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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.nupack import nupack_parser
__author__ = "Shandy Wikman"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__contributors__ = ["Shandy Wikman"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Shandy Wikman"
__email__ = "ens01svn@cs.umu.se"
__status__ = "Development"
class NupackParserTest(TestCase):
"""Provides tests for NUPACK RNA secondary structure format parsers"""
def setUp(self):
"""Setup function"""
#output
self.nupack_out = NUPACK
#expected
self.nupack_exp = [['GGCUAGUCCCUUCU',[(0,9),(1,8),(4,13),(5,12)],-23.30]]
def test_nupack_output(self):
"""Test for nupack format"""
obs = nupack_parser(self.nupack_out)
self.assertEqual(obs,self.nupack_exp)
NUPACK = ['****************************************************************\n', 'NUPACK 1.2\n',
'Copyright 2007-2009 2003, 2004 by Robert M. Dirks & Niles A. Pierce\n',
'California Institute of Technology\n', 'Pasadena, CA 91125 USA\n', '\n',
'Last Modified: 03/18/2004\n',
'****************************************************************\n', '\n',
'\n', 'Fold.out Version 1.2: Complexity O(N^5) (pseudoknots enabled)\n',
'Reading Input File...\n', 'Sequence Read.\n', 'Energy Parameters Loaded\n',
'SeqLength = 14\n', 'Sequence and a Minimum Energy Structure:\n',
'GGCUAGUCCCUUCU\n', '((..{{..))..}}\n', 'mfe = -23.30 kcal/mol\n',
'pseudoknotted!\n']
if __name__ == '__main__':
main()
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