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#!/usr/bin/env python
__author__ = "Jesse Zaneveld"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Jesse Zaneveld", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Jesse Zaneveld"
__email__ = "zaneveld@gmail.com"
__status__ = "Development"
from sys import argv
from string import strip
from os import listdir,path
from optparse import OptionParser
from datetime import datetime
def parse_kegg_taxonomy(lines):
"""Returns successive taxonomy entries from lines.
Format of return value is four levels of taxonomy (sometimes empty),
unique id, three-letter kegg code, abbreviated name, full name,
genus, species, and common name if present.
Taxonomic level information is implicit in the number of hashes read
at the beginning of the last line with hashes. Need to keep track of
the last level read.
Each hash line has a number of hashes indicating the level, and a name
for that taxonomic level. Note that this is not as detailed as the real
taxonomy in the genome file!
Maximum taxonomic level as of this writing is 4: exclude any levels more
detailed than this.
Each non-taxon line is tab-delimited: has a unique id of some kind, then
the three-letter KEGG code, then the short name (should be the same as
the names of the individual species files for genes, etc.), then the
genus and species names which may have a common name in parentheses
afterwards.
"""
max_taxonomy_length = 4
taxonomy_stack = []
for line in lines:
#bail out if it's a blank line
line = line.rstrip()
if not line:
continue
if line.startswith('#'): #line defining taxonomic level
hashes, name = line.split(None, 1)
name = name.strip()
level = len(hashes)
if level == len(taxonomy_stack): #new entry at same level
taxonomy_stack[-1] = name
elif level > len(taxonomy_stack): #add level: assume sequential
taxonomy_stack.append(name)
else: #level must be less than stack length: truncate
del taxonomy_stack[level:]
taxonomy_stack[level-1] = name
else: #line defining an individual taxonomy entry
fields = map(strip, line.split('\t'))
#add genus, species, and common name as three additional fields
raw_species_name = fields[-1]
species_fields = raw_species_name.split()
if not species_fields:
print "ERROR"
print line
genus_name = species_fields[0]
if len(species_fields) > 1:
species_name = species_fields[1]
else:
species_name = ''
#check for common name
if '(' in raw_species_name:
prefix, common_name = raw_species_name.split('(', 1)
common_name, ignored = common_name.split(')', 1)
else:
common_name = ''
output_taxon = taxonomy_stack + \
['']*(max_taxonomy_length-len(taxonomy_stack)) \
+ fields + [genus_name, species_name, common_name]
yield "\t".join(output_taxon) + "\n"
if __name__ == '__main__':
from sys import argv
filename = argv[1]
for result_line in parse_kegg_taxonomy(open(filename,"U")):
print result_line.strip()
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