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")
