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Python GenomeInfo.fullName方法代码示例

本文整理汇总了Python中quick.util.GenomeInfo.GenomeInfo.fullName方法的典型用法代码示例。如果您正苦于以下问题:Python GenomeInfo.fullName方法的具体用法?Python GenomeInfo.fullName怎么用?Python GenomeInfo.fullName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quick.util.GenomeInfo.GenomeInfo的用法示例。


在下文中一共展示了GenomeInfo.fullName方法的3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 fullName [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
开发者ID:Anderrb,项目名称:Dynamic-benchmark,代码行数:27,代码来源:GenomeInfoTool.py

示例2: execute

# 需要导入模块: from quick.util.GenomeInfo import GenomeInfo [as 别名]
# 或者: from quick.util.GenomeInfo.GenomeInfo import fullName [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()
开发者ID:Anderrb,项目名称:Dynamic-benchmark,代码行数:57,代码来源:UploadGenomeTool.py

示例3: str

# 需要导入模块: from quick.util.GenomeInfo import GenomeInfo [as 别名]
# 或者: from quick.util.GenomeInfo.GenomeInfo import fullName [as 别名]
             shutil.copytree(fromDir, toDir)
             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()
     
开发者ID:Anderrb,项目名称:Dynamic-benchmark,代码行数:32,代码来源:setup.py


注:本文中的quick.util.GenomeInfo.GenomeInfo.fullName方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。