teamcity/deprecated/full_run.sh
+@@ -1,10 +1,3 @@
+-
+-
+-
+-
+-
+-
+-
+ #!/bin/bash
+
+ ############################################################################
+@@ -26,7 +19,7 @@ mkdir $project_dir -p
+ read line < $options_dir"spades.options"
+ echo $line
+ ./cpcfg
+-python2.6 ./spades.py $line -o $project_dir --disable-gzip-output --mismatch-correction
++python3 ./spades.py $line -o $project_dir --disable-gzip-output --mismatch-correction
+
+ read line < $options_dir"quast.options"
+ echo $line
+@@ -45,7 +38,7 @@ cp $work_contigs $dir$(date +%Y%m%d_%H%M
+ cp $project_dir"/scaffolds.fasta" $dir$(date +%Y%m%d_%H%M%S)_scaf".fasta"
+
+
+-python2.6 ~/quast-1.3/quast.py $work_contigs $line -o $project_dir"/quality_results/"
++python3 ~/quast-1.3/quast.py $work_contigs $line -o $project_dir"/quality_results/"
+ rm $dir"/quast_all" -rf
+ #echo $dir"*.fasta" $line -o $dir"/quast_all"
+ dirtmp=$dir"tmp/"
+@@ -60,7 +53,7 @@ for i in $dir*.fasta ; do
+ # echo $j
+ if [ -f $j ] ;
+ then
+- compare_res=$(python2.6 ~/algorithmic-biology/assembler/src/tools/contig_analysis/compare_fasta.py $i $j)
++ compare_res=$(python3 ~/algorithmic-biology/assembler/src/tools/contig_analysis/compare_fasta.py $i $j)
+ # echo $compare_res
+ if [ $compare_res = "True" ];
+ then
+@@ -79,8 +72,8 @@ quast_line="$output_pref/quast-1.3/quast
+ quast1_2_line="$output_pref/quast-1.2/quast.py -M 500 $dirtmp* $line -o $dir/quast1_2_all/"
+
+ echo "$quast_line"
+-python2.6 $quast_line >null
+-python2.6 $quast1_2_line >null
++python3 $quast_line >null
++python3 $quast1_2_line >null
+
+ ssh -n antipov at 194.85.238.21 mkdir -p "/var/www/teamcity_runs/$1$2" &
+
+@@ -98,7 +91,7 @@ do
+ splitted_opts=$splitted_opts" "${opts[$i * 2 + 1]}
+ done
+ echo $splitted_opts
+-python src/test/teamcity/assess.py $project_dir"quality_results/transposed_report.tsv" $splitted_opts
++python3 src/test/teamcity/assess.py $project_dir"quality_results/transposed_report.tsv" $splitted_opts
+ rm $project_dir"/corrected/" -rf
+
+
+--- a/assembler/src/test/teamcity/deprecated/spades_mc_bfaecium_ant.sh
++++ b/assembler/src/test/teamcity/deprecated/spades_mc_bfaecium_ant.sh
+@@ -12,6 +12,6 @@ pushd ../../../
+ rm -rf /tmp/data/output/spades_output/BFAECIUM_QUAKE
+ ./spades.py -k 21,33,55 -m 16 --only-assembler -1 data/input/B.faecium/std_left.cor.fastq.gz -2 data/input/B.faecium/std_right.cor.fastq.gz -s data/input/B.faecium/std_right.cor_single.fastq.gz -s data/input/B.faecium/std_left.cor_single.fastq.gz -o /tmp/data/output/spades_output/BFAECIUM_QUAKE
+ rm -rf ~/quast-1.3/BFAECIUM_QUAKE/
+-python ~/quast-1.3/quast.py -R /tmp/data/input/B.faecium/ref.fasta.gz -o ~/quast-1.3/BFAECIUM_QUAKE/ /tmp/data/output/spades_output/BFAECIUM_QUAKE/contigs.fasta
+-python src/test/teamcity/assess.py ~/quast-1.3/BFAECIUM_QUAKE/transposed_report.tsv 330000 0
++python3 ~/quast-1.3/quast.py -R /tmp/data/input/B.faecium/ref.fasta.gz -o ~/quast-1.3/BFAECIUM_QUAKE/ /tmp/data/output/spades_output/BFAECIUM_QUAKE/contigs.fasta
