def __init__(self, analysis, suffix="", readFilter='all', strand='Plus'):
self.suffix = str(suffix)
self.readFilter = readFilter
self.strand = strand
LogicalStep.__init__(self, analysis, 'bamToBws_' + \
readFilter.lower() + strand + '_' + suffix)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
def writeVersions(self,raFile=None,allLevels=False):
'''Writes versions to to the log or a file.'''
if allLevels:
LogicalStep.writeVersions(self, raFile)
if raFile != None:
raFile.add('eap_run_hotspot', self.getToolVersion('eap_run_hotspot'))
raFile.add('hotspot', self.getToolVersion( \
self.ana.toolsDir+'hotspot-distr/hotspot-deploy/bin/hotspot'))
raFile.add('python2.7', self.getToolVersion('python2.7'))
raFile.add('hotspot.py', self.getToolVersion('hotspot.py'))
raFile.add('bedToBigBed', self.getToolVersion('bedToBigBed'))
raFile.add('bedmap', self.getToolVersion('bedmap'))
raFile.add('sort-bed', self.getToolVersion('sort-bed'))
raFile.add('starchcat', self.getToolVersion('starchcat'))
raFile.add('unstarch', self.getToolVersion('unstarch'))
raFile.add('intersectBed',self.getToolVersion( \
self.ana.toolsDir+'bedtools/bin/intersectBed'))
raFile.add('bedGraphPack',self.getToolVersion('bedGraphPack'))
raFile.add('bedGraphToBigWig', self.getToolVersion('bedGraphToBigWig'))
else:
self.getToolVersion('eap_run_hotspot')
self.getToolVersion(self.ana.toolsDir+'hotspot-distr/hotspot-deploy/bin/hotspot')
self.getToolVersion('python2.7')
self.getToolVersion('hotspot.py')
self.getToolVersion('bedToBigBed')
self.getToolVersion('bedmap')
self.getToolVersion('sort-bed')
self.getToolVersion('starchcat')
self.getToolVersion('unstarch')
self.getToolVersion(self.ana.toolsDir+'bedtools/bin/intersectBed')
self.getToolVersion('bedGraphPack')
self.getToolVersion('bedGraphToBigWig')
def __init__(self, analysis, suffix="", readFilter='all', strand='Plus'):
self.suffix = str(suffix)
self.readFilter = readFilter
self.strand = strand
LogicalStep.__init__(self, analysis, 'bamToBws_' + \
readFilter.lower() + strand + '_' + suffix)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
def __init__(self, analysis, replicate='1', libId='', encoding='sanger', tagLen=100):
self.replicate = str(replicate)
self.encoding = encoding
self.libId = libId
self.tagLen = int(tagLen)
LogicalStep.__init__(self, analysis, 'alignmentByTophat_' + analysis.readType + 'Rep' + \
self.replicate)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all step versions
def writeVersions(self, raFile=None, allLevels=False):
'''Writes versions to to the log or a file.'''
if allLevels:
LogicalStep.writeVersions(self, raFile)
if raFile != None:
raFile.add('samtools', samtools.version(self))
else:
samtools.version(self)
def writeVersions(self, raFile=None, allLevels=False):
"""Writes versions to to the log or a file."""
if allLevels:
LogicalStep.writeVersions(self, raFile)
if raFile != None:
raFile.add("samtools", samtools.version(self))
else:
samtools.version(self)
def writeVersions(self,raFile=None,allLevels=False):
'''Writes versions to to the log or a file.'''
if allLevels:
LogicalStep.writeVersions(self, raFile)
if raFile != None:
raFile.add('ucscUtils', ucscUtils.version(self,tool='fastqStatsAndSubsample'))
raFile.add('fastqc', self.getToolVersion('fastqc'))
else:
ucscUtils.version(self,tool='fastqStatsAndSubsample')
self.getToolVersion('fastqc')
def writeVersions(self, raFile=None, allLevels=False):
'''Writes versions to to the log or a file.'''
if allLevels:
LogicalStep.writeVersions(self, raFile)
if raFile != None:
raFile.add('ucscUtils',
ucscUtils.version(self, tool='fastqStatsAndSubsample'))
raFile.add('fastqc', self.getToolVersion('fastqc'))
else:
ucscUtils.version(self, tool='fastqStatsAndSubsample')
self.getToolVersion('fastqc')
def writeVersions(self,raFile=None,allLevels=False,scriptName=None):
'''Writes versions to to the log or a file.'''
