def illustrate(args):
data = json.load(file(args.file))
testsuite_paths = discover_testsuites(args.testsuite_directory or [])
testsuites = {}
update_testsuites(testsuites, data['info']['testsuites'], testsuite_paths)
analyser = analyse.Analyser()
lo.info('loading json-file args.file')
analyser.decode(testsuites, data)
lo.info('updating testsuites')
analyser.update_testsuites()
if args.readlengths:
rls = analyser.stats['readlengths']
hist = TextHist()
print(hist.draw(rls, indexed=True))
if args.coverage:
for name, testsuite in analyser.testsuites.items():
print(name + ':')
for test in testsuite.tests:
print(' - %s : %s' % (test, analyser[test]))
print()
if args.results:
for testsuite, results in analyser.results.items():
print('\n'+testsuite)
print('-'*len(testsuite))
pprint(results)
def show(args):
fastq = Fastq(args.file)
if args.quality:
Amin = fastq.Q2A(args.quality)
n = args.number
points = args.points
lo.info('determining readlengths with quality>=%d of %s '
'by reading %d records at %d points'%(
args.quality, args.file, n, points))
rls = fastq.lengths(Amin, n=n, points=points)
hist = TextHist()
print(hist.draw(sorted(rls)))
if args.info:
print('dQ=' + str(fastq.dQ))
print('variants=' + str(fastq.variants))
print('readlength=' + str(fastq.readlength))
print('records_approx=' + str(fastq.records_approx or '?'))