prefix of X for filler taxonomies; changed default fraction cutoff

ncbi-gtdb_map.py

@@ -94,7 +94,7 @@
 parser.add_argument('-q', '--query-taxonomy', type=str, default='ncbi_taxonomy',
  choices=['ncbi_taxonomy', 'gtdb_taxonomy'],
  help='Taxonomy of the query list (Default: %(default)s)')
-parser.add_argument('-f', '--fraction', type=float, default=0.51,
+parser.add_argument('-f', '--fraction', type=float, default=0.90,
  help='Homogeneity of LCA (fraction) in order to be used (Default: %(default)s)')
 parser.add_argument('-m', '--max-tips', type=int, default=100,
  help='Max no. of tips used for LCA determination. If more, subsampling w/out replacement (Default: %(default)s)')
@@ -205,7 +205,7 @@ def format_taxonomy(T, hierarchy, acc):
  Tx = ['' for i in range(len(hierarchy))]
  for i,x in enumerate(hierarchy[:-1]):
  if len(T) < i + 1 or T[i] == '' or T[i] == 'unclassified' or regex.search(T[i]):
- Tx[i] = '__'.join([x[0], acc])
+ Tx[i] = '__'.join(['X' + x[0], acc])
  else:
  Tx[i] = T[i]
  Tx[-1] = acc
@@ -294,7 +294,7 @@ def load_gtdb_metadata(infile, G, completeness, contamination):
  raise KeyError('Cannot find "ncbi_taxonomy"')
  if X == 'none':
  stats['no ncbi tax'] += 1
- continue 
+ continue
  # filtering by checkM stats
  try:
  X = line[header['checkm_completeness']]
@@ -351,7 +351,7 @@ def lca_frac_pass(D, lca_frac):
  mc = D.most_common(1)
  except IndexError:
  return [None,None]
- if re.search(r'^[pcofgs]__$', mc[0][0]):
+ if re.search(r'^[Xx][pcofgs]__', mc[0][0]):
  return [None,None]
  try:
  frac = mc[0][1] / float(sum(D.values()))
@@ -401,7 +401,7 @@ def _query_tax(tax_queries, G, qtax, ttax, lca_frac=1.0, max_tips=100, verbose=F
  # iterating queries
  for Q in tax_queries:
  tips = []
- try:
+ try: 
  # getting descendents of the node
  tips = [desc for desc in descendants(G[qtax], Q[0]) if \
  G[qtax].nodes[desc]['taxonomy'] == 'strain']

tests/data/ncbi-gtdb/gtdb_tax_queries.txt

@@ -1,3 +1,4 @@
+f__Gearchaeaceae
 g__Aquabacter
 s__Nitrosopumilus sp000746785
 g__Escherichia
@@ -6,5 +7,6 @@ s__Xanthomonas oryzae
 c__Gammaproteobacteria
 o__Burkholderiales
 c__Bacteroidia
+f__BM003
 s__Homo sapiens
 Blank