def test_iter_read_multi_file():
infiles = kevlar.tests.data_glob('bogus-genome/mask-chr[1,2].fa')
print(infiles)
records = [r for r in kevlar.multi_file_iter_khmer(infiles)]
assert len(records) == 4
def main(args):
timer = kevlar.Timer()
timer.start()
if (not args.num_bands) is not (not args.band):
raise ValueError('Must specify --num-bands and --band together')
myband = args.band - 1 if args.band else None
timer.start('loadall')
kevlar.plog('[kevlar::novel] Loading control samples')
timer.start('loadctrl')
controls = load_samples(
args.control_counts,
args.control,
args.ksize,
args.memory,
args.max_fpr,
args.num_bands,
myband,
args.threads,
args.save_ctrl_counts,
)
elapsed = timer.stop('loadctrl')
message = 'Control samples loaded in {:.2f} sec'.format(elapsed)
kevlar.plog('[kevlar::novel]', message)
kevlar.plog('[kevlar::novel] Loading case samples')
timer.start('loadcases')
cases = load_samples(
args.case_counts,
args.case,
args.ksize,
args.memory,
args.max_fpr,
args.num_bands,
myband,
args.threads,
args.save_case_counts,
)
elapsed = timer.stop('loadcases')
kevlar.plog(
'[kevlar::novel] Case samples loaded in {:.2f} sec'.format(elapsed))
elapsed = timer.stop('loadall')
kevlar.plog(
'[kevlar::novel] All samples loaded in {:.2f} sec'.format(elapsed))
timer.start('iter')
ncases = len(args.case)
message = 'Iterating over reads from {:d} case sample(s)'.format(ncases)
kevlar.plog('[kevlar::novel]', message)
outstream = kevlar.open(args.out, 'w')
infiles = [f for filelist in args.case for f in filelist]
caserecords = kevlar.multi_file_iter_khmer(infiles)
readstream = novel(
caserecords,
cases,
controls,
ksize=args.ksize,
abundscreen=args.abund_screen,
casemin=args.case_min,
ctrlmax=args.ctrl_max,
numbands=args.num_bands,
band=myband,
skipuntil=args.skip_until,
)
for augmented_read in readstream:
kevlar.print_augmented_fastx(augmented_read, outstream)
elapsed = timer.stop('iter')
message = 'Iterated over all case reads in {:.2f} seconds'.format(elapsed)
kevlar.plog('[kevlar::novel]', message)
total = timer.stop()
message = 'Total time: {:.2f} seconds'.format(total)
kevlar.plog('[kevlar::novel]', message)