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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,257 @@ | ||
| import os | ||
| import sys | ||
| import argparse | ||
| import subprocess | ||
|
|
||
| lastd = sys.argv[0].rfind('/') | ||
| if lastd == -1: | ||
| programdir = './' | ||
| else: | ||
| programdir = sys.argv[0][:lastd] + '/' | ||
| parser = argparse.ArgumentParser(description='Single-cell Gene Fusion Detection (c) Zjie Jin', add_help=False) | ||
| subparsers = parser.add_subparsers(help='Select the function', required=True) | ||
| parser1 = subparsers.add_parser('BuildSTARIndex', help='Build the STAR Index', add_help=False) | ||
| group11 = parser1.add_argument_group('Required parameters') | ||
| group12 = parser1.add_argument_group('Optional parameters') | ||
| group11.add_argument("-s", "--STARIndex", help='The STAR index output folder.') | ||
| group11.add_argument("-g", "--Genome", help='The reference file (*.fasta or *.fa).') | ||
| group11.add_argument("-a", "--Annotation", help='The gtf annotation file (*.gtf).') | ||
| group12.add_argument("-t", "--Thread", default='8', help='Number of threads can be used, default is 8.') | ||
| parser2 = subparsers.add_parser('Rename', help='Rename files using consecutive numbers', add_help=False) | ||
| group2 = parser2.add_argument_group('Required parameters') | ||
| group2.add_argument("-f", "--FileDir", help='The folder of input data.') | ||
| parser3 = subparsers.add_parser('RestoreName', help='Restore file names.', add_help=False) | ||
| group3 = parser3.add_argument_group('Required parameters') | ||
| group3.add_argument("-f", "--FileDir", help='The folder of input data.') | ||
| parser4 = subparsers.add_parser('Index', help='Produce some necessary files.', add_help=False) | ||
| group4 = parser4.add_argument_group('Required parameters') | ||
| group4.add_argument("-d", "--GenomeDir", help='The genome index folder.') | ||
| group4.add_argument("-g", "--Genome", help='The reference file (*.fasta or *.fa).') | ||
| group4.add_argument("-a", "--Annotation", help='The gtf annotation file (*.gtf).') | ||
| parser5 = subparsers.add_parser('ReadMapping', help='Mapping pair-end reads using STAR.', add_help=False) | ||
| group51 = parser5.add_argument_group('Required parameters') | ||
| group52 = parser5.add_argument_group('Optional parameters') | ||
| group51.add_argument("-f", "--FileDir", help='The folder of input data.') | ||
| group51.add_argument("-b", "--Begin", help='The first index of input files.') | ||
| group51.add_argument("-e", "--End", help='The last index of input files.') | ||
| group51.add_argument("-s", "--STARIndex", help='The STAR index folder.') | ||
| group52.add_argument("-o", "--OutDir", help='The output folder of the results and temporal files, default is FileDir.') | ||
| group52.add_argument("-t", "--Thread", default='8', help='Number of threads can be used, default is 8') | ||
| parser6 = subparsers.add_parser('ReadProcessing', help='Process the chimeric reads.', add_help=False) | ||
| group61 = parser6.add_argument_group('Required parameters') | ||
| group62 = parser6.add_argument_group('Optional parameters') | ||
| group61.add_argument("-d", "--GenomeDir", help='The genome index folder.') | ||
| group61.add_argument("-o", "--OutDir", help='The output folder of the results and temporal files.') | ||
| mappabilitygroup = group62.add_mutually_exclusive_group() | ||
| mappabilitygroup.add_argument("-m", "--Mappability", default=programdir + '/data/hg19mappability75.txt', | ||
| help='The mappability file, default is hg19mappability75.txt in the data folder.') | ||
| mappabilitygroup.add_argument("-M", "--NoMappabilityFilter", help='Keep all reads and do not apply mappability filter.', | ||
| action='store_true') | ||
| group61.add_argument("-b", "--Begin", help='The first index of input files.') | ||
| group61.add_argument("-e", "--End", help='The last index of input files.') | ||
