Python GenomeInfo.installedBy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 installedBy [as 别名]
 def execute(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...'
     
     tempinfofile=ExternalTrackManager.extractFnFromGalaxyTN(choices[0].split(":"))
     abbrv=GenomeImporter.getGenomeAbbrv(tempinfofile)
     gi = GenomeInfo(abbrv)
     chrNamesInFasta=gi.sourceChrNames
     
     chromNamesDict={}
     chrDict = InstallGenomeTool._getRenamedChrDictWithSelection(choices)
         
     for i, key in enumerate(chrDict.keys()):
         if chrDict[key]:
             chromNamesDict[chrNamesInFasta[i]]=key
     print 'All chromosomes chosen: ' + str(chromNamesDict)
         
     stdChrDict = InstallGenomeTool._getRenamedChrDictWithSelection(choices, stdChrs=True)
     stdChrs = [x for x in stdChrDict if stdChrDict[x]]
     print 'Standard chromosomes chosen: ' + ", ".join(stdChrs)
     
     GenomeImporter.createGenome(abbrv, gi.fullName, chromNamesDict, stdChrs, username=username)
     
     gi.installedBy = username
     gi.timeOfInstallation = datetime.now()
     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 installedBy [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 installedBy [as 别名]
            sys.exit(1)
            
    for track in ProcTrackOptions.getSubtypes('TestGenome', ['GESourceTracks']):
        ti = TrackInfo('TestGenome', ['GESourceTracks', track])
        ti.trackName = [track]
        ti.genome = 'ModelsForExternalTracks'
        ti.store()
            
    from quick.util.GenomeInfo import GenomeInfo
    from datetime import datetime
    gi = GenomeInfo('TestGenome')
    gi.fullName = 'TestGenome'
    gi.sourceUrls = ['http://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/chr21.fa.gz', \
                     'http://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/chrM.fa.gz']
    gi.sourceChrNames = ['chr21', 'chrM']
    gi.installedBy = 'Setup.py'
    gi.genomeBuildSource = 'NCBI'
    gi.genomeBuildName = 'hg18'
    gi.species = 'Homo Sapiens'
    gi.speciesTaxonomyUrl = 'http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606'
    gi.assemblyDetails = 'Chromosome 21 and M from the hg18 genome, used for testing purposes.'
    gi.isPrivate = False
    gi.privateAccessList = []
    gi.isExperimental = False
    gi.timeOfInstallation = datetime.now()
    gi.store()
        
def setupHB(galaxyPath='', ignoreVersionChecking=False, installationSetupFn=''):
    hbPath = os.path.dirname(os.path.realpath(sys.argv[0]))
    os.chdir(hbPath)