def main():
args = docopt(__doc__)
fasta_f = args['--infile']
list_f = args['--list']
invert = args['--invert']
prefix = args['--out']
output = []
out_f = BtIO.getOutFile(fasta_f, prefix, "filtered.fna")
print BtLog.status_d['1'] % ("list", list_f)
items = BtIO.parseSet(list_f)
items_count = len(items)
print BtLog.status_d['22'] % fasta_f
items_parsed = []
sequences = 0
for header, sequence in BtIO.readFasta(fasta_f):
sequences += 1
if header in items:
if not (invert):
items_parsed.append(header)
output.append(">%s\n%s\n" % (header, sequence))
else:
if (invert):
items_parsed.append(header)
output.append(">%s\n%s\n" % (header, sequence))
BtLog.progress(len(output), 10, items_count, no_limit=True)
BtLog.progress(items_count, 10, items_count)
items_parsed_count = len(items_parsed)
print BtLog.status_d['23'] % ('{:.2%}'.format(items_parsed_count/sequences), "{:,}".format(items_count), "{:,}".format(items_parsed_count), "{:,}".format(sequences))
items_parsed_count_unique = len(set(items_parsed))
if not items_parsed_count == items_parsed_count_unique:
print BtLog.warn_d['8'] % "\n\t\t\t".join(list(set([x for x in items_parsed if items_parsed.count(x) > 1])))
with open(out_f, "w") as fh:
print BtLog.status_d['24'] % out_f
fh.write("".join(output))
def main():
args = docopt(__doc__)
fasta_f = args['--infile']
list_f = args['--list']
invert = args['--invert']
prefix = args['--out']
output = []
out_f = BtIO.getOutFile(fasta_f, prefix, "filtered.fna")
print(BtLog.status_d['1'] % ("list", list_f))
items = BtIO.parseSet(list_f)
items_count = len(items)
print(BtLog.status_d['22'] % fasta_f)
items_parsed = []
with tqdm(total=items_count, desc="[%] ", ncols=200, unit_scale=True) as pbar:
for header, sequence in BtIO.readFasta(fasta_f):
if header in items:
if not (invert):
items_parsed.append(header)
output.append(">%s\n%s\n" % (header, sequence))
else:
if (invert):
items_parsed.append(header)
output.append(">%s\n%s\n" % (header, sequence))
pbar.update()
items_parsed_count = len(items_parsed)
items_parsed_count_unique = len(set(items_parsed))
if not items_parsed_count == items_parsed_count_unique:
print(BtLog.warn_d['8'] % "\n\t\t\t".join(list(set([x for x in items_parsed if items_parsed.count(x) > 1]))))
with open(out_f, "w") as fh:
print(BtLog.status_d['24'] % out_f)
fh.write("".join(output))
