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#!/usr/bin/env python
from os import remove
from cogent.util.unit_test import TestCase, main
from cogent.app.comrna import comRNA
__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 ComrnaTest(TestCase):
"""Tests for comRNA application controller"""
def setUp(self):
self.input = comrna_input
def test_input_as_lines(self):
"""Test comrna input as lines"""
c = comRNA(InputHandler='_input_as_lines')
res = c(self.input)
#Can't compare stdout since comRNA app controller uses tmp filenames
#that are impossible to predict.
self.assertEqual(res['ExitStatus'],0)
assert res['StdOut'] is not None
res.cleanUp()
def test_input_as_string(self):
"""Test comrna input as string"""
c = comRNA()
f = open('/tmp/single.fasta','w')
txt = '\n'.join([str(i).strip('\n') for i in self.input])
f.write(txt)
f.close()
res = c('/tmp/single.fasta')
#Can't compare stdout since comRNA app controller uses tmp filenames
#that are impossible to predict.
self.assertEqual(res['ExitStatus'],0)
assert res['StdOut'] is not None
res.cleanUp()
remove('/tmp/single.fasta')
def test_get_result_path(self):
"""Tests comrna result path"""
c = comRNA(InputHandler='_input_as_lines')
res = c(self.input)
self.assertEqualItems(res.keys(),['StdOut','StdErr','ExitStatus'])
self.assertEqual(res['ExitStatus'],0)
assert res['StdOut'] is not None
res.cleanUp()
comrna_input = ['>seq1\n', 'GGCTAGATAGCTCAGATGGTAGAGCAGAGGATTGAAGATCCTTGTGTCGTCGGTTCGATCCCGGCTCTGGCC\n', '>seq2\n', 'GGCTAGATAGCTCAGATGGTAGAGCAGAGGATTGAAGATCCTTGTGTCGTCGGTTCGATCCCGGCTCTGGCC\n', '>seq3\n', 'GGCTAGATAGCTCAGATGGTAGAGCAGAGGATTGAAGATCCTTGTGTCGTCGGTTCGATCCCGGCTCTGGCC\n', '>seq4\n', 'GGCTAGATAGCTCAGATGGTAGAGCAGAGGATTGAAGATCCTTGTGTCGTCGGTTCGATCCCGGCTCTGGCC']
if __name__ == '__main__':
main()
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