Python GenomeInfo.getSequenceTrackName方法代码示例

# 需要导入模块: from quick.util.GenomeInfo import GenomeInfo [as 别名]
# 或者: from quick.util.GenomeInfo.GenomeInfo import getSequenceTrackName [as 别名]
 def execute(cls, choices, galaxyFn=None , username=''):
     '''Is called when execute-button is pushed by web-user.
     Should print output as HTML to standard out, which will be directed to a results page in Galaxy history.
     If needed, StaticFile can be used to get a path where additional files can be put (e.g. generated image files).
     choices is a list of selections made by web-user in each options box.
     '''
     #print 'Executing... with choices %s'%str(choices)
     abbrv = choices[0]
     name = choices[1]
     
     #Should test that the genome is not in hyperbrowser.
     gi = GenomeInfo(abbrv)
     
     if gi.hasOrigFiles():
         sys.stderr.write( "Genome "+abbrv+ " is already in the Genomic HyperBrowser. Remove the old first.")
     else:
         gi.fullName = name
         if choices[2] == 'URL':
             urls = choices[3].split()
             gi.sourceUrls = urls
             for url in urls:
                 try:
                     GenomeImporter.downloadGenomeSequence(abbrv, url)
                 except InvalidFormatError:
                     return
         else:
             basePath =  os.sep.join([NONSTANDARD_DATA_PATH, abbrv] + GenomeInfo.getSequenceTrackName(abbrv))
             fnSource = ExternalTrackManager.extractFnFromGalaxyTN(choices[4].split(':'))
             fnDest = basePath+'/'+abbrv+'Sequence.fasta'
             ensurePathExists(fnDest)
             copyfile(fnSource, fnDest)
             
         chrs=GenomeImporter.extractChromosomesFromGenome(abbrv)
         gi.sourceChrNames = chrs
         gi.installedBy = username
         gi.genomeBuildSource = choices[5]
         gi.genomeBuildName = choices[6]
         gi.species = choices[7]
         gi.speciesTaxonomyUrl = choices[8]
         gi.assemblyDetails = choices[9]
         gi.privateAccessList = [v.strip() for v in choices[10].replace(os.linesep, ' ').replace(',', ' ').split(' ') if v.find('@')>0]
         gi.isPrivate = (choices[11] != 'All')
         gi.isExperimental = (choices[12] != 'All')
         gi.ucscClade = choices[13]
         gi.ucscGenome = choices[14]
         gi.ucscAssembly = choices[15]
         
         galaxyFile=open(galaxyFn, "w")
         galaxyFile.write( 'Genome abbreviation: ' + abbrv + os.linesep)
         galaxyFile.write( 'Genome full name: ' + name + os.linesep)
         galaxyFile.write( 'Track name: ' + ':'.join(GenomeInfo.getSequenceTrackName(abbrv)) + os.linesep)
         galaxyFile.write( 'Temp chromosome names: ' + ' || '.join(chrs) + os.linesep)
         #GenomeImporter.saveTempInfo(abbrv, name, chrs)
         #print 'Chromosomes: '+chrs
         gi.store()

# 需要导入模块: from quick.util.GenomeInfo import GenomeInfo [as 别名]
# 或者: from quick.util.GenomeInfo.GenomeInfo import getSequenceTrackName [as 别名]
 def execute(cls, choices, galaxyFn=None, username=''):
     '''
     Is called when execute-button is pushed by web-user. Should print
     output as HTML to standard out, which will be directed to a results page
     in Galaxy history. If getOutputFormat is anything else than HTML, the
     output should be written to the file with path galaxyFn. If needed,
     StaticFile can be used to get a path where additional files can be put
     (e.g. generated image files). choices is a list of selections made by
     web-user in each options box.
     '''
     
     try:
         historyInputTN = choices[0].split(':') #from history
         historyGalaxyFn = ExternalTrackManager.extractFnFromGalaxyTN( historyInputTN) #same as galaxyFn in execute of create benchmark..
         randomStatic = RunSpecificPickleFile(historyGalaxyFn) #finds path to static file created for a previous history element, and directs to a pickle file
         myInfo = randomStatic.loadPickledObject()
     except:
         return None
     
