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#!/usr/bin/env python
from os import getcwd, rmdir
from cogent.core.moltype import PROTEIN, DNA
from cogent.util.unit_test import TestCase, main
from cogent.app.cd_hit import CD_HIT, CD_HIT_EST, cdhit_from_seqs, \
cdhit_clusters_from_seqs, clean_cluster_seq_id, parse_cdhit_clstr_file
__author__ = "Daniel McDonald"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Daniel McDonald"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Daniel McDonald"
__email__ = "mcdonadt@colorado.edu"
__status__ = "Development"
class CD_HIT_Tests(TestCase):
"""Tests for the CD-HIT application controller"""
def test_base_command(self):
"""CD_HIT BaseCommand should return the correct BaseCommand"""
c = CD_HIT()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cd-hit']))
c.Parameters['-i'].on('seq.txt')
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cd-hit -i "seq.txt"']))
c.Parameters['-c'].on(0.8)
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cd-hit -c 0.8' +
' -i "seq.txt"']))
def test_changing_working_dir(self):
"""CD_HIT BaseCommand should change according to WorkingDir"""
c = CD_HIT(WorkingDir='/tmp/cdhit_test')
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/cdhit_test','/"; ','cd-hit']))
c = CD_HIT()
c.WorkingDir = '/tmp/cdhit_test2'
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/cdhit_test2','/"; ','cd-hit']))
#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/cdhit_test')
rmdir('/tmp/cdhit_test2')
def test_cdhit_from_seqs(self):
"""CD_HIT should return expected seqs"""
res = cdhit_from_seqs(protein_seqs, PROTEIN, {'-c':0.8})
self.assertEqual(res.toFasta(), protein_expected)
class CD_HIT_EST_Tests(TestCase):
"""Tests for the CD-HIT application controller"""
def test_base_command(self):
"""CD_HIT_EST BaseCommand should return the correct BaseCommand"""
c = CD_HIT_EST()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cd-hit-est']))
c.Parameters['-i'].on('seq.txt')
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cd-hit-est -i "seq.txt"']))
c.Parameters['-c'].on(0.8)
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cd-hit-est -c 0.8' +
' -i "seq.txt"']))
def test_changing_working_dir(self):
"""CD_HIT_EST BaseCommand should change according to WorkingDir"""
c = CD_HIT_EST(WorkingDir='/tmp/cdhitest_test')
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/cdhitest_test','/"; ','cd-hit-est']))
c = CD_HIT_EST()
c.WorkingDir = '/tmp/cdhitest_test2'
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/cdhitest_test2','/"; ','cd-hit-est']))
#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/cdhitest_test')
rmdir('/tmp/cdhitest_test2')
def test_cdhit_from_seqs(self):
"""CD_HIT should return expected seqs"""
res = cdhit_from_seqs(dna_seqs, DNA, {'-c':0.8})
self.assertEqual(res.toFasta(), dna_expected)
def test_cdhit_from_seqs_synonym(self):
"""CD_HIT should return expected seqs with -c synonym"""
res = cdhit_from_seqs(dna_seqs, DNA, {'Similarity':0.8})
self.assertEqual(res.toFasta(), dna_expected)
class CD_HIT_SupportMethodTests(TestCase):
"""Tests for supporting methods"""
def test_clean_cluster_seq_id(self):
"""clean_cluster_seq_id returns a cleaned sequence id"""
data = ">foobar..."
