Python GenomeInfo.sourceUrls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 sourceUrls [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 getOutputFormat is anything else than HTML, the output should be written to the file with path galaxyFn.gtr
     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.
     '''
     gi=GenomeInfo(choices[0])
     gi.fullName = choices[1]
     urls = choices[2].split()
     gi.sourceUrls = urls
 
     gi.genomeBuildSource = choices[3]
     gi.genomeBuildName = choices[4]
     gi.species = choices[5]
     gi.speciesTaxonomyUrl = choices[6]
     gi.assemblyDetails = choices[7]
     gi.privateAccessList = [v.strip()  for v in choices[8].replace(os.linesep, ' ').replace(',', ' ').split(' ') if v.find('@')>0]
     gi.isPrivate = (choices[9] == 'Owners only')
     gi.isExperimental = (choices[10] == 'Experimental only')
     gi.ucscClade = choices[11]
     gi.ucscGenome = choices[12]
     gi.ucscAssembly = choices[13]
     gi.store()
     
     return "Updated genome %s." % gi.fullName

# 需要导入模块: from quick.util.GenomeInfo import GenomeInfo [as 别名]
# 或者: from quick.util.GenomeInfo.GenomeInfo import sourceUrls [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 sourceUrls [as 别名]
                print 'OK: Copied from %s to %s.' % (fromDir, toDir)
        except Exception, e:
            print 'FAILED: Error occurred copying from %s to %s: ' % (fromDir, toDir) + str(e).strip()
            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]))