update valid args

urmi-21 · Jan 17, 2021 · 6c3f9fe · 6c3f9fe
1 parent 5c767a2
commit 6c3f9fe
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Showing 4 changed files with 113 additions and 40 deletions.
diff --git a/case_studies/Covid_RNA-Seq/Snakemake/Snakefile b/case_studies/Covid_RNA-Seq/Snakemake/Snakefile
@@ -68,11 +68,11 @@ rule merge:
 		#gene counts
 		df_gene=df[['GeneID']+names].copy()
 		df_gene = df_gene.groupby(['GeneID'],as_index = False).sum()
-                df_gene['GeneID']=df_gene['GeneID'].str.split('.').str[0]
-                #add gene metadata
-                md=pd.read_csv('Ens_gene_metadata.txt',sep='\t',skiprows=0) 
-                md.rename(columns={ md.columns[0]: "GeneID" }, inplace = True)
-                df_gene=md.merge(df_gene, on=['GeneID'], how='right')
-                #reorder
-                df_gene = df_gene[ ['Gene name'] + [ col for col in df_gene.columns if col != 'Gene name' ] ]
+        df_gene['GeneID']=df_gene['GeneID'].str.split('.').str[0]
+        #add gene metadata
+        md=pd.read_csv('Ens_gene_metadata.txt',sep='\t',skiprows=0) 
+        md.rename(columns={ md.columns[0]: "GeneID" }, inplace = True)
+        df_gene=md.merge(df_gene, on=['GeneID'], how='right')
+        #reorder
+        df_gene = df_gene[ ['Gene name'] + [ col for col in df_gene.columns if col != 'Gene name' ] ]
 		df_gene.to_csv(DIR+'/results_TPM_gene.tsv',sep='\t',index=False)
diff --git a/pyrpipe/mapping.py b/pyrpipe/mapping.py
@@ -141,9 +141,8 @@ def build_index(self,index_path,genome,objectid="NA"):
                 raise OSError("Error creating hisat2 index. Failed to create index directory.")
 
 
-        hisat2Buildvalid_args=['-c','--large-index','-a','-p','--bmax','--bmaxdivn','--dcv','--nodc','-r','-3','-o',
-                                  '-t','--localoffrate','--localftabchars','--snp','--haplotype','--ss','--exon',
-                                  '--seed','-q','-h','--usage','--version']
+        hisat2Buildvalid_args=valid_args._args_HISAT2BUILD
+
 
         args=(genome,index_path)
         internal_kwargs={"-p":self._threads}

diff --git a/pyrpipe/quant.py b/pyrpipe/quant.py
@@ -121,7 +121,7 @@ def build_index(self,index_path,transcriptome,objectid="NA"):
         #add positional args
         internal_kwargs['--']=args
 
-        validArgsIndex=['-i','--index','-k','--kmer-size','--make-unique']
+        validArgsIndex=valid_args._args_KALLISTO_INDEX
 
         kallisto_cmd=['kallisto','index']
         kallisto_cmd.extend(pu.parse_unix_args(validArgsIndex,internal_kwargs))
@@ -280,9 +280,8 @@ def build_index(self,index_path,transcriptome,objectid="NA"):
                 raise OSError("Error creating salmon index. Failed to create index directory.")
 
 
-        validArgsIndex=['-v','-t','--transcripts','-k','--kmerLen','-i',
-                             '--index','--gencode','--keepDuplicates','-p','--threads','--perfectHash',
-                             '--type','-s','--sasamp','-d','--decoys']
+        validArgsIndex=valid_args._args_SALMON_INDEX
+
 
         internal_kwargs={"--threads":_threads,"-t":transcriptome,"-i":index_path}
         #read build parameters

diff --git a/pyrpipe/valid_args.py b/pyrpipe/valid_args.py
@@ -8,11 +8,12 @@
 This module contains a list of valid arguments for the tools
 """
 
+#version 2.10.0
 _args_FASTERQDUMP=['-e','-f','-t','-s','-N','-X','-a','-p','-c','-o','-O','-h','-V',
                    '-L','-v','-q','-b','-m','-x','-S','-3','-P','-M',
                    '-B','--option-file','--strict','--table','--include-technical',
                    '--skip-technical','--concatenate-reads']
-
+#version 0.6.6
 _args_TRIM_GALORE=['--cores','-v','-q','--phred33','--phred64','--fastqc','--fastqc_args','-a','-a2',
                    '--illumina','--nextera','--small_rna','--consider_already_trimmed',
                    '--max_length','--stringency','-e','--gzip','--dont_gzip','--length',
@@ -22,7 +23,7 @@
                    '--clock','--polyA','--rrbs','--non_directional','--keep','--paired','-t',
                    '--retain_unpaired','-r1','-r2']
 