exp = "foobar"
obs = clean_cluster_seq_id(data)
self.assertEqual(obs, exp)
def test_parse_cdhit_clstr_file(self):
"""parse_cdhit_clstr_file returns the correct clusters"""
data = cdhit_clstr_file.split('\n')
exp = [['seq0'],['seq1','seq10','seq3','seq23','seq145'],\
['seq7','seq17','seq69','seq1231']]
obs = parse_cdhit_clstr_file(data)
self.assertEqual(obs, exp)
def test_cdhit_clusters_from_seqs(self):
"""cdhit_clusters_from_seqs returns expected clusters"""
exp = [['cdhit_test_seqs_0'],['cdhit_test_seqs_1'],\
['cdhit_test_seqs_2'],['cdhit_test_seqs_3'],\
['cdhit_test_seqs_4'],['cdhit_test_seqs_5'],\
['cdhit_test_seqs_6','cdhit_test_seqs_8'],\
['cdhit_test_seqs_7'],['cdhit_test_seqs_9']]
obs = cdhit_clusters_from_seqs(dna_seqs, DNA)
self.assertEqual(obs, exp)
dna_seqs = """>cdhit_test_seqs_0
AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT
>cdhit_test_seqs_1
ACCCACACGGTGGATGCAACAGATCCCATACACCGAGTTGGATGCTTAAGACGCATCGCGTGAGTTTTGCGTCAAGGCT
>cdhit_test_seqs_2
CCCCCACGGTGGCAGCAACACGTCACATACAACGGGTTGGATTCTAAAGACAAACCGCGTCAAAGTTGTGTCAGAACT
>cdhit_test_seqs_3
CCCCACGGTAGCTGCAACACGTCCCATACCACGGGTAGGATGCTAAAGACACATCGGGTCTGTTTTGTGTCAGGGCT
>cdhit_test_seqs_4
GCCACGGTGGGTACAACACGTCCACTACATCGGCTTGGAAGGTAAAGACACGTCGCGTCAGTATTGCGTCAGGGCT
>cdhit_test_seqs_5
CCGCGGTAGGTGCAACACGTCCCATACAACGGGTTGGAAGGTTAAGACACAACGCGTTAATTTTGTGTCAGGGCA
>cdhit_test_seqs_6
CGCGGTGGCTGCAAGACGTCCCATACAACGGGTTGGATGCTTAAGACACATCGCAACAGTTTTGAGTCAGGGCT
>cdhit_test_seqs_7
ACGGTGGCTACAAGACGTCCCATCCAACGGGTTGGATACTTAAGGCACATCACGTCAGTTTTGTGTCAGAGCT
>cdhit_test_seqs_8
CGGTGGCTGCAACACGTGGCATACAACGGGTTGGATGCTTAAGACACATCGCCTCAGTTTTGTGTCAGGGCT
>cdhit_test_seqs_9
GGTGGCTGAAACACATCCCATACAACGGGTTGGATGCTTAAGACACATCGCATCAGTTTTATGTCAGGGGA"""
dna_expected = """>cdhit_test_seqs_0
AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT
>cdhit_test_seqs_1
ACCCACACGGTGGATGCAACAGATCCCATACACCGAGTTGGATGCTTAAGACGCATCGCGTGAGTTTTGCGTCAAGGCT
>cdhit_test_seqs_2
CCCCCACGGTGGCAGCAACACGTCACATACAACGGGTTGGATTCTAAAGACAAACCGCGTCAAAGTTGTGTCAGAACT
>cdhit_test_seqs_4
GCCACGGTGGGTACAACACGTCCACTACATCGGCTTGGAAGGTAAAGACACGTCGCGTCAGTATTGCGTCAGGGCT
>cdhit_test_seqs_5