     galaxyTN = myInfo[3].split(':')
     myFileName = ExternalTrackManager.extractFnFromGalaxyTN(galaxyTN)
     genome = myInfo[0]
     
     gtrackSource = GtrackGenomeElementSource(myFileName, genome)
     regionList = []
     
     for obj in gtrackSource:
         regionList.append(GenomeRegion(obj.genome, obj.chr, obj.start, obj.end))
     
     extractor = TrackExtractor()
             
     fn = extractor.extract(GenomeInfo.getSequenceTrackName(genome), regionList, galaxyFn, 'fasta')

# 需要导入模块: from quick.util.GenomeInfo import GenomeInfo [as 别名]
# 或者: from quick.util.GenomeInfo.GenomeInfo import getSequenceTrackName [as 别名]
 def createNmerChains(self, n):
     for chr in GenomeInfo.getChrList(self._genome):
         print 'Creating chains of nmers of length ', n, ' for chromosome ', chr
         chrLen = GenomeInfo.getChrLen(self._genome,chr)
         chrReg = GenomeRegion( self._genome, chr, 0, chrLen )
         seqTV = PlainTrack( GenomeInfo.getSequenceTrackName(self._genome) ).getTrackView(chrReg)
         
         #nmersAsInts = NmerAsIntSlidingWindow(n, FuncValTvWrapper(seqTV))
         nmersAsInts = NmerAsIntSlidingWindow(n, seqTV.valsAsNumpyArray())
         SameValueIndexChainsFactory.generate( nmersAsInts, chrLen, 4**n, self._createPath(n), chr )

# 需要导入模块: from quick.util.GenomeInfo import GenomeInfo [as 别名]
# 或者: from quick.util.GenomeInfo.GenomeInfo import getSequenceTrackName [as 别名]
 def retrieveTrack(self, regionTrackName, fastaFileName):
     
     regionTrackName = regionTrackName.split(':')
     myFileName = ExternalTrackManager.extractFnFromGalaxyTN(regionTrackName)
     gtrackSource = GtrackGenomeElementSource(myFileName, self._genome)
     regionList = []
     
     for obj in gtrackSource:
         regionList.append(GenomeRegion(obj.genome, obj.chr, obj.start, obj.end))
     
     return self._extractor.extract(GenomeInfo.getSequenceTrackName(self._genome), regionList, fastaFileName, 'fasta')

# 需要导入模块: from quick.util.GenomeInfo import GenomeInfo [as 别名]
# 或者: from quick.util.GenomeInfo.GenomeInfo import getSequenceTrackName [as 别名]
 def createGenome(cls, genome, fullName, chromNamesDict, standardChromosomes, username=''):        
     basePath = cls.getBasePath(genome)
     trackName=GenomeInfo.getSequenceTrackName(genome)
     print("Splitting genome file into chromosomes.")
     SplitFasta.parseFiles(genome, trackName, chromNamesDict=chromNamesDict)
     print("Processing genome")
     PreProcessAllTracksJob(genome).process()
     
     #print "Writing name file.:", fullName  
     #nameFn=createOrigPath(genome,[], "_name.txt" if experimental else "#name.txt")
     #ensurePathExists(nameFn)
     #f=open(nameFn, "w")
     #f.write(fullName)
     #f.close()
     
     print("Creating chromosome file")
     createChromosomeFile(genome, ",".join(standardChromosomes))
     print("Creating assembly gaps file")
     createAssemblyGapsFile(genome)
     print("Processing genome")
     PreProcessAllTracksJob(genome).process()
     print(genome + " genome added")

# 需要导入模块: from quick.util.GenomeInfo import GenomeInfo [as 别名]
# 或者: from quick.util.GenomeInfo.GenomeInfo import getSequenceTrackName [as 别名]
 def getBasePath(cls, abbrv):
     return os.sep.join([NONSTANDARD_DATA_PATH, abbrv] + GenomeInfo.getSequenceTrackName(abbrv))