def gb2info(seqname, seq, record):
return {
'seqname': seqname,
'tax_id': tax_of_genbank(record),
'accession': record.id,
'description': record.description,
'length': len(seq),
'ambig_count': count_ambiguous(seq)
}
def gb2info(seqname, seq, record):
return {
"seqname": seqname,
"tax_id": tax_of_genbank(record),
"accession": record.id,
"description": record.description,
"length": len(seq),
"ambig_count": count_ambiguous(seq),
}
def action(args):
records = islice(SeqIO.parse(args.infile, "genbank"), args.limit)
if args.type_strains:
records = (r for r in records if is_type(r))
if args.filter:
fltr = lambda r: not UNCLASSIFIED_REGEX.search(r.description)
records = (r for r in records if fltr(r))
info = []
if args.features:
args.features = set(args.features)
# Parse out product locations
for r in records:
for f in r.features:
products = set(f.qualifiers.get("product", []))
if products & args.features:
tag = f.qualifiers.get("locus_tag", ["unspecified"])[0]
name = "{}_{}".format(r.name, tag)
start, end = f.location.start.position, f.location.end.position
seq = r.seq[start:end]
length = len(seq)
if (args.minus and f.location.strand == 1) or f.location.strand == -1:
seq = seq.reverse_complement()
ambig_count = count_ambiguous(seq)
if length < args.min_length:
log.warning("dropping seq {} because of length {}".format(name, length))
log.debug("Record and Feature information for short seq:")
log.debug(r)
log.debug(f)
elif ambig_count > args.max_ambiguous:
log.warning("dropping seq {} because of {} ambiguous bases".format(name, ambig_count))
else:
args.out.write(">{} {} {}\n{}\n".format(name, r.id, r.description, seq))
info.append(gb2info(name, seq, r))
else:
# if no product specified output entire seq
for r in records:
if args.region:
start, end = args.region[0], args.region[1]
seq = r.seq[start:end]
name = "{}_{}_{}".format(r.name, start, end)
else:
seq = r.seq
name = r.name
length = len(seq)
if length < args.min_length:
log.warning("dropping seq {} because of length {}".format(name, length))
log.debug("Record and Feature information for short seq:")
log.debug(r)
log.debug(f)
else:
type_source = lambda f: f.type == "source"
src = next((f for f in r.features if type_source(f)), None)
if src and ((args.minus and src.location.strand == 1) or src.location.strand == -1):
seq = seq.reverse_complement()
args.out.write(">{} {} {}\n{}\n".format(name, r.id, r.description, seq))
info.append(gb2info(name, seq, r))
if args.info_out:
args.info_out.writeheader()
args.info_out.writerows(info)
def action(args):
records = islice(SeqIO.parse(args.infile, 'genbank'), args.limit)
if args.type_strains:
records = (r for r in records if is_type(r))
if args.filter:
fltr = lambda r: not UNCLASSIFIED_REGEX.search(r.description)
records = (r for r in records if fltr(r))
info = []
if args.features:
args.features = set(args.features)
# Parse out product locations
for r in records:
for f in r.features:
products = set(f.qualifiers.get('product', []))
if products & args.features:
tag = f.qualifiers.get('locus_tag', ['unspecified'])[0]
name = '{}_{}'.format(r.name, tag)
start, end = f.location.start.position, f.location.end.position
seq = r.seq[start:end]
length = len(seq)
if (args.minus and f.location.strand
== 1) or f.location.strand == -1:
seq = seq.reverse_complement()
ambig_count = count_ambiguous(seq)
if length < args.min_length:
log.warning(
'dropping seq {} because of length {}'.format(
name, length))
log.debug(
'Record and Feature information for short seq:')
log.debug(r)
log.debug(f)
elif ambig_count > args.max_ambiguous:
log.warning(
'dropping seq {} because of {} ambiguous bases'.
format(name, ambig_count))
else:
args.out.write('>{} {} {}\n{}\n'.format(
name, r.id, r.description, seq))
info.append(gb2info(name, seq, r))
else:
# if no product specified output entire seq
for r in records:
if args.region:
start, end = args.region[0], args.region[1]
seq = r.seq[start:end]
name = '{}_{}_{}'.format(r.name, start, end)
else:
seq = r.seq
name = r.name
length = len(seq)
if length < args.min_length:
log.warning('dropping seq {} because of length {}'.format(
name, length))
log.debug('Record and Feature information for short seq:')
log.debug(r)
log.debug(f)
else:
type_source = lambda f: f.type == 'source'
src = next((f for f in r.features if type_source(f)), None)
if src and ((args.minus and src.location.strand == 1)
or src.location.strand == -1):
seq = seq.reverse_complement()
args.out.write('>{} {} {}\n{}\n'.format(
name, r.id, r.description, seq))
info.append(gb2info(name, seq, r))
if args.info_out:
args.info_out.writeheader()
args.info_out.writerows(info)
