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)