| parser7 = subparsers.add_parser('FusionCandidate', help='Identify the fusion candidates', add_help=False) | ||
| group71 = parser7.add_argument_group('Required parameters') | ||
| group72 = parser7.add_argument_group('Optional parameters') | ||
| group71.add_argument("-o", "--OutDir", help='The output folder of the results and temporal files.') | ||
| group71.add_argument("-b", "--Begin", help='The first index of input files.') | ||
| group71.add_argument("-e", "--End", help='The last index of input files.') | ||
| group71.add_argument("-d", "--GenomeDir", help='The genome index folder.') | ||
| group72.add_argument("-p", "--Prefix", default='.', | ||
| help='The prefix of result file, default is blank. This should be specified if users want to compare the results of different settings.') | ||
| parser8 = subparsers.add_parser('Retrain', help='Retrain the network using current data.', add_help=False) | ||
| group81 = parser8.add_argument_group('Required parameters') | ||
| group82 = parser8.add_argument_group('Optional parameters') | ||
| group81.add_argument("-o", "--OutDir", help='The output folder of the results and temporal files.') | ||
| group82.add_argument("-p", "--Prefix", default='.', | ||
| help='The prefix of result file, default is blank. This should be specified if users want to compare the results of different settings.') | ||
| group82.add_argument("-w", "--Weight", default=programdir + '/data/weight-V9-2.hdf5', | ||
| help='The initial weight file of the deep-learning network, default is "weight-V9-2.hdf5" in the data folder.') | ||
| group82.add_argument("-c", "--Epoch", default='10', | ||
| help='The number of epochs in the retraining step, default is 10') | ||
| parser9 = subparsers.add_parser('ArtifactScoring', help='Find the artifacts', add_help=False) | ||
| group91 = parser9.add_argument_group('Required parameters') | ||
| group92 = parser9.add_argument_group('Optional parameters') | ||
| group91.add_argument("-d", "--GenomeDir", help='The genome index folder.') | ||
| group91.add_argument("-o", "--OutDir", help='The output folder of the results and temporal files.') | ||
| group91.add_argument("-b", "--Begin", help='The first index of input files.') | ||
| group91.add_argument("-e", "--End", help='The last index of input files.') | ||
| group92.add_argument("-p", "--Prefix", default='.', | ||
| help='The prefix of result file, default is blank. This should be specified if users want to compare the results of different settings.') | ||
| group92.add_argument("-w", "--Weight", default=programdir + '/data/weight-V9-2.hdf5', | ||
| help='The weight file used in the deep-learning network, default is "weight-V9-2.hdf5" in the data folder.') | ||
| parser10 = subparsers.add_parser('FusionReport', help='Report gene fusions.', add_help=False) | ||
| group101 = parser10.add_argument_group('Required parameters') | ||
| group102 = parser10.add_argument_group('Optional parameters') | ||
| group101.add_argument("-f", "--FileDir", help='The folder of input data.') | ||
| group101.add_argument("-d", "--GenomeDir", help='The genome index folder.') | ||
| group102.add_argument("-o", "--OutDir", help='The output folder of the results and temporal files, default is FileDir.') | ||
| group101.add_argument("-b", "--Begin", help='The first index of input files.') | ||
| group101.add_argument("-e", "--End", help='The last index of input files.') | ||
| group102.add_argument("-p", "--Prefix", default='.', | ||
| help='The prefix of result file, default is blank. This should be specified if users want to compare the results of different settings.') | ||
| group102.add_argument("-v", "--PvalueCutoff", default='0.05', help='Pvalue(FDR) cutoff of the statistical model, default is 0.05.') | ||
| group102.add_argument("-n", "--ArtifactScoreCutoff", default='0.75', help='Artifact score cutoff, default is 0.75') | ||
