def checkOptions( parser, options, args ): if not options.seqdir: raise InputOptionError("Input directory is required, none was given.\n") if not os.path.isdir( options.seqdir ): raise InputOptionError("Input directory (%s) is not a directory\n" %options.seqdir) if not os.path.exists( options.outdir ): system( "mkdir %s\n" %(options.outdir) ) #options.cutoffs = [ float(p) for p in options.minReadPercentage.strip(',').split(',') ] analyses = ['geneusage', 'cdr3len', 'aausage'] if options.analyses == 'all': options.analyses = analyses else: options.analyses = options.analyses.split(',') for analysis in options.analyses: if analysis not in analyses: raise ValueError("Option for analysis %s is not valid." %analysis) if options.vgenes: options.vgenes = iseqlib.readList(options.vgenes, ',') if options.jgenes: options.jgenes = iseqlib.readList(options.jgenes, ',') if options.dgenes: options.dgenes = iseqlib.readList(options.dgenes, ',') if options.group2samplesFile: options.group2samples, options.sample2group = iseqlib.readGroup2samples(options.group2samplesFile) if options.vs: options.vs = options.vs.split(',') if options.js: options.js = options.js.split(',')
def checkOptions( parser, options, args ): if options.group2samplesFile: options.group2samples, options.sample2group = iseqlib.readGroup2samples(options.group2samplesFile) if options.vs: options.vs = options.vs.split(',') if options.js: options.js = options.js.split(',') analyses = ["pairwiseOverlap", "numsamVsClones"] if options.analyses == 'all': options.analyses = analyses else: options.analyses = options.analyses.split(',') for a in options.analyses: if a not in analyses: raise ValueError("Invalid analysis choice %s. Valid choices are: pairwiseOverlap, numsamVsClones")