本文整理汇总了Python中quick.util.GenomeInfo.GenomeInfo.hasOrigFiles方法的典型用法代码示例。如果您正苦于以下问题：Python GenomeInfo.hasOrigFiles方法的具体用法？Python GenomeInfo.hasOrigFiles怎么用？Python GenomeInfo.hasOrigFiles使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类quick.util.GenomeInfo.GenomeInfo的用法示例。
在下文中一共展示了GenomeInfo.hasOrigFiles方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: execute
# 需要导入模块: from quick.util.GenomeInfo import GenomeInfo [as 别名]
# 或者: from quick.util.GenomeInfo.GenomeInfo import hasOrigFiles [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()