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#!/usr/bin/env python
from os import getcwd, remove, rmdir, mkdir, path
from subprocess import Popen, PIPE, STDOUT
import tempfile, shutil
from cogent.core.moltype import RNA, DNA
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from cogent.app.muscle_v38 import Muscle, muscle_seqs, aln_tree_seqs, \
align_unaligned_seqs, build_tree_from_alignment, \
align_and_build_tree, add_seqs_to_alignment, align_two_alignments
__author__ = "Catherine Lozupone"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Catherine Lozupone", "Rob Knight", "Daniel McDonald",
"Jai Ram Rideout"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Catherine Lozupone"
__email__ = "lozupone@colorado.edu"
__status__ = "Production"
class GeneralSetUp(TestCase):
def setUp(self):
"""Muscle general setUp method for all tests"""
# Check if muscle version is supported for this test
acceptable_version = (3,8)
command = "muscle -version"
proc = Popen(command,shell=True,universal_newlines=True,\
stdout=PIPE,stderr=STDOUT)
stdout = proc.stdout.read()
version_string = stdout.strip().split(' ')[1].strip()[1:]
try:
version = tuple(map(int,version_string.split('.')))
pass_test = version[:2] == acceptable_version
except ValueError:
pass_test = False
version_string = stdout
self.assertTrue(pass_test,\
"Unsupported muscle version. %s is required, but running %s." \
% ('.'.join(map(str,acceptable_version)), version_string))
self.seqs1 = ['ACUGCUAGCUAGUAGCGUACGUA','GCUACGUAGCUAC',
'GCGGCUAUUAGAUCGUA']
self.labels1 = ['>1','>2','>3']
self.lines1 = flatten(zip(self.labels1,self.seqs1))
self.seqs2=['UAGGCUCUGAUAUAAUAGCUCUC','UAUCGCUUCGACGAUUCUCUGAUAGAGA',
'UGACUACGCAU']
self.labels2=['>a','>b','>c']
self.lines2 = flatten(zip(self.labels2,self.seqs2))
self.temp_dir = tempfile.mkdtemp()
self.temp_dir_spaces = '/tmp/test for muscle/'
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
def tearDown(self):
"""cleans up all files initially created"""
# remove the tempdir and contents
shutil.rmtree(self.temp_dir)
shutil.rmtree(self.temp_dir_spaces)
class MuscleTests(GeneralSetUp):
"""Tests for the Muscle application controller"""
def test_base_command(self):
"""Muscle BaseCommand should return the correct BaseCommand"""
c = Muscle()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','muscle']))
c.Parameters['-in'].on('seq.txt')
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','muscle -in "seq.txt"']))
c.Parameters['-cluster2'].on('neighborjoining')
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','muscle -cluster2 neighborjoining' +
' -in "seq.txt"']))
def test_maxmb(self):
"""maxmb option should not break Muscle"""
app = Muscle()
app.Parameters['-maxmb'].on('250')
outfile = tempfile.NamedTemporaryFile()
app.Parameters['-out'].on(outfile.name)
infile = tempfile.NamedTemporaryFile()
infile.write(
">Seq1\nAAAGGGTTTCCCCT\n"
">Seq2\nAAAGGGGGTTTCCACT\n")
infile.flush()
result = app(infile.name)
observed = result['MuscleOut'].read()
expected = (
">Seq1\nAAA--GGGTTTCCCCT\n"
">Seq2\nAAAGGGGGTTTCCACT\n"
