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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.consan import Consan
__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 ConsanTest(TestCase):
"""Tests for Consan application controller"""
def setUp(self):
self.input1 = consan_input1
self.input2 = consan_input2
def test_stdout_input_as_lines(self):
"""Test Consan stdout input as lines"""
c = Consan(InputHandler='_input_as_lines')
input = self.input1
input.extend(self.input2)
res = c(input)
#Impossible to compare stdout since copmutation time is in the output
#which may differ between runs
self.assertEqual(res['ExitStatus'],0)
assert res['StdOut'] is not None
res.cleanUp()
def test_input_as_string(self):
"""Test Consan stdout input as string"""
c = Consan()
f = open('/tmp/seq1.fasta','w')
txt = '\n'.join([str(i).strip('\n') for i in self.input1])
f.write(txt)
f.close()
s = open('/tmp/seq2.fasta','w')
txt = '\n'.join([str(i).strip('\n') for i in self.input2])
s.write(txt)
s.close()
res = c(['/tmp/seq1.fasta','/tmp/seq2.fasta'])
#Impossible to compare stdout since copmutation time is in the output
#which may differ between runs
self.assertEqual(res['ExitStatus'],0)
assert res['StdOut'] is not None
res.cleanUp()
def test_get_result_path(self):
"""Tests Consan result path"""
c = Consan(InputHandler='_input_as_lines')
input = self.input1
input.extend(self.input2)
res = c(input)
self.assertEqualItems(res.keys(),['StdOut','StdErr','ExitStatus'])
self.assertEqual(res['ExitStatus'],0)
res.cleanUp()
consan_input1 = ['>seq1\n',
'GGCCACGTAGCTCAGTCGGTAGAGCAAAGGACTGAAAATCCTTGTGTCGTTGGTTCAATTCCAACCGTGGCCACCA']
consan_input2 = ['>seq2\n',
'GCCAGATAGCTCAGTCGGTAGAGCGTTCGCCTGAAAAGTGAAAGGTCGCCGGTTCGATCCCGGCTCTGGCCACCA']
if __name__ == '__main__':
main()
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