-
+#version 38.76
 _args_BBDUK=['in','in2','ref','literal','touppercase','interleaved','qin','reads','copyundefined',
              'samplerate','samref','out','out2','outm','outm2','outs','stats','refstats','rpkm',
              'dump','duk','nzo','overwrite','showspeed','ziplevel','fastawrap','qout','statscolumns',
@@ -42,11 +43,15 @@
              'entropyk','minbasefrequency','entropytrim','entropymask','entropymark','cardinality',
              'cardinalityout','loglogk','loglogbuckets','-Xmx','-eoom','-da']
 
-_args_STAR=['--parametersFiles','--sysShell','--runMode','--runThreadN','--runDirPerm','--runRNGseed','--quantMode','--quantTranscriptomeBAMcompression','--quantTranscriptomeBan','--twopassMode','--twopass1readsN',
-            '--genomeDir','--genomeLoad','--genomeFastaFiles','--genomeChrBinNbits','--genomeSAindexNbases','--genomeSAsparseD','--genomeSuffixLengthMax','--genomeChainFiles','--genomeFileSizes',
+#STAR version 2.7.6a
+_args_STAR=['--help','--parametersFiles','--sysShell','--runMode','--runThreadN','--runDirPerm','--runRNGseed','--quantMode','--outFilterIntronStrands','--alignInsertionFlush','--peOverlapMMp',
+            '--quantTranscriptomeBAMcompression','--quantTranscriptomeBan','--twopassMode','--twopass1readsN','--chimMultimapScoreRange','--chimNonchimScoreDropMin','--chimOutJunctionFormat',
+            '--genomeDir','--genomeLoad','--genomeFastaFiles','--genomeType','--genomeTransformType','--genomeTransformVCF','--outSAMtlen','--outBAMsortingBinsN','--peOverlapNbasesMin','--waspOutputMode',
+            '--genomeChrBinNbits','--genomeSAindexNbases','--genomeSAsparseD','--genomeSuffixLengthMax','--readFilesManifest','--readFilesPrefix','--readQualityScoreBase','--seedMapMin',
+            '--genomeChainFiles','--genomeFileSizes','--genomeConsensusFile','--sjdbGTFtagExonParentGeneName','--sjdbGTFtagExonParentGeneType','--varVCFfile','--readFilesType','--limitNreadsSoft','--seedSplitMin',
             '--sjdbFileChrStartEnd','--sjdbGTFfile','--sjdbGTFchrPrefix','--sjdbGTFfeatureExon','--sjdbGTFtagExonParentTranscript','--sjdbGTFtagExonParentGene','--sjdbOverhang','--sjdbScore','--sjdbInsertSave',
             '--inputBAMfile','--readFilesIn','--readFilesCommand','--readMapNumber','--readMatesLengthsIn','--readNameSeparator','--clip3pNbases','--clip5pNbases','--clip3pAdapterSeq','--clip3pAdapterMMp','--clip3pAfterAdapterNbases',
-            '--limitGenomeGenerateRAM','--limitIObufferSize','--limitOutSAMoneReadBytes','--limitOutSJoneRead','--limitOutSJcollapsed','--limitBAMsortRAM','--limitSjdbInsertNsj','--outFileNamePrefix','--outTmpDir','--outTmpKeep',
+            '--limitGenomeGenerateRAM','--limitIObufferSize','--limitOutSAMoneReadBytes','--limitOutSJoneRead','--limitOutSJcollapsed','--limitBAMsortRAM ','--limitSjdbInsertNsj','--outFileNamePrefix','--outTmpDir','--outTmpKeep',
             '--outStd','--outReadsUnmapped','--outQSconversionAdd','--outMultimapperOrder','--outSAMtype','--outSAMmode','--outSAMstrandField','--outSAMattributes','--outSAMattrIHstart','--outSAMunmapped','--outSAMorder',
             '--outSAMprimaryFlag','--outSAMreadID','--outSAMmapqUnique','--outSAMflagOR','--outSAMflagAND','--outSAMattrRGline','--outSAMheaderHD','--outSAMheaderPG','--outSAMheaderCommentFile','--outSAMfilter','--outSAMmultNmax',
             '--outBAMcompression','--outBAMsortingThreadN','--bamRemoveDuplicatesType','--bamRemoveDuplicatesMate2basesN','--outWigType','--outWigStrand','--outWigReferencesPrefix','--outWigNorm','--outFilterType',
@@ -56,8 +61,11 @@
             '--seedSearchStartLmax','--seedSearchStartLmaxOverLread','--seedSearchLmax','--seedMultimapNmax','--seedPerReadNmax','--seedPerWindowNmax','--seedNoneLociPerWindow','--alignIntronMin','--alignIntronMax','--alignMatesGapMax',
             '--alignSJoverhangMin','--alignSJstitchMismatchNmax','--alignSJDBoverhangMin','--alignSplicedMateMapLmin','--alignSplicedMateMapLminOverLmate','--alignWindowsPerReadNmax','--alignTranscriptsPerWindowNmax','--alignTranscriptsPerReadNmax',
             '--alignEndsType','--alignEndsProtrude','--alignSoftClipAtReferenceEnds','--winAnchorMultimapNmax','--winBinNbits','--winAnchorDistNbins','--winFlankNbins','--winReadCoverageRelativeMin','--winReadCoverageBasesMin',
-            '--chimOutType','--chimSegmentMin','--chimScoreMin','--chimScoreDropMax','--chimScoreSeparation','--chimScoreJunctionNonGTAG','--chimJunctionOverhangMin','--chimSegmentReadGapMax','--chimFilter','--chimMainSegmentMultNmax']
+            '--chimOutType','--chimSegmentMin','--chimScoreMin','--chimScoreDropMax','--chimScoreSeparation','--chimScoreJunctionNonGTAG','--chimJunctionOverhangMin','--chimSegmentReadGapMax','--chimFilter','--chimMainSegmentMultNmax',
+            '--soloCBwhitelist','--soloType','--soloCBstart','--soloCBlen','--soloUMIstart','--soloUMIlen','--soloBarcodeReadLength','--soloCBposition','--soloUMIposition','--soloAdapterSequence','--soloAdapterMismatchesNmax','--soloCBmatchWLtype',
+            '--soloStrand','--soloFeatures','--soloUMIdedup','--soloUMIfiltering','--soloOutFileNames','--soloCellFilter','--soloOutFormatFeaturesGeneField3','--soloClusterCBfile']
 
