New subcommand taxit named that filters unclassified, unnamed taxonom…

…y ids

CHANGES.rst

@@ -6,6 +6,7 @@ Upcoming
 ========
 
 * Updated NCBI taxdmp.zip download protocol from ftp to https [GH-156]
+* New subcommand `taxit named` that filters unclassified, unnamed taxonomy ids
 
 0.10.1
 ======

taxtastic/subcommands/named.py

@@ -0,0 +1,79 @@
+# This file is part of taxtastic.
+#
+#    taxtastic is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    taxtastic is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with taxtastic.  If not, see <http://www.gnu.org/licenses/>.
+"""
+Filters unclassified, unnamed taxonomy ids
+"""
+import argparse
+import csv
+import sqlalchemy
+import sys
+from taxtastic.utils import add_database_args
+from taxtastic.taxonomy import Taxonomy
+
+
+def build_parser(parser):
+    parser = add_database_args(parser)
+    input_group = parser.add_mutually_exclusive_group(required=True)
+    input_group.add_argument(
+        '-t', '--tax-ids',
+        nargs='+',
+        help='one or more space-delimited tax_ids (eg "-t 47770 33945")')
+    input_group.add_argument(
+        '-f', '--tax-id-file',
+        metavar='FILE',
+        type=argparse.FileType('rt'),
+        help=('File containing a whitespace-delimited list of '
+              'tax_ids (ie, separated by tabs, spaces, or newlines.'))
+    input_group.add_argument(
+        '-i', '--seq-info',
+        type=argparse.FileType('rt'),
+        help=('Read tax_ids from sequence info file, minimally '
+              'containing a column named "tax_id"'))
+    parser.add_argument(
+        '--ranked',
+        action='store_true',
+        help='Ignore "no rank" taxonomies [%(default)s]')
+    parser.add_argument(
+        '-o', '--outfile',
+        type=argparse.FileType('wt'),
+        default=sys.stdout,
+        metavar='FILE',
+        help=('Output file containing named taxonomy ids;'
+              'writes to stdout if unspecified'))
+
+
+def action(args):
+    engine = sqlalchemy.create_engine(args.url, echo=args.verbosity > 3)
+    tax = Taxonomy(engine, schema=args.schema)
+    if args.tax_ids:
+        tax_ids = args.tax_ids
+    elif args.tax_id_file:
+        tax_ids = (i.strip() for i in args.tax_id_file)
+        tax_ids = [i for i in tax_ids if i]
+    elif args.seq_info:
+        seq_info = csv.DictReader(args.seq_info)
+        tax_ids = (row['tax_id'] for row in seq_info)
+    named = set(tax.named(set(tax_ids), no_rank=not args.ranked))
+    if args.seq_info:
+        out = csv.DictWriter(args.outfile, fieldnames=seq_info.fieldnames)
+        out.writeheader()
+        args.seq_info.seek(0)
+        for i in csv.DictReader(args.seq_info):
+            if i['tax_id'] in named:
+                out.writerow(i)
+    else:
+        for i in tax_ids:
+            if i in named:
+                args.outfile.write(i + '\n')

taxtastic/taxonomy.py

@@ -824,3 +824,13 @@ def species_below(self, tax_id):
             newc = self.species_below(c)
             assert self.is_ancestor_of(newc, tax_id)
             return newc
+
+    def named(self, taxids, no_rank=True):
+        nodes = self.nodes
+        s = select(nodes.c.tax_id).\
+            where(and_(
+                nodes.c.tax_id.in_(taxids),
+                nodes.c.is_valid))
+        if not no_rank:
+            s = s.where(nodes.c.rank != 'no_rank')
+        return [f[0] for f in self.fetchall(s)]