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#!/usr/bin/env python
from cogent.util.unit_test import TestCase, main
from cogent.parse.cut import cut_parser
__author__ = "Rob Knight"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__contributors__ = ["Rob Knight"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Rob Knight"
__email__ = "rob@spot.colorado.edu"
__status__ = "Development"
class CutParserTest(TestCase):
"""Provides tests for codon usage table parser"""
def test_cut_parser(self):
"""cut_parser should work on first few lines of supplied file"""
lines = """#Species: Saccharomyces cerevisiae
#Division: gbpln
#Release: TranstermMay1994
#CdsCount: 24
#Coding GC 44.99%
#1st letter GC 47.28%
#2nd letter GC 40.83%
#3rd letter GC 46.86%
#Codon AA Fraction Frequency Number
GCA A 0.010 1.040 6
GCC A 0.240 22.420 130
GCG A 0.000 0.000 0
GCT A 0.750 71.610 411
TGC C 0.070 0.520 3
"""
result = cut_parser(lines.splitlines())
self.assertEqual(result, \
{'GCA':6,'GCC':130,'GCG':0,'GCT':411,'TGC':3})
if __name__ == '__main__':
main()
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