+#HISAT2 version 2.2.1
 _args_HISAT2=['-x','-1','-2','-U','--sra-acc','-S','-q','--qseq','-f','-r','-c','-s',
               '-u','-5','-3','--phred33','--phred64','--int-quals',
               '--sra-acc','--n-ceil','--ignore-quals','--nofw','--norc','--pen-cansplice',
@@ -72,7 +80,11 @@
               '--met','--no-head','--no-sq','--rg-id','--rgit-sec-seq','-o','-p',
               '--reorder','--mm','--qc-filter','--seed','--non-deterministic',
               '--remove-chrname','--add-chrname','--version']
+_args_HISAT2BUILD=['-c','--large-index','-a','-p','--bmax','--bmaxdivn','--dcv','--nodc','-r','-3','-o',
+                '-t','--localoffrate','--localftabchars','--snp','--haplotype','--ss','--exon',
+                '--repeat-ref','--repeat-info','--repeat-snp','--repeat-haplotype','--seed','-q','-h','--usage','--version']
 
+#bowtie2 version 2.3.5.1
 _args_BOWTIE2=['-x','-1','-2','-U','--interleaved','-S','-b','-q','--tab5','--tab6','--qseq','-f','-r','-F','-c','-s','-u','-5','-3',
                 '--trim-to','--phred33','--phred64','--int-quals','--very-fast','--fast',
                 '--sensitive','--very-sensitive','--very-fast-local','--fast-local',
@@ -87,10 +99,12 @@
                 '-p','--threads','--reorder','--mm','--qc-filter','--seed','--non-deterministic',
                 ]
 
+#stringtie version 2.1.4
 _args_STRINGTIE=['-G','--version','--conservative','--rf','--fr','-o','-l',
                 '-f','-L','-m','-a','-j','-t','-c','-s','-v','-g','-M',
                 '-p','-A','-B','-b','-e','-x','-u','-h','--merge','-F','-T','-i']
 