| group102.add_argument("--LncRNAFilterOff", help='turn off the LncRNA filter', action='store_true') | ||
| group102.add_argument("--NoApprovedSymbolFilterOff", help='turn off the no-approved-symbol filter', action='store_true') | ||
|
|
||
| if len(sys.argv) == 1: | ||
| parser.print_help() | ||
| exit() | ||
|
|
||
| args = parser.parse_args() | ||
|
|
||
| if sys.argv[1] == 'Rename': | ||
| if not args.FileDir: | ||
| parser2.print_help() | ||
| print('Please specify all required parameters!') | ||
| exit() | ||
| aa = os.system('python ' + programdir + '/bin/RenameFastqFiles.py ' + args.FileDir) | ||
| if aa == 0: | ||
| print('Successfully rename files to consecutive numbers!') | ||
| print('Please keep RenameList.txt carefully, or the file names can not be restored.') | ||
| else: | ||
| print('ERROR!!!!!') | ||
|
|
||
| if sys.argv[1] == 'RestoreName': | ||
| if not args.FileDir: | ||
| parser3.print_help() | ||
| print('Please specify all required parameters!') | ||
| exit() | ||
| aa = os.system( | ||
| 'python ' + programdir + '/bin/RenameFastqFiles.py ' + args.FileDir + ' ' + args.FileDir + '/RenameList.txt') | ||
| if aa == 0: | ||
| print('Successfully restore file names!') | ||
| else: | ||
| print('ERROR!!!!!') | ||
|
|
||
| if sys.argv[1] == 'BuildSTARIndex': | ||
| if not args.STARIndex or not args.Genome or not args.Annotation: | ||
| parser1.print_help() | ||
| print('Please specify all required parameters!') | ||
| exit() | ||
| os.system('STAR --runMode genomeGenerate --genomeDir ' + args.STARIndex + ' --runThreadN ' + | ||
| args.Thread + ' --genomeFastaFiles ' + args.Genome + ' --sjdbGTFfile ' + | ||
| args.Annotation) | ||
|
|
||
| if sys.argv[1] == 'Index': | ||
| if not args.GenomeDir or not args.Genome or not args.Annotation: | ||
| parser4.print_help() | ||
| print('Please specify all required parameters!') | ||
| exit() | ||
| aa = os.system('mkdir -p ' + args.GenomeDir + ' && cp ' + args.Genome + ' ' + args.GenomeDir + '/ref.fa && cp ' + | ||
| args.Annotation + ' ' + args.GenomeDir + '/ref_annot.gtf && python ' + programdir + | ||
| '/bin/Addchr2gtf.py ' + args.GenomeDir + '/ref_annot.gtf > ' + args.GenomeDir + | ||
| '/ref_annot.gtf.added && python ' + programdir + '/bin/GetExonPos.py ' + args.GenomeDir + | ||
| '/ref_annot.gtf.added > ' + args.GenomeDir + '/exon_probe.hg19.gene.new.bed && python ' + programdir + | ||
| '/bin/GetGenePos.py ' + args.GenomeDir + '/ref_annot.gtf.added > ' + args.GenomeDir + | ||
| '/GenePos.txt && pyensembl install --reference-name GRCH37 --annotation-name my_genome_features --gtf ' | ||
| + args.GenomeDir + '/ref_annot.gtf.added') | ||
| if aa == 0: | ||
| print('Finish Indexing!') | ||
| else: | ||
| print('ERROR!!!!!') | ||
|
|
||
| if sys.argv[1] == 'ReadMapping': | ||
| if not args.OutDir and args.FileDir: | ||
| args.OutDir = args.FileDir | ||
| if not args.FileDir or not args.OutDir or not args.Begin or not args.End or not args.STARIndex: | ||
| parser5.print_help() | ||
| print('Please specify all required parameters!') | ||
| exit() | ||
| aa = os.system( | ||
| 'sh ' + programdir + '/bin/StarMapping_Chimeric.sh ' + args.FileDir + ' ' + args.Begin + ' ' + args.End + ' ' + args.OutDir + | ||
| 'STARMapping/ ' + args.STARIndex + ' ' + args.Thread) | ||
| if aa == 0: | ||
| print('Finish mapping! Index: ' + args.Begin + ' ~ ' + args.End) | ||
| else: | ||
| print('ERROR!!!!!') | ||
|
|
||
| if sys.argv[1] == 'ReadProcessing': | ||
| if not args.OutDir or not args.Begin or not args.End or not args.GenomeDir or not args.NoMappabilityFilter and not args.Mappability: | ||
| parser6.print_help() | ||
| print('Please specify all required parameters!') | ||
| exit() | ||
| if args.NoMappabilityFilter: | ||
| aa = os.system( | ||
| 'sh ' + programdir + '/bin/CombinePipeline_before_FS_NoMappa.sh ' + args.OutDir + ' ' + args.Begin + ' ' + args.End + ' ' + | ||
| args.GenomeDir + '/ref_annot.gtf.added ' + args.GenomeDir + '/exon_probe.hg19.gene.new.bed ' + programdir + '/bin/') | ||
