Author: Andreas Tille Last-Update: Tue, 12 Nov 2019 17:11:17 +0100 Description: Make sure Python3 interpreter is used in scripts --- a/assembler/changer_of_K.py +++ b/assembler/changer_of_K.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 import os import shutil --- a/assembler/spades.py +++ b/assembler/spades.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/spades_init.py +++ b/assembler/spades_init.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/src/spades_pipeline/easy_align.py +++ b/assembler/src/spades_pipeline/easy_align.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 import os import sys --- a/assembler/src/spades_pipeline/process_cfg.py +++ b/assembler/src/spades_pipeline/process_cfg.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/src/spades_pipeline/truspades/moleculo_filter_contigs.py +++ b/assembler/src/spades_pipeline/truspades/moleculo_filter_contigs.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/truspades.py +++ b/assembler/truspades.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # 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 @@ -#!/usr/bin/env python +#!/usr/bin/python3 from __future__ import (print_function) import pandas --- a/assembler/src/spades_pipeline/hammer_logic.py +++ b/assembler/src/spades_pipeline/hammer_logic.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/src/spades_pipeline/options_storage.py +++ b/assembler/src/spades_pipeline/options_storage.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/src/spades_pipeline/run_contig_breaker.py +++ b/assembler/src/spades_pipeline/run_contig_breaker.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/src/spades_pipeline/truspades/break_by_coverage.py +++ b/assembler/src/spades_pipeline/truspades/break_by_coverage.py @@ -1,4 +1,4 @@ -#! /usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/src/projects/mts/scripts/split_bins.py +++ b/assembler/src/projects/mts/scripts/split_bins.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import print_function +#!/usr/bin/python3 from operator import itemgetter import os --- a/assembler/src/spades_pipeline/spades_logic.py +++ b/assembler/src/spades_pipeline/spades_logic.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University @@ -214,7 +214,7 @@ def run_iteration(configs_dir, execution lines = [] with open(cfg_file) as infile: for line in infile: - for src, target in replacements.iteritems(): + for src, target in replacements.items(): line = line.replace(src, target) lines.append(line) with open(cfg_file, 'w') as outfile: @@ -275,7 +275,7 @@ def run_scaffold_correction(configs_dir, lines = [] with open(cfg_file) as infile: for line in infile: - for src, target in replacements.iteritems(): + for src, target in replacements.items(): line = line.replace(src, target) lines.append(line) with open(cfg_file, 'w') as outfile: --- a/assembler/src/spades_pipeline/truspades/reference_construction.py +++ b/assembler/src/spades_pipeline/truspades/reference_construction.py @@ -1,4 +1,4 @@ -#! /usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/src/test/cap/tests/synthetic/test_generator.py +++ b/assembler/src/test/cap/tests/synthetic/test_generator.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/src/projects/mts/scripts/choose_samples.py +++ b/assembler/src/projects/mts/scripts/choose_samples.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import (print_function) +#!/usr/bin/python3 import argparse from operator import itemgetter --- a/assembler/src/projects/mts/scripts/clusters2csv.py +++ b/assembler/src/projects/mts/scripts/clusters2csv.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import print_function +#!/usr/bin/python3 import sys from Bio import SeqIO --- a/assembler/src/projects/mts/scripts/combine_contigs.py +++ b/assembler/src/projects/mts/scripts/combine_contigs.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import print_function +#!/usr/bin/python3 import sys import os import os.path --- a/assembler/src/projects/mts/scripts/multi_stats.py +++ b/assembler/src/projects/mts/scripts/multi_stats.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import (print_function) +#!/usr/bin/python3 import argparse import os --- a/assembler/src/spades_pipeline/support.py +++ b/assembler/src/spades_pipeline/support.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2016 Saint Petersburg State University --- a/assembler/src/projects/mts/scripts/cut_fasta.py +++ b/assembler/src/projects/mts/scripts/cut_fasta.py @@ -1,7 +1,6 @@ -#!/usr/bin/env python +#!/usr/bin/python3 """Cut up fasta file in non-overlapping or overlapping parts of equal length. """ -from __future__ import print_function import argparse import sys from Bio import SeqIO --- a/assembler/src/projects/mts/scripts/bhtsne.py +++ b/assembler/src/projects/mts/scripts/bhtsne.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ''' 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 @@ -#!/usr/bin/env python -from __future__ import (print_function) +#!/usr/bin/python3 import re import sys --- a/assembler/src/projects/mts/scripts/subsample.py +++ b/assembler/src/projects/mts/scripts/subsample.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import (print_function) +#!/usr/bin/python3 import argparse import gzip --- a/assembler/src/projects/mts/multirun.py +++ b/assembler/src/projects/mts/multirun.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import (print_function) +#!/usr/bin/python3 import argparse import os --- a/assembler/src/projects/mts/scripts/contig_name_filter.py +++ b/assembler/src/projects/mts/scripts/contig_name_filter.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import print_function +#!/usr/bin/python3 import sys from Bio import SeqIO --- a/assembler/src/projects/mts/scripts/gather_stats.py +++ b/assembler/src/projects/mts/scripts/gather_stats.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import (print_function) +#!/usr/bin/python3 import argparse from collections import OrderedDict --- a/assembler/src/tools/misc/copyrighter.py +++ b/assembler/src/tools/misc/copyrighter.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/src/tools/misc/datasets_converter.py +++ b/assembler/src/tools/misc/datasets_converter.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/src/tools/misc/datasets_info2yaml_converter.py +++ b/assembler/src/tools/misc/datasets_info2yaml_converter.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/src/tools/misc/sv_simulator.py +++ b/assembler/src/tools/misc/sv_simulator.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/src/tools/reads_utils/crop/crop_bfaecium.py +++ b/assembler/src/tools/reads_utils/crop/crop_bfaecium.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/src/projects/mts/mts.py +++ b/assembler/src/projects/mts/mts.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import (print_function) +#!/usr/bin/python3 import argparse import subprocess --- a/assembler/src/tools/misc/assembler_runner/runner.py +++ b/assembler/src/tools/misc/assembler_runner/runner.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/src/tools/misc/txt2gff.py +++ b/assembler/src/tools/misc/txt2gff.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/src/tools/reads_utils/ideal_by_fasta.py +++ b/assembler/src/tools/reads_utils/ideal_by_fasta.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/src/tools/truseq/quast_all.py +++ b/assembler/src/tools/truseq/quast_all.py @@ -1,4 +1,4 @@ -#! /usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/src/tools/misc/datasets_info_cleaner.py +++ b/assembler/src/tools/misc/datasets_info_cleaner.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University --- a/assembler/src/tools/spades_pipeline/spades_download_binary.py +++ b/assembler/src/tools/spades_pipeline/spades_download_binary.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # 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@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 --- a/assembler/src/spades_pipeline/truspades/generate_quality.py +++ b/assembler/src/spades_pipeline/truspades/generate_quality.py @@ -52,7 +52,7 @@ def CountContigQuality(contigs, qual): for pos in range(len(contigs[i])): q = qual[i][pos] if q[1] != 0: - qual_list[pos] = chr(q[0] / q[1]) + qual_list[pos] = chr(q[0] // q[1]) else: cnt += 1 contigs[i].qual = "".join(qual_list)