if allLevels:
LogicalStep.writeVersions(self, raFile)
if raFile != None:
if scriptName != None:
raFile.add(scriptName, self.getToolVersion(scriptName))
raFile.add('bwa', self.getToolVersion('bwa'))
raFile.add('samtools', self.getToolVersion('samtools'))
else:
if scriptName != None:
self.getToolVersion(scriptName)
self.getToolVersion('bwa')
self.getToolVersion('samtools')
def writeVersions(self,raFile=None,allLevels=False,scriptName=None):
'''Writes versions to to the log or a file.'''
if allLevels:
LogicalStep.writeVersions(self, raFile)
if raFile != None:
if scriptName != None:
raFile.add(scriptName, self.getToolVersion(scriptName))
raFile.add('edwBamStats', self.getToolVersion('edwBamStats'))
raFile.add('samtools', self.getToolVersion('samtools'))
raFile.add('Rscript', self.getToolVersion('Rscript'))
raFile.add('run_spp.R', self.getToolVersion(self.ana.toolsDir+'run_spp.R'))
else:
if scriptName != None:
self.getToolVersion(scriptName)
self.getToolVersion('edwBamStats')
self.getToolVersion('samtools')
self.getToolVersion('Rscript')
self.getToolVersion(self.ana.toolsDir+'run_spp.R')
def writeVersions(self,raFile=None,allLevels=False,scriptName=None):
'''Writes versions to to the log or a file.'''
if allLevels:
LogicalStep.writeVersions(self, raFile)
if raFile != None:
if scriptName != None:
raFile.add(scriptName, self.getToolVersion(scriptName))
raFile.add('tophat', self.getToolVersion('tophat'))
raFile.add('bowtie2', self.getToolVersion('bowtie2'))
raFile.add('samtools', self.getToolVersion('samtools'))
raFile.add('tophat_bam_xsA_tag_fix.pl', self.getToolVersion('tophat_bam_xsA_tag_fix.pl'))
else:
if scriptName != None:
self.getToolVersion(scriptName)
self.getToolVersion('tophat')
self.getToolVersion('bowtie2')
self.getToolVersion('samtools')
self.getToolVersion('tophat_bam_xsA_tag_fix.pl')
def writeVersions(self,raFile=None,allLevels=False,scriptName=None):
'''Writes versions to to the log or a file.'''
if allLevels:
LogicalStep.writeVersions(self, raFile)
if raFile != None:
if scriptName != None:
raFile.add(scriptName, self.getToolVersion(scriptName))
raFile.add('macs', self.getToolVersion('macs2'))
raFile.add('eap_macs2_xls_to_narrowPeak',
self.getToolVersion('eap_macs2_xls_to_narrowPeak'))
raFile.add('eap_narrowPeak_to_bigBed', self.getToolVersion('eap_narrowPeak_to_bigBed'))
raFile.add('bedGraphToBigWig', self.getToolVersion('bedGraphToBigWig'))
else:
if scriptName != None:
self.getToolVersion(scriptName)
self.getToolVersion('macs2')
self.getToolVersion('eap_macs2_xls_to_narrowPeak')
self.getToolVersion('eap_narrowPeak_to_bigBed')
self.getToolVersion('bedGraphToBigWig')
def writeVersions(self,raFile=None,allLevels=False,scriptName=None):
'''Writes versions to to the log or a file.'''
if allLevels:
LogicalStep.writeVersions(self, raFile)
if raFile != None:
if scriptName != None:
raFile.add(scriptName,self.getToolVersion(scriptName))
raFile.add('samtools', self.getToolVersion('samtools'))
raFile.add('makewigglefromBAM-NH.py', \
self.getToolVersion('makewigglefromBAM-NH.py'))
raFile.add('python2.7', self.getToolVersion('python2.7'))
raFile.add('wigToBigWig', self.getToolVersion('wigToBigWig'))
#raFile.add('perl', self.getToolVersion('perl'))
else:
if scriptName != None:
self.getToolVersion(scriptName)
self.getToolVersion('samtools')
self.getToolVersion('makewigglefromBAM-NH.py')
self.getToolVersion('python2.7')
self.getToolVersion('wigToBigWig')
def writeVersions(self, raFile=None, allLevels=False, scriptName=None):
'''Writes versions to to the log or a file.'''