CCGCGGTAGGTGCAACACGTCCCATACAACGGGTTGGAAGGTTAAGACACAACGCGTTAATTTTGTGTCAGGGCA
>cdhit_test_seqs_7
ACGGTGGCTACAAGACGTCCCATCCAACGGGTTGGATACTTAAGGCACATCACGTCAGTTTTGTGTCAGAGCT"""
protein_seqs = """>seq1
MGNKWSKSWPQVRDRMRRAAPAPAADGVGAVSQDLAKHGAITSSNTAATNDDCAWLEAQTEEEVGFPVRPQVPLRPMTYK
>seq2
MGGKWSKSSIVGWSTVRERMRKTPPAADGVGAVSQDLDKHGAVTSSNTAFNNPDCAWLEAQEDEDVGFPVRPQVPLRPT
>seq3
MGGKWSKSSIVGWPAIRERMRRARPAADRVGTQPAADGVGAVSQDLARHGAVTSSNTSHNNPDCAWLEAQEEEEVGVR
>seq4
MGKIWSKSSIVGWPEIRERMRRQRPHEPAVEPAVGVGAASQDLANRGALTTSNTRTNNPTVAWVEAQEEEGEVVRPQ
>seq5
MGKIWSKSSLVGWPEIRERMRRQTQEPAVEPAVGAGAASQDLANRGAITIRNTRDNNESIAWLEAQEEEFPVRPQV
>seq6
MGKIWSKSSLVGWPEIRERIRRQTPEPAVGVGAVSQDLANRGAITTSNTKDNNQTVAWLEAQEEPVRPQVPLRPM
>seq7
MGNALRKGKFEGWAAVRERMRRTRTFPESEPCAPGVGQISRELAARGGIPSSHTPQNNESHQEEEVGFPVAPQV
>seq8
MGNAWSKSKFAGWSEVRDRMRRSSSDPQQPCAPGVGAVSRELATRGGISSSALAFLDSHKDEDVGFPVRPQVP
>seq9
MGNVLGKDKFKGWAAVRERMRKTSSDPDPQPCAPGVGPVSRELSYTPQNNAALAFLESHEDEDVGFPVXPQV
>seq10
MGNVLGKDKFKGWSAVRERMRKTSPEPEPCAPGVRGGISNSHTPQNNAALAFLESHQDEDVGFPVRPQVPL"""
protein_expected = """>seq1
MGNKWSKSWPQVRDRMRRAAPAPAADGVGAVSQDLAKHGAITSSNTAATNDDCAWLEAQTEEEVGFPVRPQVPLRPMTYK
>seq2
MGGKWSKSSIVGWSTVRERMRKTPPAADGVGAVSQDLDKHGAVTSSNTAFNNPDCAWLEAQEDEDVGFPVRPQVPLRPT
>seq3
MGGKWSKSSIVGWPAIRERMRRARPAADRVGTQPAADGVGAVSQDLARHGAVTSSNTSHNNPDCAWLEAQEEEEVGVR
>seq4
MGKIWSKSSIVGWPEIRERMRRQRPHEPAVEPAVGVGAASQDLANRGALTTSNTRTNNPTVAWVEAQEEEGEVVRPQ
>seq5
MGKIWSKSSLVGWPEIRERMRRQTQEPAVEPAVGAGAASQDLANRGAITIRNTRDNNESIAWLEAQEEEFPVRPQV
>seq7
MGNALRKGKFEGWAAVRERMRRTRTFPESEPCAPGVGQISRELAARGGIPSSHTPQNNESHQEEEVGFPVAPQV
>seq8
MGNAWSKSKFAGWSEVRDRMRRSSSDPQQPCAPGVGAVSRELATRGGISSSALAFLDSHKDEDVGFPVRPQVP
>seq9
MGNVLGKDKFKGWAAVRERMRKTSSDPDPQPCAPGVGPVSRELSYTPQNNAALAFLESHEDEDVGFPVXPQV"""
cdhit_clstr_file = """>Cluster 0
0 2799aa, >seq0... *
>Cluster 1
0 2214aa, >seq1... at 80%
1 2215aa, >seq10... at 84%
2 2217aa, >seq3... *
3 2216aa, >seq23... at 84%
4 527aa, >seq145... at 63%
>Cluster 2
0 2202aa, >seq7... at 60%
1 2208aa, >seq17... *
2 2207aa, >seq69... at 73%
3 2208aa, >seq1231... at 69%"""
if __name__ == '__main__':
main()
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