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See help text below about usage. Script was created to create consensus taxonomy strings for all sequence taxa strings in the Silva 119 release.
#!/usr/bin/env python
# USAGE
# python create_consensus_taxonomy.py X Y Z A
# where X is the taxonomy mapping file for all NR seqs, Y is the representative
# file (i.e. one of the rep_set/ files with the 119 release), Z is the OTU
# mapping file created from running pick_otus.py, and A is the output
# consensus mapping file
from sys import argv
from cogent.parse.fasta import MinimalFastaParser
silva_taxa = open(argv[1], "U")
id_to_taxa = {}
for line in silva_taxa:
curr_id = line.split()[0].strip()
curr_taxa = " ".join(line.split()[1:]).strip()
id_to_taxa[curr_id] = curr_taxa
rep_set_fasta = open(argv[2], "U")
ordered_ids = []
for label,seq in MinimalFastaParser(rep_set_fasta):
ordered_ids.append(label)
ordered_ids = set(ordered_ids)
otu_mapping = open(argv[3], "U")
matched_ids = {}
for line in otu_mapping:
if len(line.strip()) == 0:
continue
curr_line = line.strip().split('\t')
curr_otu = curr_line[0]
all_seqs = curr_line[1:]
for seq in all_seqs:
if seq in ordered_ids:
matched_ids[seq] = all_seqs
output_taxa_mapping = open(argv[4], "w")
for id in ordered_ids:
taxa_data = []
final_taxa_string = []
for curr_seq in matched_ids[id]:
# Used example from http://stackoverflow.com/questions/3844801/check-if-all-elements-in-a-list-are-identical for comparing equality of elements
# Have to step backwards through the bottom taxa up to the top taxa
taxa_data.append(id_to_taxa[curr_seq].split(';')[::-1])
levels = len(taxa_data[0])
final_taxa_string = []
for n in range(levels):
curr_taxa_strings = []
for tax in taxa_data:
curr_taxa_strings.append(tax[n])
match = all(x==curr_taxa_strings[0] for x in curr_taxa_strings)
if match:
final_taxa_string.append(curr_taxa_strings[0])
else:
final_taxa_string.append("Ambiguous_taxa")
fixed_taxa_string = ";".join(final_taxa_string[::-1])
output_taxa_mapping.write("%s\t%s\n" % (id, fixed_taxa_string))
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