| else: | ||
| aa = os.system( | ||
| 'sh ' + programdir + '/bin/CombinePipeline_before_FS.sh ' + args.OutDir + ' ' + args.Begin + ' ' + args.End + ' ' + | ||
| args.GenomeDir + '/ref_annot.gtf.added ' + args.Mappability + ' ' + args.GenomeDir + '/exon_probe.hg19.gene.new.bed ' + programdir + '/bin/') | ||
| if aa == 0: | ||
| print('Finish Read Processing! Index: ' + args.Begin + ' ~ ' + args.End) | ||
| else: | ||
| print('ERROR!!!!!') | ||
|
|
||
| if sys.argv[1] == 'FusionCandidate': | ||
| if not args.OutDir or not args.Begin or not args.End or not args.GenomeDir: | ||
| parser7.print_help() | ||
| print('Please specify all required parameters!') | ||
| exit() | ||
| aa = os.system( | ||
| 'sh ' + programdir + '/bin/CombinePipeline_startwith_FS.sh ' + args.OutDir + ' ' + args.Begin + ' ' + args.End + ' ' + args.Prefix + ' ' + args.GenomeDir + '/ref.fa ' + args.GenomeDir + '/ref_annot.gtf.added ' + programdir + '/bin/') | ||
| if aa == 0: | ||
| print('Finish identifying fusion candidates') | ||
| else: | ||
| print('ERROR!!!!!') | ||
|
|
||
| if sys.argv[1] == 'Retrain': | ||
| if not args.OutDir: | ||
| parser8.print_help() | ||
| print('Please specify all required parameters!') | ||
| exit() | ||
| aa = os.system( | ||
| 'sh ' + programdir + '/bin/CombinePipeline_Retrain.sh ' + args.OutDir + ' ' + args.Prefix + ' ' + args.Weight + ' ' + args.Epoch + ' ' + programdir + '/bin/') | ||
| if aa == 0: | ||
| print('Finish Retraining!') | ||
| print('New weight file was saved at ' + args.OutDir + '/weights/RetrainWeight.hdf5') | ||
| else: | ||
| print('ERROR!!!!!') | ||
|
|
||
| if sys.argv[1] == 'ArtifactScoring': | ||
| if not args.OutDir or not args.Begin or not args.End or not args.GenomeDir: | ||
| parser9.print_help() | ||
| print('Please specify all required parameters!') | ||
| exit() | ||
| aa = os.system( | ||
| 'sh ' + programdir + '/bin/CombinePipeline_Predict.sh ' + args.OutDir + ' ' + args.Begin + ' ' + args.End + ' ' + args.Prefix + ' ' + | ||
| args.Weight + ' ' + args.GenomeDir + '/ref.fa ' + args.GenomeDir + '/ref_annot.gtf.added ' + programdir + '/bin/') | ||
| if aa == 0: | ||
| print('Finish ArtifactScoring Step!') | ||
| else: | ||
| print('ERROR!!!!!') | ||
|
|
||
| if sys.argv[1] == 'FusionReport': | ||
| if not args.OutDir and args.FileDir: | ||
| args.OutDir = args.FileDir | ||
| if not args.FileDir or not args.OutDir or not args.Begin or not args.End or not args.GenomeDir: | ||
| parser10.print_help() | ||
| print('Please specify all required parameters!') | ||
| exit() | ||
| numcell = 0 | ||
| for i in range(int(args.Begin), int(args.End) + 1): | ||
| if os.path.exists(args.FileDir + str(i) + '_2.fastq') or os.path.exists(args.FileDir + str(i) + '_2.fastq.gz'): | ||
| numcell += 1 | ||
| if args.LncRNAFilterOff: | ||
| lncfilter = '1' | ||
| else: | ||
| lncfilter = '0' | ||
| if args.NoApprovedSymbolFilterOff: | ||
| nasfilter = '1' | ||
| else: | ||
| nasfilter = '0' | ||
| aa = os.system( | ||
| 'sh ' + programdir + '/bin/CombinePipeline_startwith_ChiDist.sh ' + args.OutDir + ' ' + args.Prefix + ' ' + str(numcell) + | ||
| ' ' + args.PvalueCutoff + ' ' + args.ArtifactScoreCutoff + ' ' + args.GenomeDir + '/ref_annot.gtf.added ' + args.GenomeDir + '/GenePos.txt ' + programdir + '/bin/ ' + lncfilter + ' ' + nasfilter) | ||
| if aa == 0: | ||
| if args.Prefix == '.': | ||
| args.Prefix = '' | ||
| print('Final Results are in ' + args.OutDir + '/FinalResult/' + args.Prefix + 'FinalOutput.abridged.txt') | ||
| os.system( | ||
| 'cat ' + args.OutDir + '/FinalResult/' + args.Prefix + 'FinalOutput.abridged.txt > ' + args.OutDir + '/Result.abridged.txt') | ||
| os.system( | ||
| 'cat ' + args.OutDir + '/FinalResult/' + args.Prefix + 'FinalOutput.full.txt > ' + args.OutDir + '/Result.full.txt') | ||
| os.system('mv ' + args.OutDir + '/FinalResult/ ' + args.OutDir + '/Resulttemp/') | ||
| else: | ||
| print('ERROR!!!!!') |