def scan(args):
testsuite_paths = discover_testsuites(args.testsuite_directory or [])
if args.select_all:
testsuites = load_testsuites(testsuite_paths, testsuite_paths.keys())
else:
testsuites = load_testsuites(testsuite_paths, args.select)
if not testsuites:
sys.stderr.write('\n*** you must specify at least one testsuite! ***\n\n')
sys.stderr.write('(use the -t command line switch)\n\n')
sys.exit(ERROR_COMMAND_LINE_SWITCH)
# prepare scanning {{{2
try:
fastq = Fastq(args.fastq, paired=not args.no_paired, variant=args.variant)
except FastqFileFormatException, e:
lo.error('cannot open file %s : %s'%(args.fastq, str(e)))
sys.exit(ERROR_FASTQ_FORMAT_ERROR)
def do_export():
js = JsonSummary()
for jpath in self.jpaths:
if bj.canceled:
break
bj.message = 'extracting from ' + os.path.basename(jpath)
try:
js.add(jpath)
stats['n'] += 1
except Exception as e:
lo.error('could not load %s : %s'%(jpath, e))
continue
try:
js.dump(file(fname, 'w'))
except IOError as e:
lo.error('could not write to file %s : %s' % (fname, e))
sys.exit(ERROR_FASTQ_FORMAT_ERROR)
engine.config(
nthreads=args.threads,
maxerrors=args.errors,
Amin=fastq.Q2A(args.quality),
Azero=fastq.Azero,
minreadlength=args.readlength,
minoverlap=args.overlap
)
analyser = analyse.Analyser()
if not args.force:
if os.path.exists(args.json):
lo.error('will not overwrite file ' + args.json)
sys.exit(ERROR_FILE_EXISTS)
if args.extract_hits and os.path.exists(args.extract_hits):
lo.error('will not overwrite file ' + args.extract_hits)
sys.exit(ERROR_FILE_EXISTS)
# do scanning {{{2
mb = os.path.getsize(args.fastq) / 1024 / 1024
lo.info('scanning {} ({})...'.format(
', '.join(fastq.filenames()),
', '.join(['%.2f MB' % (filesize/1024.**2) for filesize in fastq.filesizes()])
))
t0 = time.time()
class AnalyseThread(threading.Thread):