+#cufflinks version 2.2.1
 _args_CUFFLINKS=['-o','--output-dir','-p','--num-threads','--seed','-G','--GTF','-g','--GTF-guide','-M','--mask-file','-b','--frag-bias-correct','-u','--multi-read-correct','--library-type','--library-norm-method',
                 '-m','--frag-len-mean','-s','--frag-len-std-dev','--max-mle-iterations','--compatible-hits-norm','--total-hits-norm','--num-frag-count-draws','--num-frag-assign-draws','--max-frag-multihits','--no-effective-length-correction',
                 '--no-length-correction','-N','--upper-quartile-norm','--raw-mapped-norm','-L','--label','-F','--min-isoform-fraction','-j','--pre-mrna-fraction','-I','--max-intron-length','-a','--junc-alpha','-A','--small-anchor-fraction',
@@ -108,23 +122,84 @@
               '--normalize_by_read_set','--genome_guided_max_intron','--genome_guided_min_coverage','--genome_guided_min_reads_per_partition',
               '--grid_conf','--grid_node_CPU','--grid_node_max_memory']
 
-_args_KALLISTO=['-i','--index','-o','--output-dir','--bias','-b','--bootstrap-samples',
-                '--seed','--plaintext','--fusion','--single','--fr-stranded','--rf-stranded',
-                '-l','--fragment-length','-s','--sd','-t','--threads','--pseudobam']
-
-_args_SALMON=['--help-reads','-i','--index','-l','--libType','-r','--unmatedReads',
-              '-1','--mates1','-2','--mates2','-o','--output','--discardOrphansQuasi',
-              '--allowOrphansFMD','--seqBias','--gcBias','-p','--threads','--incompatPrior',
-              '-g','--geneMap','-z','--writeMappings','--meta','--alternativeInitMode',
-              '--auxDir','-c','--consistentHits','--dumpEq','-d','--dumpEqWeights',
-              '--fasterMapping','--minAssignedFrags','--reduceGCMemory','--biasSpeedSamp',
-              '--strictIntersect','--fldMax','--fldMean','--fldSD','-f','--forgettingFactor',
-              '-m','--maxOcc','--initUniform','-w','--maxReadOcc','--noLengthCorrection',
-              '--noEffectiveLengthCorrection','--noFragLengthDist','--noBiasLengthThreshold',
-              '--numBiasSamples','--numAuxModelSamples','--numPreAuxModelSamples','--useVBOpt',
-              '--rangeFactorizationBins','--numGibbsSamples','--numBootstraps','--thinningFactor',
-              '-q','--perTranscriptPrior','--vbPrior','--writeOrphanLinks','--writeUnmappedNames',
-              '-x','--quasiCoverage','--validateMappings']
-
-
-_args_SAMTOOLS=None
+
+
+
+
+#kallisto version 0.46.2
+_args_KALLISTO_INDEX=['-i','--index','-k','--kmer-size','--make-unique']
+_args_KALLISTO_QUANT=['-i','--index','-o','--output-dir','--bias','-b','--bootstrap-samples','--genomebam','--verbose',
+                     '--seed','--plaintext','--fusion','--single','--fr-stranded','--rf-stranded','-g','-c',
+                     '-l','--fragment-length','-s','--sd','-t','--threads','--pseudobam','--single-overhang']
+_args_KALLISTO_BUS=['-i','-o','-x','-l','-t','-b','-n','--verbose']
+_args_KALLISTO_H5DUMP=['-o','--output-dir']
+_args_KALLISTO_INSPECT=['-g','-G','-b']
+_args_KALLISTO_MERGE=['-i','-o','--output-dir']
+_args_KALLISTO_PSEUDO=['-i','--index','-o','--output-dir','-u','--umi','-b','--batch','--single','-l','--fragment-length','-s','--sd','-t','--threads']
+_args_KALLISTO={}
+_args_KALLISTO['index']=_args_KALLISTO_INDEX
+_args_KALLISTO['quant']=_args_KALLISTO_QUANT
+_args_KALLISTO['bus']=_args_KALLISTO_BUS
+_args_KALLISTO['pseudo']=_args_KALLISTO_PSEUDO
+_args_KALLISTO['h5dump']=_args_KALLISTO_H5DUMP
+_args_KALLISTO['inspect']=_args_KALLISTO_INSPECT
