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#!/usr/bin/env python
from cogent.util.unit_test import TestCase, main
from cogent.parse.kegg_pos import parse_pos_lines, parse_pos_file
__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_pos.py in cogent.parse.
"""
class ParsePosTests(TestCase):
def test_parse_pos_lines(self):
"""Parse pos lines should parse given lines and filename"""
test_lines = \
['YPO0021 hemN 28982 28982..30355 1374\n',\
'YPO0022 glnG, glnT, ntrC 30409 complement(30409..31821) 1413\n',\
'YPO0023 glnL, ntrB 31829 complement(31829..32878) 1050\n',\
'YPO0024 glnA 33131 complement(33131..34540) 1410\n']
obs = parse_pos_lines(test_lines, file_name = 'y.pestis.pos')
exp = ['y.pestis\tYPO0021 hemN 28982 28982..30355 1374\n',\
'y.pestis\tYPO0022 glnG, glnT, ntrC 30409 complement(30409..31821) 1413\n',\
'y.pestis\tYPO0023 glnL, ntrB 31829 complement(31829..32878) 1050\n',\
'y.pestis\tYPO0024 glnA 33131 complement(33131..34540) 1410\n']
for i,parsed_line in enumerate(obs):
self.assertEqual(parsed_line, exp[i])
def test_pos_to_fields(self):
"""parse_pos_to_fields should open files and extract fields"""
# Note that this test is set to pass, as this is just a simple
# open/yield wrapper equivalent to the demo blocks for other parsers.
# It is kept as an independent function to allow calling by handlers.
pass
if __name__=="__main__":
main()
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