++python3 src/test/teamcity/assess.py ~/quast-1.3/BFAECIUM_QUAKE/transposed_report.tsv 330000 0
+ popd
+--- a/assembler/src/test/teamcity/deprecated/spades_sc_phepa.sh
++++ b/assembler/src/test/teamcity/deprecated/spades_sc_phepa.sh
+@@ -17,8 +17,8 @@ rm -rf /tmp/data/output/spades_output/PH
+
+ rm -rf ~/quast-1.3/PHEPARINUS/
+
+-python ~/quast-1.3/quast.py -R data/input/P.heparinus/ref.fasta -G data/input/P.heparinus/PHE_genes.txt -o ~/quast-1.3/PHEPARINUS/ /tmp/data/output/spades_output/PHEPARINUS/contigs.fasta
+-python src/test/teamcity/assess.py ~/quast-1.3/PHEPARINUS/transposed_report.tsv 140000 6 4140 98.0 8.0 2.0
++python3 ~/quast-1.3/quast.py -R data/input/P.heparinus/ref.fasta -G data/input/P.heparinus/PHE_genes.txt -o ~/quast-1.3/PHEPARINUS/ /tmp/data/output/spades_output/PHEPARINUS/contigs.fasta
++python3 src/test/teamcity/assess.py ~/quast-1.3/PHEPARINUS/transposed_report.tsv 140000 6 4140 98.0 8.0 2.0
+ exitlvl=$?
+ popd
+
+--- a/assembler/spades_dev.sh
++++ b/assembler/spades_dev.sh
+@@ -8,5 +8,5 @@ mkdir -p bin;
+ rm bin/*;
+ cp build/release/debruijn/spades bin/spades;
+ cp build/release/hammer/hammer bin/hammer;
+-python spades.py "$@";
++python3 spades.py "$@";
+
+--- a/assembler/src/tools/dataset_hammer
++++ b/assembler/src/tools/dataset_hammer
+@@ -3,7 +3,7 @@
+ DIR="$( cd "$( dirname "$0" )" && pwd )"
+ BASE="$( cd "$( dirname "$0" )" && cd ../.. && pwd )"
+ #pushd $BASE/data/input > /dev/null
+-python $BASE/src/tools/dataset.py hammer $1
++python3 $BASE/src/tools/dataset.py hammer $1
+ #src/tools/dataset_hammer /mnt/ace/acestorage/snikolenko/090408_ultrashort/09
+ #src/tools/dataset_hammer /mnt/ace/acestorage/data/input/x5/makarich.fbb.msu.ru/run1_fca/Quaked/
+ #src/tools/dataset_hammer ~/temp/02
=====================================
debian/patches/yaml_load.patch
=====================================
@@ -14,6 +14,42 @@ Description: Specify yaml loader
dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(cfg["dataset"].yaml_filename))
support.pretty_print_reads(dataset_data, log)
+@@ -425,7 +425,7 @@ def fill_cfg(options_to_parse, log, seco
+ if load_processed_dataset:
+ if os.path.isfile(processed_dataset_fpath):
+ try:
+- existing_dataset_data = pyyaml.load(open(processed_dataset_fpath, 'r'))
++ existing_dataset_data = pyyaml.load(open(processed_dataset_fpath, 'r'), Loader=pyyaml.FullLoader)
+ except pyyaml.YAMLError:
+ existing_dataset_data = None
+ if existing_dataset_data is not None:
+@@ -433,7 +433,7 @@ def fill_cfg(options_to_parse, log, seco
+ else:
+ if options_storage.dataset_yaml_filename:
+ try:
+- dataset_data = pyyaml.load(open(options_storage.dataset_yaml_filename, 'r'))
++ dataset_data = pyyaml.load(open(options_storage.dataset_yaml_filename, 'r'), Loader=pyyaml.FullLoader)
+ except pyyaml.YAMLError:
+ _, exc, _ = sys.exc_info()
+ support.error('exception caught while parsing YAML file (' + options_storage.dataset_yaml_filename + '):\n' + str(exc))
+@@ -792,7 +792,7 @@ def main(args):
+ if os.path.isfile(corrected_dataset_yaml_filename) and options_storage.continue_mode \
