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#!/usr/bin/env python
from os import remove
from cogent.util.unit_test import TestCase, main
from cogent.core.info import Info
from cogent.app.knetfold import Knetfold
__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 KnetfoldTest(TestCase):
"""Tests for Knetfold application controller"""
def setUp(self):
self.input = knetfold_input
def test_input_as_lines(self):
"""Test Knetfold stdout input as lines"""
k = Knetfold(InputHandler='_input_as_lines')
res = k(self.input)
self.assertEqual(res['ExitStatus'],0)
assert res['StdOut'] is not None
res.cleanUp()
def test_input_as_string(self):
"""Test Knetfold stdout input as string"""
k = Knetfold()
f = open('/tmp/single.fasta','w')
f.write('\n'.join(self.input))
f.close()
res = k('/tmp/single.fasta')
self.assertEqual(res['ExitStatus'],0)
assert res['StdOut'] is not None
res.cleanUp()
remove('/tmp/single.fasta')
def test_get_result_path(self):
"""Tests knetfold result path"""
k = Knetfold(InputHandler='_input_as_lines')
res = k(self.input)
self.assertEqualItems(res.keys(),['StdOut','StdErr','ExitStatus',
'ct','coll','sec','fasta','pdf','mx0','mx1','mx2','mx3'])
self.assertEqual(res['ExitStatus'],0)
assert res['ct'] is not None
assert res['coll'] is not None
assert res['sec'] is not None
assert res['fasta'] is not None
res.cleanUp()
knetfold_input = ['>seq1\n',
'GGCUAGAUAGCUCAGAUGGUAGAGCAGAGGAUUGAAGAUCCUUGUGUCGUCGGUUCGAUCCCGGCUCUGGC\n',
'\n']
if __name__ == '__main__':
main()
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