#!/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()