if allLevels:
LogicalStep.writeVersions(self, raFile)
if raFile != None:
if scriptName != None:
raFile.add(scriptName, self.getToolVersion(scriptName))
raFile.add('samtools', self.getToolVersion('samtools'))
raFile.add('makewigglefromBAM-NH.py', \
self.getToolVersion('makewigglefromBAM-NH.py'))
raFile.add('python2.7', self.getToolVersion('python2.7'))
raFile.add('wigToBigWig', self.getToolVersion('wigToBigWig'))
#raFile.add('perl', self.getToolVersion('perl'))
else:
if scriptName != None:
self.getToolVersion(scriptName)
self.getToolVersion('samtools')
self.getToolVersion('makewigglefromBAM-NH.py')
self.getToolVersion('python2.7')
self.getToolVersion('wigToBigWig')
def writeVersions(self, raFile=None, allLevels=False, scriptName=None):
'''Writes versions to to the log or a file.'''
if allLevels:
LogicalStep.writeVersions(self, raFile)
if raFile != None:
if scriptName != None:
raFile.add(scriptName, self.getToolVersion(scriptName))
raFile.add('macs', self.getToolVersion('macs2'))
raFile.add('eap_macs2_xls_to_narrowPeak',
self.getToolVersion('eap_macs2_xls_to_narrowPeak'))
raFile.add('eap_narrowPeak_to_bigBed',
self.getToolVersion('eap_narrowPeak_to_bigBed'))
raFile.add('bedGraphToBigWig',
self.getToolVersion('bedGraphToBigWig'))
else:
if scriptName != None:
self.getToolVersion(scriptName)
self.getToolVersion('macs2')
self.getToolVersion('eap_macs2_xls_to_narrowPeak')
self.getToolVersion('eap_narrowPeak_to_bigBed')
self.getToolVersion('bedGraphToBigWig')
def writeVersions(self, raFile=None, allLevels=False):
'''Writes versions to to the log or a file.'''
if allLevels:
LogicalStep.writeVersions(self, raFile)
if raFile != None:
raFile.add('eap_run_hotspot',
self.getToolVersion('eap_run_hotspot'))
raFile.add('hotspot', self.getToolVersion( \
self.ana.toolsDir+'hotspot-distr/hotspot-deploy/bin/hotspot'))
raFile.add('python2.7', self.getToolVersion('python2.7'))
raFile.add('hotspot.py', self.getToolVersion('hotspot.py'))
raFile.add('bedToBigBed', self.getToolVersion('bedToBigBed'))
raFile.add('bedmap', self.getToolVersion('bedmap'))
raFile.add('sort-bed', self.getToolVersion('sort-bed'))
raFile.add('starchcat', self.getToolVersion('starchcat'))
raFile.add('unstarch', self.getToolVersion('unstarch'))
raFile.add('intersectBed',self.getToolVersion( \
self.ana.toolsDir+'bedtools/bin/intersectBed'))
raFile.add('bedGraphPack', self.getToolVersion('bedGraphPack'))
raFile.add('bedGraphToBigWig',
self.getToolVersion('bedGraphToBigWig'))
else:
self.getToolVersion('eap_run_hotspot')
self.getToolVersion(self.ana.toolsDir +
'hotspot-distr/hotspot-deploy/bin/hotspot')
self.getToolVersion('python2.7')
self.getToolVersion('hotspot.py')
self.getToolVersion('bedToBigBed')
self.getToolVersion('bedmap')
self.getToolVersion('sort-bed')
self.getToolVersion('starchcat')
self.getToolVersion('unstarch')
self.getToolVersion(self.ana.toolsDir +
'bedtools/bin/intersectBed')
self.getToolVersion('bedGraphPack')
self.getToolVersion('bedGraphToBigWig')
def __init__(self, analysis, replicate1="1", replicate2="2"):
self.replicate1 = str(replicate1)
self.replicate2 = str(replicate2)
LogicalStep.__init__(self, analysis, "mergeBam_Rep" + self.replicate1 + "Rep" + self.replicate2)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
def __init__(self, analysis, suffix=""):
self.suffix = str(suffix)
LogicalStep.__init__(self, analysis, 'quantitateRsem_' + analysis.readType + '_' + suffix)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all step versions
seed = e3.getSetting('fastqSampleSeed', '12345')
# Establish up tool locations
toolPath = e3.getSetting('toolPath')
fastqcToolPath = e3.getSetting('fastqcToolPath', toolPath)
# Get nonGalaxy paths
e3.registerFile('fastq', 'galaxyInput', galaxyInputFile)
e3.registerFile('validated', 'galaxyOutput', galaxyOutputFile)
nonGalaxyInput = e3.nonGalaxyInput('fastq')
resultsDir = e3.resultsDir(galaxyPath)
runningLog = e3.declareLogFile()
e3.log.empty() # start with an empty log
# Begin logging
step = LogicalStep(e3, stepName)
