def main():
parser = iseqlib.initOptions()
addOptions(parser)
options, args = parser.parse_args()
group2keywords = {} #key = keywordGroup, val = list of keywords
if options.keywords:
if options.keywords == '-':
group2keywords = getDefaultKeywords()
else:
group2keywords, kw2group = iseqlib.readGroup2samples(options.keywords)
clones, clone2hits = readNcbiXml(options.infile, options.minPos, options.minNumSamples, options.minLen)
#printTab(clones, clone2hits, group2keywords, options, options.outdir)
printTexTab(clones, clone2hits, group2keywords, options, options.outdir)
def main():
parser = iseqlib.initOptions()
addOptions(parser)
options, args = parser.parse_args()
group2keywords = {} # key = keywordGroup, val = list of keywords
if options.keywords:
if options.keywords == "-":
group2keywords = getDefaultKeywords()
else:
group2keywords, kw2group = iseqlib.readGroup2samples(options.keywords)
group2sample2host = {}
if options.sample2host:
group2sample2host = readSample2host(options.sample2host)
# clones, clone2hits = readNcbiXml(options.infile, options.minPos, options.minNumSamples, options.minLen, options.minNumPatients, options.minNumControls, options.minPatientCount, options.minControlCount, group2sample2host)
clones, clone2hits = readNcbiXml(options, group2sample2host)
outbasename = os.path.join(options.outdir, options.basename)
printTab(clones, clone2hits, group2keywords, options, outbasename)
printTexTab(clones, clone2hits, group2keywords, options, outbasename)
