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#!/usr/bin/env python
from cogent.util.unit_test import TestCase, main
from cogent.parse.kegg_taxonomy import parse_kegg_taxonomy
__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__ = "Production"
"""
Test code for kegg_taxonomy.py in cogent.parse.
"""
class ParseKEGGTaxonomy(TestCase):
def test_parse_kegg_taxonomy(self):
"""parse_kegg_taxonomy should return successive taxonomy entries from
lines"""
test_lines =\
['# Eukaryotes\n',\
'## Animals\n',\
'### Vertebrates\n',\
'#### Mammals\n',\
'T01001(2000)\thsa\tH.sapiens\tHomo sapiens (human)\n',\
'#### Birds\n',\
'T01006(2005)\tgga\tG.gallus\tGallus gallus (chicken)\n',\
'### Arthropods\n',\
'#### Insects\n',\
'T00030(2000)\tdme\tD.melanogaster\tDrosophila melanogaster (fruit fly)\n']
exp =\
['Eukaryotes\tAnimals\tVertebrates\tMammals\tT01001(2000)\thsa\tH.sapiens\tHomo sapiens (human)\tHomo\tsapiens\thuman\n',\
'Eukaryotes\tAnimals\tVertebrates\tBirds\tT01006(2005)\tgga\tG.gallus\tGallus gallus (chicken)\tGallus\tgallus\tchicken\n',\
'Eukaryotes\tAnimals\tArthropods\tInsects\tT00030(2000)\tdme\tD.melanogaster\tDrosophila melanogaster (fruit fly)\tDrosophila\tmelanogaster\tfruit fly\n']
obs = parse_kegg_taxonomy(test_lines)
for i,res in enumerate(obs):
self.assertEqual(res,exp[i])
if __name__=="__main__":
main()
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