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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.cove import coves_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 CovesParserTest(TestCase):
"""Provides tests for Coves RNA secondary structure parsers"""
def setUp(self):
"""Setup function """
#output
self.cove_out = COVE
#expected
self.cove_exp = [['UAGAUGGCUCUCAU',[(0,13),(2,11),(3,10)]]]
def test_cove_output(self):
"""Test coves format parser"""
obs = coves_parser(self.cove_out)
self.assertEqual(obs,self.cove_exp)
COVE = ['coves - scoring and structure prediction of RNA sequences\n', ' using a covariance model\n',
' version 2.4.4, January 1996\n', '\n',
'---------------------------------------------------\n',
'Database to search/score: single.fasta\n',
'Model: single.fasta.cm\n',
'GC% of background model: 50%\n',
'---------------------------------------------------\n', '\n',
'-32.55 bits : seq1\n', ' seq1 UAGAUGGCUCUCAU\n',
' seq1 >.>>......<<.<\n', '\n']
if __name__ == '__main__':
main()
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