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#!/usr/bin/env python
from os import remove
from cogent.util.unit_test import TestCase, main
from cogent.app.foldalign import foldalign
__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 FoldalignTest(TestCase):
"""Tests for Foldalign application controller"""
def setUp(self):
self.input = FOLDALIGN_INPUT
def test_input_as_lines(self):
"""Test foldalign stdout input as lines"""
f = foldalign(InputHandler='_input_as_lines')
res = f(self.input)
self.assertEqual(res['ExitStatus'],0)
assert res['StdOut'] is not None
res.cleanUp()
def test_input_as_string(self):
"""Test foldalign stdout input as string"""
f = foldalign()
t = open('/tmp/single.col','w')
t.write('\n'.join(self.input))
t.close()
res = f('/tmp/single.col')
self.assertEqual(res['ExitStatus'],0)
assert res['StdOut'] is not None
res.cleanUp()
remove('/tmp/single.col')
def test_get_result_path(self):
"""Tests foldalign result path"""
f = foldalign(InputHandler='_input_as_lines')
res = f(self.input)
self.assertEqualItems(res.keys(),['StdOut','StdErr','ExitStatus'])
self.assertEqual(res['ExitStatus'],0)
assert res['StdOut'] is not None
res.cleanUp()
FOLDALIGN_INPUT = ['>seq1\n', 'GGCCACGTAGCTCAGTCGGTAGAGCAAAGGACTGAAAATCCTTGTGTCGTTGGTTCAATTCCAACCGTGGCCACCA','>seq2\n', 'GCCAGATAGCTCAGTCGGTAGAGCGTTCGCCTGAAAAGTGAAAGGTCGCCGGTTCGATCCCGGCTCTGGCCACCA']
if __name__ == '__main__':
main()
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