)
self.assertEqual(observed, expected)
def test_changing_working_dir(self):
"""Muscle BaseCommand should change according to WorkingDir"""
c = Muscle(WorkingDir='/tmp/muscle_test')
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/muscle_test','/"; ','muscle']))
c = Muscle()
c.WorkingDir = '/tmp/muscle_test2'
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/muscle_test2','/"; ','muscle']))
#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/muscle_test')
rmdir('/tmp/muscle_test2')
def test_aln_tree_seqs(self):
"aln_tree_seqs returns the muscle alignment and tree from iteration2"
tree, aln = aln_tree_seqs(path.join(self.temp_dir, 'seq1.txt'),
tree_type="neighborjoining",
WorkingDir=self.temp_dir,
clean_up=True)
self.assertEqual(str(tree), '((1:1.125,2:1.125):0.375,3:1.5);')
self.assertEqual(len(aln), 6)
self.assertEqual(aln[-2], '>3\n')
self.assertEqual(aln[-1], 'GCGGCUAUUAGAUCGUA------\n')
def test_aln_tree_seqs_spaces(self):
"aln_tree_seqs should work on filename with spaces"
try:
#create sequence files
f = open(path.join(self.temp_dir_spaces, 'muscle_test_seq1.txt'),'w')
f.write('\n'.join(self.lines1))
f.close()
except OSError:
pass
tree, aln = aln_tree_seqs(path.join(self.temp_dir_spaces,\
'muscle_test_seq1.txt'),
tree_type="neighborjoining",
WorkingDir=getcwd(),
clean_up=True)
self.assertEqual(str(tree), '((1:1.125,2:1.125):0.375,3:1.5);')
self.assertEqual(len(aln), 6)
self.assertEqual(aln[-2], '>3\n')
self.assertEqual(aln[-1], 'GCGGCUAUUAGAUCGUA------\n')
remove(self.temp_dir_spaces+'/muscle_test_seq1.txt')
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)
def test_build_tree_from_alignment(self):
"""Muscle should return a tree built from the passed alignment"""
tree_short = build_tree_from_alignment(build_tree_seqs_short, DNA)
num_seqs = flatten(build_tree_seqs_short).count('>')
self.assertEqual(len(tree_short.tips()), num_seqs)
tree_long = build_tree_from_alignment(build_tree_seqs_long, DNA)
seq_names = []
for line in build_tree_seqs_long.split('\n'):
if line.startswith('>'):
seq_names.append(line[1:])
for node in tree_long.tips():
if node.Name not in seq_names:
self.fail()
def test_align_and_build_tree(self):
"""Should align and build a tree from a set of sequences"""
res = align_and_build_tree(self.seqs1, RNA)
self.assertEqual(res['Align'].toFasta(), align1)
tree = res['Tree']
seq_names = []
for line in align1.split('\n'):
if line.startswith('>'):
seq_names.append(line[1:])
for node in tree.tips():
if node.Name not in seq_names:
self.fail()
def test_add_seqs_to_alignment(self):
"""Should add sequences to an alignment"""
res = add_seqs_to_alignment(seqs_to_add, align1)
self.assertEqual(res.toFasta(), added_align_result)
def test_align_two_alignments(self):
"""Should align to multiple sequence alignments"""
res = align_two_alignments(align1, aln_to_merge)
self.assertEqual(res.toFasta(), merged_align_result)
align1 = ">seq_0\nACUGCUAGCUAGUAGCGUACGUA\n>seq_1\n---GCUACGUAGCUAC-------\n>seq_2\nGCGGCUAUUAGAUCGUA------"
# for use in test_add_seqs_to_alignment()
seqs_to_add = ">foo\nGCUACGUAGCU\n>bar\nGCUACGUAGCC"
