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#!/usr/bin/env python
from os import remove
from cogent.util.unit_test import TestCase, main
from cogent.app.nupack import Nupack
__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 NupackTest(TestCase):
"""Tests for Nupack application controller"""
def setUp(self):
self.input = nupack_input
def test_input_as_lines(self):
"""Test nupack input as lines"""
n = Nupack(InputHandler='_input_as_lines')
exp = '%s\n' % '\n'.join([str(i).strip('\n') for i in nupack_stdout])
res = n(self.input)
obs = res['StdOut'].read()
self.assertEqual(obs,exp)
res.cleanUp()
def test_input_as_string(self):
"""Test nupack input as string"""
n = Nupack()
exp = '%s\n' % '\n'.join([str(i).strip('\n') for i in nupack_stdout])
f = open('/tmp/single.fasta','w')
txt = '\n'.join([str(i).strip('\n') for i in self.input])
f.write(txt)
f.close()
res = n('/tmp/single.fasta')
obs = res['StdOut'].read()
self.assertEqual(obs,exp)
res.cleanUp()
remove('/tmp/single.fasta')
def test_get_result_path(self):
"""Tests nupack result path"""
n = Nupack(InputHandler='_input_as_lines')
res = n(self.input)
self.assertEqualItems(res.keys(),['StdOut','StdErr','ExitStatus',
'pair','ene'])
assert res['pair'] is not None
assert res['ene'] is not None
res.cleanUp()
nupack_input = ['>seq1\n',
'GGCUAGAUAGCUCAGAUGGUAGAGCAGAGGAUUGAAGAUCCUUGUGUCGUCGGUUCGAUCCCGGCUCUGGC\n',
'\n']
nupack_stdout = ['****************************************************************\n',
'NUPACK 1.2\n', 'Copyright 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 = 71\n', 'Sequence and a Minimum Energy Structure:\n',
'GGCUAGAUAGCUCAGAUGGUAGAGCAGAGGAUUGAAGAUCCUUGUGUCGUCGGUUCGAUCCCGGCUCUGGC\n',
'.....((..((.((...{.{{{{{{.{.{{{{{{{{......)).))..))..}}}}}}}}}.}}}}}}.}\n',
'mfe = -23.30 kcal/mol\n', 'pseudoknotted!\n']
if __name__ == '__main__':
main()
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