def impInitIO(self, ): faInput1 = self.getParamIO('faInput1') gtfInput1 = self.getParamIO('gtfInput1') assembliesInput = self.getParamIO('assembliesInput') gtfOutputDir = self.getParamIO('gtfOutputDir') if gtfOutputDir is None: self.setParamIO('gtfOutputDir', Configure.getTmpDir()) #set all input files self.setInputDirOrFile('assembliesInput', assembliesInput) if faInput1 is None: faInput1 = Configure.getConfig('') self.setIput('faInput1', faInput1) self.setParamIO('faInput1', faInput1) else: self.setInput('faInput1', faInput1) if gtfInput1 is None: gtfInput1 = Configure.getConfig('') self.setIput('gtfInput1', gtfInput1) self.setParamIO('gtfInput1', gtfInput1) else: self.setInput('gtfInput1', gtfInput1) if assembliesInput is not None: self._setInputSize(len(self.getInputList('assembliesInput'))) merged_gtf = list() for i in range(len(self.getInputList('assembliesInput'))): merged_gtf.append( os.path.join(gtfOutputDir, 'cuffmerge_' + str(i), 'merged.gtf')) self.setOutput('merged_gtf', merged_gtf) else: self.setOutput('merged_gtf', None)
def impInitIO(self, ): # obtain all input and output parameters #fastqInput1 = self.getParamIO('fastqInput1') fastqInput1 = self.getParamIO('fastqInput1') fastqInput2 = self.getParamIO('fastqInput2') samOutputDir = self.getParamIO('samOutputDir') ht2Idx = self.getParamIO('ht2Idx') if samOutputDir is None: self.setParamIO('samOutputDir', Configure.getTmpDir()) # print(ht2Idx) #set all input files #self.setInputDirOrFile('fastqInput1',fastqInput1) self.setInputDirOrFile('fastqInput1', fastqInput1) self.setInputDirOrFile('fastqInput2', fastqInput2) if ht2Idx is None: self.setInput('ht2IdxFile', Configure.getConfig('ht2IdxFile')) self.setParamIO('ht2Idx', Configure.getConfig('ht2Indx')) else: suffix = [ '.1.ht2', '.2.ht2', '.3.ht2', '.4.ht2', '.5.ht2', '.6.ht2', '.7.ht2', '.8.ht2' ] ht2IdxFiles = [ht2Idx + s for s in suffix] self.setInput('ht2IdxFiles', ht2IdxFiles) # create output file paths and set self.setOutputDir1To1('samOutput', samOutputDir, 'hisat', 'sam', 'fastqInput1') # set how many sample are there if fastqInput1 is not None: self._setInputSize(len(self.getInputList('fastqInput1')))
def impInitIO(self, ): """ This function is to initialize all of the input and output files from the io parameters set in __init__() """ # obtain all input and output parameters fastqInput1 = self.getParamIO('fastqInput1') fastqInput2 = self.getParamIO('fastqInput2') bt2Idx = self.getParamIO('bt2Idx') samOutputDir = self.getParamIO('samOutputDir') mapRsOutputDir = self.getParamIO('mapRsOutputDir') #set all input files self.setInputDirOrFile('fastqInput1', fastqInput1) self.setInputDirOrFile('fastqInput2', fastqInput2) #some special input from __init__ or configure if bt2Idx is None: self.setInput('bt2IdxFiles', Configure.getConfig('bt2IdxFiles')) self.setParamIO('bt2Idx', Configure.getConfig('bt2Idx')) else: suffix = [ '.1.bt2', '.2.bt2', '.3.bt2', '.4.bt2', '.rev.1.bt2', '.rev.2.bt2' ] bt2IdxFiles = [bt2Idx + s for s in suffix] self.setInput('bt2IdxFiles', bt2IdxFiles) # create output file paths and set if samOutputDir is None: self.setParamIO('samOutputDir', Configure.getTmpDir()) if mapRsOutputDir is None: self.setParamIO('mapRsOutputDir', Configure.getTmpDir()) self.setOutputDir1To1('samOutput', samOutputDir, None, 'sam', 'fastqInput1') self.setOutputDir1To1('mapRsOutput', mapRsOutputDir, None, 'result.txt', 'fastqInput1') # set how many sample are there if fastqInput1 is not None: self._setInputSize(len(self.getInputList('fastqInput1')))
def impInitIO(self,): bamInput = self.getParamIO('bamInput') gtfInput = self.getParamIO('gtfInput') outputDir = self.getParamIO('outputDir') #fragBiasCorrectInput = self.getParamIO('fragBiasCorrectInput') if outputDir is None: self.setParamIO('outputDir',Configure.getTmpDir()) self.setInputDirOrFile('bamInput',bamInput) if gtfInput is None: gtfInput=Configure.getConfig('') self.setIput('gtfInput',gtfInput) self.setParamIO('gtfInput',gtfInput) else: self.setInput('gtfInput',gtfInput) self.setOutput('assembliesOutput',os.path.join(Configure.getTmpDir(), 'assemblies.txt')) if bamInput is not None: self._setInputSize(len(self.getInputList('bamInput'))) genes_fpkm_tracking=list() isoforms_fpkm_tracking=list() skipped_gtf=list() transcripts_gtf=list() for i in range(len(self.getInputList('bamInput'))): genes_fpkm_tracking.append(os.path.join(outputDir, 'cufflinks_'+str(i),'genes.fpkm_tracking')) isoforms_fpkm_tracking.append(os.path.join(outputDir, 'cufflinks_'+str(i),'isoforms.fpkm_tracking')) skipped_gtf.append(os.path.join(outputDir, 'cufflinks_'+str(i),'skipped.gtf')) transcripts_gtf.append(os.path.join(outputDir, 'cufflinks_'+str(i),'transcripts.gtf')) self.setOutput('genes_fpkm_tracking',genes_fpkm_tracking) self.setOutput('isoforms_fpkm_tracking',isoforms_fpkm_tracking) self.setOutput('skipped_gtf',skipped_gtf) self.setOutput('transcripts_gtf',transcripts_gtf) else: self.setOutput('genes_fpkm_tracking',None) self.setOutput('isoforms_fpkm_tracking',None) self.setOutput('skipped_gtf',None) self.setOutput('transcripts_gtf',None)