# Establish temporary and Permenant outputs
sampleOf = step.declareGarbageFile('sampleOf_s' + reads, suffix='fastq')
sampledStats = step.declareGarbageFile('sampledStats', suffix='txt')
# The following 2 are bound together by the same nameKey:
stepFile = step.declareTargetFile(
'validateRep' + repNo, suffix='html') # will become nonGalaxyOutput
nonGalaxyOutput = e3.createOutFile('validateRep'+repNo,'nonGalaxyOutput', \
'%s_s'+reads+'_fastqc/fastqc_report', ext='html' )
# FAKING step.run()
step._status = 'Running'
step.declareLogFile() # Ensures that the logical step dir and log exist
step.log.out("--- Beginning '" + stepName + "' [" +
datetime.now().strftime("%Y-%m-%d %X (%A)") + '] ---')
def __init__(self, analysis, suffix='', tagLen=50):
self.suffix = str(suffix)
self.tagLen = int(tagLen)
LogicalStep.__init__(self, analysis, 'peaksByHotspot_' + self.suffix)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
def __init__(self, analysis, suffix='', expType='ChIPseq',isPaired=False):
self.suffix = str(suffix)
self.expType = str(expType)
self.isPaired = isPaired
LogicalStep.__init__(self, analysis, 'peaksByMacs_' + self.suffix)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
def __init__(self, analysis, suffix=''):
self.suffix = str(suffix)
LogicalStep.__init__(self, analysis, 'fastqValidation_' + self.suffix)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
def __init__(self, analysis, replicate1='1', replicate2='2'):
self.replicate1 = str(replicate1)
self.replicate2 = str(replicate2)
LogicalStep.__init__(self, analysis, \
'mergeBam_Rep' + self.replicate1 + 'Rep' + self.replicate2)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
def __init__(self, analysis, suffix='', tagLen=50):
self.suffix = str(suffix)
self.tagLen = int(tagLen)
LogicalStep.__init__(self, analysis, 'peaksByHotspot_' + self.suffix)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
seed = e3.getSetting('fastqSampleSeed','12345')
# Establish up tool locations
toolPath = e3.getSetting('toolPath')
fastqcToolPath = e3.getSetting('fastqcToolPath',toolPath)
# Get nonGalaxy paths
e3.registerFile('fastq','galaxyInput',galaxyInputFile)
e3.registerFile('validated','galaxyOutput',galaxyOutputFile)
nonGalaxyInput = e3.nonGalaxyInput('fastq')
resultsDir = e3.resultsDir(galaxyPath)
runningLog = e3.declareLogFile()
e3.log.empty() # start with an empty log
# Begin logging
step = LogicalStep(e3,stepName)
# Establish temporary and Permenant outputs
sampleOf = step.declareGarbageFile('sampleOf_s' + reads, suffix='fastq')
sampledStats = step.declareGarbageFile('sampledStats', suffix='txt')
# The following 2 are bound together by the same nameKey:
stepFile = step.declareTargetFile('validateRep'+repNo, suffix='html') # will become nonGalaxyOutput
nonGalaxyOutput = e3.createOutFile('validateRep'+repNo,'nonGalaxyOutput', \
'%s_s'+reads+'_fastqc/fastqc_report', ext='html' )
# FAKING step.run()
step._status = 'Running'
step.declareLogFile() # Ensures that the logical step dir and log exist
step.log.out("--- Beginning '" + stepName + "' [" +
datetime.now().strftime("%Y-%m-%d %X (%A)")+ '] ---')
def __init__(self, analysis, suffix='', expType='ChIPseq', isPaired=False):
self.suffix = str(suffix)
self.expType = str(expType)
self.isPaired = isPaired
LogicalStep.__init__(self, analysis, 'peaksByMacs_' + self.suffix)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
def __init__(self, analysis, suffix=''):
self.suffix = str(suffix)
LogicalStep.__init__(self, analysis, 'fastqValidation_' + self.suffix)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
def __init__(self, analysis, replicate="1", suffix=""):
self.replicate = str(replicate)
self.suffix = suffix
LogicalStep.__init__(self, analysis, 'bamEvaluate' + self.suffix)
def __init__(self, analysis, replicate="1", encoding='sanger'):
self.replicate = str(replicate)
self.encoding = encoding
LogicalStep.__init__(self, analysis, 'alignmentByBwa_' + analysis.readType + 'Rep' + \
self.replicate)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all step versions