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#!/usr/bin/env python
from cogent.util.unit_test import TestCase, main
from cogent.core.info import Info
from cogent.parse.pknotsrg import pknotsrg_parser
__author__ = "Shandy Wikman"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__contributors__ = ["Shandy Wikman"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Shandy Wikman"
__email__ = "ens01svn@cs.umu.se"
__status__ = "Development"
class PknotsrgParserTest(TestCase):
"""Provides tests for pknotsRG RNA secondary structure format parsers"""
def setUp(self):
"""Setup function"""
#output
self.pknotsrg_out = PKNOTSRG
#expected
self.pknotsrg_exp = [['UGCAUAAUAGCUCC',[(0,8),(3,11),(5,13)],-22.40]]
def test_pknotsrg_output(self):
"""Test for pknotsrg format parser"""
obs = pknotsrg_parser(self.pknotsrg_out)
self.assertEqual(obs,self.pknotsrg_exp)
PKNOTSRG = ['UGCAUAAUAGCUCC\n', '(..{.[..)..}.] (-22.40)\n']
if __name__ == '__main__':
main()
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