+_args_KALLISTO['merge']=_args_KALLISTO_MERGE
+
+
+
+#salmon version 0.14.1
+_args_SALMON_ALEVIN=['-l','-i','-r','-1','-2','-v','-h','-o','-p','--tgMap','--hash',
+                    '--dropseq','--chromiumV3','--chromium','--gemcode','--celseq','--celseq2',
+                    '--whitelist','--noQuant','--numCellBootstraps','--forceCells','--expectCells',
+                    '--mrna','--rrna','--keepCBFraction','--dumpfq','--dumpBfh','--dumpUmiGraph',
+                    '--dumpFeatures','--dumpMtx','--lowRegionMinNumBarcodes','--maxNumBarcodes']
+_args_SALMON_INDEX=['-v','--version','-h','--help','-t','--transcripts','-k','--kmerLen','-i',
+                     '--index','--gencode','--keepDuplicates','-p','--threads','--perfectHash',
+                     '--type','-d','--decoys']
+_args_SALMON_QUANT=['--help-reads','-i','--index','-l','--libType','-r','--unmatedReads',
+                    '-1','--mates1','-2','--mates2','-o','--output','--discardOrphansQuasi',
+                    '--allowOrphansFMD','--seqBias','--gcBias','-p','--threads','--incompatPrior',
+                    '-g','--geneMap','-z','--writeMappings','--meta','--alternativeInitMode',
+                    '--auxDir','-c','--consistentHits','--dumpEq','-d','--dumpEqWeights',
+                    '--fasterMapping','--minAssignedFrags','--reduceGCMemory','--biasSpeedSamp',
+                    '--strictIntersect','--fldMax','--fldMean','--fldSD','-f','--forgettingFactor',
+                    '-m','--maxOcc','--initUniform','-w','--maxReadOcc','--noLengthCorrection',
+                    '--noEffectiveLengthCorrection','--noFragLengthDist','--noBiasLengthThreshold',
+                    '--numBiasSamples','--numAuxModelSamples','--numPreAuxModelSamples','--useVBOpt',
+                    '--rangeFactorizationBins','--numGibbsSamples','--numBootstraps','--thinningFactor',
+                    '-q','--perTranscriptPrior','--vbPrior','--writeOrphanLinks','--writeUnmappedNames',
+                    '-x','--quasiCoverage','--validateMappings','--consensusSlack','--minScoreFraction',
+                    '--maxMMPExtension','--ma','--mp','--go','--ge','--bandwidth','--allowDovetail','--recoverOrphans',
+                    '--mimicBT2','--mimicStrictBT2','--hardFilter','--skipQuant','--useEM','--noGammaDraw',
+                    '--bootstrapReproject','--sigDigits']
+_args_SALMON_QUANTMERGE=['--quants','--names','-c','--column','-o','--output','--genes','--missing']
+
+_args_SALMON={}
+_args_SALMON['index']=_args_SALMON_INDEX
+_args_SALMON['quant']=_args_SALMON_QUANT
+_args_SALMON['alevin']=_args_SALMON_ALEVIN
+_args_SALMON['quantmerge']=_args_SALMON_QUANTMERGE
+
+
+#samtools version 1.9
+_args_SAMTOOLS_SORT=['-l','-m','-n','-t','-o','-T','-O','-@','--input-fmt-option','--output-fmt','--output-fmt-option','--reference','--threads']
+_args_SAMTOOLS_VIEW=['-b','-C','-1','-u','-h','-H','-c','-o','-U','-t','-L','-r','-R','-q','-l','-m','-f','-F','-G','-s','-M','-x','-B','-?','-S','O','T','@',
+                    '--input-fmt-option','--output-fmt','--output-fmt-option','--reference','--threads']
+_args_SAMTOOLS_MERGE=['-n','-t','-r','-u','-f','-1','-l','-R','-h','-c','-p','-s','-b','-O','-@','--input-fmt-option',
+                      '--output-fmt','--output-fmt-option','--reference','--threads']
+_args_SAMTOOLS={}
+_args_SAMTOOLS['sort']=_args_SAMTOOLS_SORT
+_args_SAMTOOLS['view']=_args_SAMTOOLS_VIEW
+_args_SAMTOOLS['merge']=_args_SAMTOOLS_MERGE
+
+
+
+
+
+
+
+
+
+
+
+