def action(args):
engine = create_engine(
'sqlite:///%s' % args.database_file, echo=args.verbosity > 2)
tax = Taxonomy(engine, ncbi.ranks)
taxids = set()
if args.taxids:
if os.access(args.taxids, os.F_OK):
for line in getlines(args.taxids):
taxids.update(set(re.split(r'[\s,;]+', line)))
else:
taxids.update([x.strip()
for x in re.split(r'[\s,;]+', args.taxids)])
if args.taxnames:
for taxname in getlines(args.taxnames):
for name in re.split(r'\s*[,;]\s*', taxname):
tax_id, primary_name, is_primary = tax.primary_from_name(
name.strip())
taxids.add(tax_id)
if args.seq_info:
with args.seq_info:
reader = csv.DictReader(args.seq_info)
taxids.update(frozenset(i['tax_id']
for i in reader if i['tax_id']))
# Before digging into lineages, make sure all the taxids exist in
# the taxonomy database.
valid_taxids = True
for t in taxids:
try:
tax._node(t)
except KeyError:
# Check for merged
m = tax._get_merged(t)
if m and m != t:
msg = ("Taxid {0} has been replaced by {1}. "
"Please update your records").format(t, m)
print >> sys.stderr, msg
else:
print >>sys.stderr, "Taxid %s not found in taxonomy." % t
valid_taxids = False
if not(valid_taxids):
print >>sys.stderr, "Some taxids were invalid. Exiting."
return 1 # exits with code 1
# Extract all the taxids to be exported in the CSV file.
taxids_to_export = set()
for t in taxids:
taxids_to_export.update([y for (x, y) in tax._get_lineage(t)])
tax.write_table(taxids_to_export, csvfile=args.out_file, full=args.full)
engine.dispose()
return 0
def action(args):
engine = create_engine(
'sqlite:///%s' % args.database_file, echo=args.verbosity > 2)
tax = Taxonomy(engine, ncbi.RANKS)
if any([args.taxids, args.taxnames, args.seq_info]):
taxids = set()
if args.taxids:
if os.access(args.taxids, os.F_OK):
for line in getlines(args.taxids):
taxids.update(set(re.split(r'[\s,;]+', line)))
else:
taxids.update(
[x.strip() for x in re.split(r'[\s,;]+', args.taxids)])
if args.seq_info:
with args.seq_info:
reader = csv.DictReader(args.seq_info)
taxids.update(
frozenset(i['tax_id'] for i in reader if i['tax_id']))
if not(are_valid(taxids, tax)):
return "Some taxids were invalid. Exiting."
if args.taxnames:
for taxname in getlines(args.taxnames):
for name in re.split(r'\s*[,;]\s*', taxname):
tax_id, primary_name, is_primary = tax.primary_from_name(
name.strip())
taxids.add(tax_id)
else:
taxids = set(tax.tax_ids())
# Extract all the taxids to be exported in the CSV file.
taxids_to_export = set()
for t in taxids:
taxids_to_export.update([y for (x, y) in tax._get_lineage(t)])
tax.write_table(taxids_to_export, csvfile=args.out_file, full=args.full)
engine.dispose()
return 0
def action(args):
engine = create_engine('sqlite:///%s' % args.database_file,
echo=args.verbosity > 2)
tax = Taxonomy(engine, ncbi.RANKS)
if any([args.taxids, args.taxnames, args.seq_info]):
taxids = set()
if args.taxids:
if os.access(args.taxids, os.F_OK):
for line in getlines(args.taxids):
taxids.update(set(re.split(r'[\s,;]+', line)))
else:
taxids.update(
[x.strip() for x in re.split(r'[\s,;]+', args.taxids)])
if args.seq_info:
with args.seq_info:
reader = csv.DictReader(args.seq_info)
taxids.update(
frozenset(i['tax_id'] for i in reader if i['tax_id']))
if not (are_valid(taxids, tax)):
return "Some taxids were invalid. Exiting."
if args.taxnames:
for taxname in getlines(args.taxnames):
for name in re.split(r'\s*[,;]\s*', taxname):
tax_id, primary_name, is_primary = tax.primary_from_name(
name.strip())
taxids.add(tax_id)
else:
taxids = set(tax.tax_ids())
# Extract all the taxids to be exported in the CSV file.
taxids_to_export = set()
for t in taxids:
taxids_to_export.update([y for (x, y) in tax._get_lineage(t)])
tax.write_table(taxids_to_export, csvfile=args.out_file, full=args.full)
engine.dispose()
return 0
