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#!/usr/bin/env python
from os import getcwd, remove, rmdir, mkdir, path
import tempfile, shutil
from cogent.core.moltype import RNA
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from cogent.app.mafft import Mafft, align_unaligned_seqs, \
add_seqs_to_alignment, align_two_alignments
__author__ = "Jeremy Widmann"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Jeremy Widmann"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Jeremy Widmann"
__email__ = "jeremy.widmann@colorado.edu"
__status__ = "Development"
class GeneralSetUp(TestCase):
def setUp(self):
"""Mafft general setUp method for all tests"""
self.seqs1 = ['ACUGCUAGCUAGUAGCGUACGUA','GCUACGUAGCUAC',
'GCGGCUAUUAGAUCGUA']
self.labels1 = ['>1','>2','>3']
self.lines1 = flatten(zip(self.labels1,self.seqs1))
self.aligned1 = {'1': 'acugcuagcuaguagcguacgua',\
'2': 'gcuacguagcuac----------',\
'3': 'gcggcuauuagau------cgua',\
}
self.seqs2=['UAGGCUCUGAUAUAAUAGCUCUC','UAUCGCUUCGACGAUUCUCUGAUAGAGA',
'UGACUACGCAU']
self.labels2=['>a','>b','>c']
self.lines2 = flatten(zip(self.labels2,self.seqs2))
self.aligned2 = {'a': 'UAGGCUCUGAUAUAAUAGCUCUC---------',\
'b': 'UA----UCGCUUCGACGAUUCUCUGAUAGAGA',\
'c': 'UG------------ACUACGCAU---------',\
}
self.temp_dir = tempfile.mkdtemp()
self.temp_dir_spaces = '/tmp/test for mafft/'
try:
mkdir(self.temp_dir_spaces)
except OSError:
pass
try:
#create sequence files
f = open(path.join(self.temp_dir, 'seq1.txt'),'w')
f.write('\n'.join(self.lines1))
f.close()
g = open(path.join(self.temp_dir, 'seq2.txt'),'w')
g.write('\n'.join(self.lines2))
g.close()
except OSError:
pass
class MafftTests(GeneralSetUp):
"""Tests for the Mafft application controller"""
def test_base_command(self):
"""Mafft BaseCommand should return the correct BaseCommand"""
c = Mafft()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','mafft']))
c.Parameters['--quiet'].on()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','mafft --quiet']))
c.Parameters['--globalpair'].on()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','mafft --globalpair --quiet']))
c.Parameters['--maxiterate'].on(1000)
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ',"""mafft --maxiterate 1000 --globalpair --quiet"""]))
def test_changing_working_dir(self):
"""Mafft BaseCommand should change according to WorkingDir"""
c = Mafft(WorkingDir='/tmp/mafft_test')
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/mafft_test','/"; ','mafft']))
c = Mafft()
c.WorkingDir = '/tmp/mafft_test2'
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/mafft_test2','/"; ','mafft']))
#removing the dirs is proof that they were created at the same time
#if the dirs are not there, an OSError will be raised
rmdir('/tmp/mafft_test')
rmdir('/tmp/mafft_test2')
def test_general_cleanUp(self):
"""Last test executed: cleans up all files initially created"""
# remove the tempdir and contents
shutil.rmtree(self.temp_dir)
shutil.rmtree(self.temp_dir_spaces)
def test_align_unaligned_seqs(self):
"""align_unaligned_seqs should work as expected"""
res = align_unaligned_seqs(self.seqs1, RNA)
self.assertEqual(res.toFasta(), align1)
res = align_unaligned_seqs(self.lines2, RNA)
self.assertEqual(res.toFasta(), align2)
def test_add_seqs_to_alignment(self):
"""add_seqs_to_alignment should work as expected."""
res = add_seqs_to_alignment(self.lines1,self.aligned2, RNA)
self.assertEqual(res.toFasta(), add_seqs_align)
def test_align_two_alignments(self):
"""align_two_alignments should work as expected."""
res = align_two_alignments(self.aligned1, self.aligned2, RNA)
self.assertEqual(res.toFasta(), align_two_align)
align1 = ">seq_0\nACUGCUAGCUAGUAGCGUACGUA\n>seq_1\nGCUACGUAGCUAC----------\n>seq_2\nGCGGCUAUUAGAU------CGUA"
align2 = ">a\nUAGGCUCUGAUAUAAUAGCUCUC---------\n>b\nUA----UCGCUUCGACGAUUCUCUGAUAGAGA\n>c\nUG------------ACUACGCAU---------"
add_seqs_align = """>1\nACUGC-UAGCUAGUAGCGUACGUA--------\n>2\nGCUACGUAGCUA-----------C--------\n>3\nGCGGCUAUUAGAUCGUA---------------\n>a\nUAGGCUCUGAUAUAAUAGCUCUC---------\n>b\nUA----UCGCUUCGACGAUUCUCUGAUAGAGA\n>c\nUG------------ACUACGCAU---------"""
align_two_align = """>1\nACUGCUAGCUAGUAGCGUACGUA---------\n>2\nGCUACGUAGCUAC-------------------\n>3\nGCGGCUAUUAGAU------CGUA---------\n>a\nUAGGCUCUGAUAUAAUAGCUCUC---------\n>b\nUA----UCGCUUCGACGAUUCUCUGAUAGAGA\n>c\nUG------------ACUACGCAU---------"""
if __name__ == '__main__':
main()
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