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#!/usr/bin/env python
from os import remove
from cogent.util.unit_test import TestCase, main
from cogent.app.rnaalifold import RNAalifold, rnaalifold_from_alignment
from cogent.core.alignment import DataError
__author__ = "Shandy Wikman"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__contributors__ = ["Shandy Wikman","Jeremy Widmann"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Shandy Wikman"
__email__ = "ens01svn@cs.umu.se"
__status__ = "Development"
class RnaalifoldTest(TestCase):
"""Tests for Rnaalifold application controller"""
def setUp(self):
self.input = RNAALIFOLD_INPUT
self.unaligned = \
{'seq_0': 'GGUAGGUCGCUGGACUUGUCUCCUUGACUGUCCGGAAGGAGCGGU',
'seq_1': 'GGUAGGUCGCUGGAUUGAUAUGAGUAUUGUCCGGAAGGAGCGGA',
'seq_2': 'GGUAGGACGCGGGACUUCUGUUCAGGACUGUCCCGAAGGUGCGGU',
'seq_3': 'GGUAGGUCGCCGCACGUCGCUUCAGGACUGUGCGGAAGGAGCGGU',
'seq_4': 'GGUAGGUCGCUGUACUUCUAUCAGGACUGUACGGAAGGAGCGGU',
}
self.alignment = \
{'seq_0': 'GGUAGGUCGCUGGAC-UUGUCUCCUUGACU-GUCCGGAAGGAGCGGU',
'seq_1': 'GGUAGGUCGCUGGAU-UGAUAUGAGUAUU--GUCCGGAAGGAGCGGA',
'seq_2': 'GGUAGGACGCGGGAC-UUCUGUUCAGGACU-GUCCCGAAGGUGCGGU',
'seq_3': 'GGUAGGUCGCCGCACGUCGCUUCAGGAC--UGUGCGGAAGGAGCGGU',
'seq_4': 'GGUAGGUCGCUGUAC-UUCUAUCAGGACU--GUACGGAAGGAGCGGU',
}
self.old_struct = '....(.((.((((((..(((....)))....))))))...)).)...'
#from version 1.4
self.new_struct = '....(.((.((((((................))))))...)).)...'
#from version 1.8 - no easy way to check version so putting both in
def test_input_as_lines(self):
"""Test rnaalifold stdout input as lines"""
r = RNAalifold(InputHandler='_input_as_lines')
res = r(self.input)
self.assertEqual(res['ExitStatus'],0)
assert res['StdOut'] is not None
res.cleanUp()
def test_input_as_string(self):
"""Test rnaalifold stdout input as string"""
r = RNAalifold()
f = open('/tmp/clustal','w')
f.write('\n'.join(self.input))
f.close()
res = r('/tmp/clustal')
self.assertEqual(res['ExitStatus'],0)
assert res['StdOut'] is not None
res.cleanUp()
remove('/tmp/clustal')
def test_get_result_path(self):
"""Tests rnaalifold result path"""
r = RNAalifold(InputHandler='_input_as_lines')
res = r(self.input)
self.assertEqualItems(res.keys(),['StdOut','StdErr','ExitStatus','SS'])
self.assertEqual(res['ExitStatus'],0)
assert res['StdOut'] is not None
res.cleanUp()
def test_rnaalifold_from_alignment_unaligned(self):
"""rnaalifold_from_alignment should handle unaligned seqs.
"""
self.assertRaises(DataError,rnaalifold_from_alignment,self.unaligned)
def test_rnaalifold_from_alignment(self):
"""rnaalifold_from_alignment should give correct result.
"""
[[seq, struct,energy]] = rnaalifold_from_alignment(aln=self.alignment)
try:
self.assertEqual(struct,self.old_struct)
except AssertionError:
self.assertEqual(struct,self.new_struct)
RNAALIFOLD_INPUT = ['CLUSTAL\n', '\n', 'seq1 GGCTAGATAGCTCAGATGGT-AGAGCAGAGGATTGAAGATCCTTGTGTCGTCGGTTCGATCCCGGCTCTGGCC----\n']
if __name__ == '__main__':
main()
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