+ and not options_storage.restart_from == "ec":
+ if not bh_cfg.gzip_output or \
+- support.dataset_has_gzipped_reads(pyyaml.load(open(corrected_dataset_yaml_filename, 'r'))):
++ support.dataset_has_gzipped_reads(pyyaml.load(open(corrected_dataset_yaml_filename, 'r')), Loader=pyyaml.FullLoader):
+ log.info("\n===== Skipping %s (already processed). \n" % STAGE_NAME)
+ ec_is_needed = False
+ else:
+@@ -869,7 +869,7 @@ def main(args):
+ support.continue_from_here(log)
+
+ if os.path.isfile(corrected_dataset_yaml_filename):
+- dataset_data = pyyaml.load(open(corrected_dataset_yaml_filename, 'r'))
++ dataset_data = pyyaml.load(open(corrected_dataset_yaml_filename, 'r'), Loader=pyyaml.FullLoader)
+ dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(corrected_dataset_yaml_filename))
+ if spades_cfg.disable_rr:
+ spades_cfg.__dict__["rr_enable"] = False
--- a/assembler/src/spades_pipeline/hammer_logic.py
+++ b/assembler/src/spades_pipeline/hammer_logic.py
@@ -94,7 +94,7 @@ def prepare_config_ih(filename, cfg, ext
@@ -34,3 +70,36 @@ Description: Specify yaml loader
remove_not_corrected_reads(cfg.output_dir)
is_changed = False
if cfg.gzip_output:
+--- a/assembler/src/spades_pipeline/spades_logic.py
++++ b/assembler/src/spades_pipeline/spades_logic.py
+@@ -94,7 +94,7 @@ def get_read_length(output_dir, K, ext_p
+ import pyyaml2 as pyyaml
+ elif sys.version.startswith('3.'):
+ import pyyaml3 as pyyaml
+- est_params_data = pyyaml.load(open(est_params_filename, 'r'))
++ est_params_data = pyyaml.load(open(est_params_filename, 'r'), Loader=pyyaml.FullLoader)
+ max_read_length = int(est_params_data['nomerge max read length'])
+ log.info("Max read length detected as %d" % max_read_length)
+ if max_read_length == 0:
+--- a/assembler/src/spades_pipeline/corrector_logic.py
++++ b/assembler/src/spades_pipeline/corrector_logic.py
+@@ -24,7 +24,7 @@ def prepare_config_corr(filename, cfg, e
+ import pyyaml2 as pyyaml
+ elif sys.version.startswith('3.'):
+ import pyyaml3 as pyyaml
+- data = pyyaml.load(open(filename, 'r'))
++ data = pyyaml.load(open(filename, 'r'), Loader=pyyaml.FullLoader)
+ data["dataset"] = cfg.dataset
+ data["output_dir"] = cfg.output_dir
+ data["work_dir"] = cfg.tmp_dir
+--- a/assembler/src/tools/reads_utils/reads_quality.py
++++ b/assembler/src/tools/reads_utils/reads_quality.py
+@@ -148,7 +148,7 @@ print("Analyzing datasets")
+ for dataset in datasets:
+
+ try:
+- dataset_data = pyyaml.load(file(dataset, 'r'))
++ dataset_data = pyyaml.load(file(dataset, 'r'), Loader=pyyaml.FullLoader)
+ except pyyaml.YAMLError, exc:
+ support.warning('skipping ' + dataset + ': exception caught while parsing YAML file (' + options_storage.dataset_yaml_filename + '):\n' + str(exc))
+ continue
View it on GitLab: https://salsa.debian.org/med-team/spades/commit/2dd0d58b8f01d2914d2d134c21123ade6d05f28b
--
View it on GitLab: https://salsa.debian.org/med-team/spades/commit/2dd0d58b8f01d2914d2d134c21123ade6d05f28b
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