Python LogicalStep.writeVersions Exemples

Exemple #1

Fichier : hotspotStep.py Projet : ENCODE-DCC/uniformAnalysis

 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')

Exemple #2

 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)

Exemple #3

Fichier : mergeBamStep.py Projet : cuskinfor/uniformAnalysis

 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)

Exemple #4

Fichier : fastqValidationStep.py Projet : ENCODE-DCC/uniformAnalysis

 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')

Exemple #5

 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')

Exemple #6

Fichier : bwaAlignmentStep.py Projet : sirusb/uniformAnalysis

 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')

Exemple #7

 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')

Exemple #8

 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')

Exemple #9

Fichier : macsStep.py Projet : ENCODE-DCC/uniformAnalysis

 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')

Exemple #10

Fichier : bamToBwStep.py Projet : sirusb/uniformAnalysis

 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')

Exemple #11

Fichier : bamToBwStep.py Projet : ENCODE-DCC/uniformAnalysis

 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')

Exemple #12

 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')

Exemple #13

Fichier : hotspotStep.py Projet : sirusb/uniformAnalysis

 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')