added_align_result = ">bar\n---GCUACGUAGCC---------\n>foo\n---GCUACGUAGCU---------\n>seq_0\nACUGCUAGCUAGUAGCGUACGUA\n>seq_1\n---GCUACGUAGCUAC-------\n>seq_2\nGCGGCUAUUAGAUCGUA------"
# for use in test_align_two_alignments()
aln_to_merge = ">foo\nGCUACGUAGCU\n>bar\n--UACGUAGCC"
merged_align_result = ">bar\n-----UACGUAGCC---------\n>foo\n---GCUACGUAGCU---------\n>seq_0\nACUGCUAGCUAGUAGCGUACGUA\n>seq_1\n---GCUACGUAGCUAC-------\n>seq_2\nGCGGCUAUUAGAUCGUA------"
build_tree_seqs_short = """>muscle_test_seqs_0
AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT
AGCTTTAAATCATGCCAGTG
>muscle_test_seqs_1
GACCCACACGGTGGATGCAACAGATCCCATACACCGAGTTGGATGCTTAAGACGCATCGCGTGAGTTTTGCGTCAAGGCT
TGCTTTCAATAATGCCAGTG
>muscle_test_seqs_2
AACCCCCACGGTGGCAGCAACACGTCACATACAACGGGTTGGATTCTAAAGACAAACCGCGTCAAAGTTGTGTCAGAACT
TGCTTTGAATCATGCCAGTA
>muscle_test_seqs_3
AAACCCCACGGTAGCTGCAACACGTCCCATACCACGGGTAGGATGCTAAAGACACATCGGGTCTGTTTTGTGTCAGGGCT
TGCTTTACATCATGCAAGTG
>muscle_test_seqs_4
AACCGCCACGGTGGGTACAACACGTCCACTACATCGGCTTGGAAGGTAAAGACACGTCGCGTCAGTATTGCGTCAGGGCT
TGCTTTAAATCATGCCAGTG
>muscle_test_seqs_5
AACCCCCGCGGTAGGTGCAACACGTCCCATACAACGGGTTGGAAGGTTAAGACACAACGCGTTAATTTTGTGTCAGGGCA
TGCTTTAAATCATGCCAGTT
>muscle_test_seqs_6
GACCCCCGCGGTGGCTGCAAGACGTCCCATACAACGGGTTGGATGCTTAAGACACATCGCAACAGTTTTGAGTCAGGGCT
TACTTTAGATCATGCCGGTG
>muscle_test_seqs_7
AACCCCCACGGTGGCTACAAGACGTCCCATCCAACGGGTTGGATACTTAAGGCACATCACGTCAGTTTTGTGTCAGAGCT
TGCTTTAAATCATGCCAGTG
>muscle_test_seqs_8
AACCCCCACGGTGGCTGCAACACGTGGCATACAACGGGTTGGATGCTTAAGACACATCGCCTCAGTTTTGTGTCAGGGCT
TGCATTAAATCATGCCAGTG
>muscle_test_seqs_9
AAGCCCCACGGTGGCTGAAACACATCCCATACAACGGGTTGGATGCTTAAGACACATCGCATCAGTTTTATGTCAGGGGA
TGCTTTAAATCCTGACAGCG
"""
build_tree_seqs_long = """>muscle_test_seqs_0
AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT
AGCTTTAAATCATGCCAGTG
>muscle_test_seqsaaaaaaaa_1
GACCCACACGGTGGATGCAACAGATCCCATACACCGAGTTGGATGCTTAAGACGCATCGCGTGAGTTTTGCGTCAAGGCT
TGCTTTCAATAATGCCAGTG
>muscle_test_seqsaaaaaaaa_2
AACCCCCACGGTGGCAGCAACACGTCACATACAACGGGTTGGATTCTAAAGACAAACCGCGTCAAAGTTGTGTCAGAACT
TGCTTTGAATCATGCCAGTA
>muscle_test_seqsaaaaaaaa_3
AAACCCCACGGTAGCTGCAACACGTCCCATACCACGGGTAGGATGCTAAAGACACATCGGGTCTGTTTTGTGTCAGGGCT
TGCTTTACATCATGCAAGTG
>muscle_test_seqsaaaaaaaa_4
AACCGCCACGGTGGGTACAACACGTCCACTACATCGGCTTGGAAGGTAAAGACACGTCGCGTCAGTATTGCGTCAGGGCT
TGCTTTAAATCATGCCAGTG
>muscle_test_seqsaaaaaaaa_5
AACCCCCGCGGTAGGTGCAACACGTCCCATACAACGGGTTGGAAGGTTAAGACACAACGCGTTAATTTTGTGTCAGGGCA
TGCTTTAAATCATGCCAGTT
>muscle_test_seqsaaaaaaaa_6
GACCCCCGCGGTGGCTGCAAGACGTCCCATACAACGGGTTGGATGCTTAAGACACATCGCAACAGTTTTGAGTCAGGGCT
TACTTTAGATCATGCCGGTG
>muscle_test_seqsaaaaaaaa_7
AACCCCCACGGTGGCTACAAGACGTCCCATCCAACGGGTTGGATACTTAAGGCACATCACGTCAGTTTTGTGTCAGAGCT
TGCTTTAAATCATGCCAGTG
>muscle_test_seqsaaaaaaaa_8
AACCCCCACGGTGGCTGCAACACGTGGCATACAACGGGTTGGATGCTTAAGACACATCGCCTCAGTTTTGTGTCAGGGCT
TGCATTAAATCATGCCAGTG
>muscle_test_seqsaaaaaaaa_9
AAGCCCCACGGTGGCTGAAACACATCCCATACAACGGGTTGGATGCTTAAGACACATCGCATCAGTTTTATGTCAGGGGA
TGCTTTAAATCCTGACAGCG
"""
if __name__ == '__main__':
main()
|
