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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.consan import consan_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 ConsanParserTest(TestCase):
"""Provides tests for CONSAN RNA secondary structure parsers"""
def setUp(self):
"""Setup function"""
#output
self.consan_out = CONSAN
#expected
self.consan_exp = [{'seq1':'GGACACGUCGCUCA','seq2':'G.ACAGAUCGCUCA'},
[(0,13),(2,11),(5,8)]]
def test_consan_output(self):
"""Test for consan format parser"""
obs = consan_parser(self.consan_out)
self.assertEqual(obs,self.consan_exp)
CONSAN = ['Using standard STA scoring\n',
'Using QRADIUS constraints (Quality > 0.9500 SPACED 20) !\n',
'# STOCKHOLM 1.0\n', '\n', '#=GF SC\t 1.000000\n', '#=GF PI\t 0.720000\n',
'#=GF ME\t QRadius Num: 3 Win: 20 Cutoff: 0.95\n',
'\n', 'seq1 \tGGACACGUCGCUCA\n',
'seq2 \tG.ACAGAUCGCUCA\n',
'#=GC SS_cons\t\t >.>..>..<..<.<\n',
'#=GC PN \t\t .......*......\n', '\n', '\n', '\n',
'#=GF TIME 43.0\n', '\n', '//\n']
if __name__ == '__main__':
main()
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