#!/usr/bin/env python __author__ = "David Soergel" __copyright__ = "Copyright 2007-2012, The Cogent Project" __credits__ = ["David Soergel"] #remember to add yourself __license__ = "GPL" __version__ = "1.5.3" __maintainer__ = "David Soergel" __email__ = "soergel@cs.umass.edu" __status__ = "Production" from cogent.util.misc import remove_files from unittest import TestCase, main from cogent.app.rtax import Rtax, assign_taxonomy from cogent.app.util import get_tmp_filename class RtaxClassifierTests(TestCase): """ Tests of the RTAX classifier module """ def setUp(self): self.maxDiff = None self.id_to_taxonomy_fp = get_tmp_filename(\ prefix='RtaxTaxonAssignerTests_',suffix='.txt') self.input_seqs_fp = get_tmp_filename(\ prefix='RtaxTaxonAssignerTests_',suffix='.fasta') self.reference_seqs_fp = get_tmp_filename(\ prefix='RtaxTaxonAssignerTests_',suffix='.fasta') self.read_1_seqs_fp = get_tmp_filename(\ prefix='RtaxTaxonAssignerTests_',suffix='.fasta') self.read_2_seqs_fp = get_tmp_filename(\ prefix='RtaxTaxonAssignerTests_',suffix='.fasta') self._paths_to_clean_up = [self.id_to_taxonomy_fp,self.input_seqs_fp,self.reference_seqs_fp, self.read_1_seqs_fp,self.read_2_seqs_fp] a = open(self.id_to_taxonomy_fp,'w') a.write(rtax_reference_taxonomy) a.close() b = open(self.reference_seqs_fp,'w') b.write(rtax_reference_fasta) b.close() c = open(self.input_seqs_fp,'w') c.write(rtax_test_repset_fasta) c.close() d = open(self.read_1_seqs_fp,'w') d.write(rtax_test_read1_fasta) d.close() e = open(self.read_2_seqs_fp,'w') e.write(rtax_test_read2_fasta) e.close() def tearDown(self): remove_files(set(self._paths_to_clean_up),error_on_missing=False) def test_paired_end_classification(self): self._paths_to_clean_up += cleanAll(self.read_1_seqs_fp) self._paths_to_clean_up += cleanAll(self.read_2_seqs_fp) result = assign_taxonomy(self.input_seqs_fp, self.reference_seqs_fp, self.id_to_taxonomy_fp, self.read_1_seqs_fp, self.read_2_seqs_fp,single_ok=False,header_id_regex="\\S+\\s+(\\S+?)\/") self.assertEqual(result, rtax_expected_result_paired) def test_paired_end_classification_with_fallback(self): self._paths_to_clean_up += cleanAll(self.read_1_seqs_fp) self._paths_to_clean_up += cleanAll(self.read_2_seqs_fp) result = assign_taxonomy(self.input_seqs_fp, self.reference_seqs_fp, self.id_to_taxonomy_fp, self.read_1_seqs_fp, self.read_2_seqs_fp,single_ok=True,header_id_regex="\\S+\\s+(\\S+?)\/") self.assertEqual(result, rtax_expected_result_paired_with_fallback) def test_single_end_classification(self): self._paths_to_clean_up += cleanAll(self.read_1_seqs_fp) result = assign_taxonomy(self.input_seqs_fp, self.reference_seqs_fp, self.id_to_taxonomy_fp, self.read_1_seqs_fp, None ,header_id_regex="\\S+\\s+(\\S+?)\/") self.assertEqual(result, rtax_expected_result_single) # I'd like to add tests here that involve the TOOMANYHITS case. However, that requires either a reference # database with >16,000 sequences, which we don't have handy for tests, or adjusting the maxMaxAccepts parameter to rtaxSearch.pl. # However the "rtax" wrapper shell script currently doesn't allow setting that option, and I'd prefer to leave that as is # unless someone actually wants to use it. Thus the TOOMANYHITS situation is not easily testable at the moment. def cleanAll(path): return [path, path + ".pos.db", path + ".pos.dir", path + ".pos.pag", path + ".lines.db", path + ".lines.dir", path + ".lines.pag"] # sample data copied from GreenGenes rtax_reference_taxonomy = """508720 99.0 k__Bacteria p__Actinobacteria c__Actinobacteria o__Actinomycetales f__Propionibacteriaceae g__Propionibacterium s__Propionibacterium acnes 508050 99.0 k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Burkholderiales f__Comamonadaceae g__Diaphorobacter s__ 502492 99.0 k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Burkholderiales f__ g__Aquabacterium s__ """ rtax_reference_fasta = """>508720 GACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTGCTTTTGTGGGGTGCTCGAGTGGCGAACG GGTGAGTAACACGTGAGTAACCTGCCCTTGACTTTGGGATAACTTCAGGAAACTGGGGCTAATACCGGATAGGAGCTCCT GCTGCATGGTGGGGGTTGGAAAGTTTCGGCGGTTGGGGATGGACTCGCGGCTTATCAGCTTGTTGGTGGGGTAGTGGCTT ACCAAGGCTTTGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACATTGGGACTGAGATACGGCCCAGACTCCTACGGGA GGCAGCAGTGGGGAATATTGCACAATGGGCGGAAGCCTGATGCAGCAACGCCGCGTGCGGGATGACGGCCTTCGGGTTGT AAACCGCTTTCGCCTGTGACGAAGCGTGAGTGACGGTAATGGGTAAAGAAGCACCGGCTAACTACGTGCCAGCAGCCGCG GTGATACGTAGGGTGCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGCTCGTAGGTGGTTGATCGCGTCGGAAGTGTAA TCTTGGGGCTTAACCCTGAGCGTGCTTTCGATACGGGTTGACTTGAGGAAGGTAGGGGAGAATGGAATTCCTGGTGGAGC GGTGGAATGCGCAGATATCAGGAGGAACACCAGTGGCGAAGGCGGTTCTCTGGGCCTTTCCTGACGCTGAGGAGCGAAAG CGTGGGGAGCGAACAGGCTTAGATACCCTGGTAGTCCACGCTGTAAACGGTGGGTACTAGGTGTGGGGTCCATTCCACGG GTTCCGTGCCGTAGCTAACGCTTTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGG GCCCCGCACAAGCGGCGGAGCATGCGGATTAATTCGATGCAACGCGTAGAACCTTACCTGGGTTTGACATGGATCGGGAG TGCTCAGAGATGGGTGTGCCTCTTTTGGGGTCGGTTCACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTT GGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTCACTGTTGCCAGCACGTTATGGTGGGGACTCAGTGGAGACCGCCGGG GTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACGCATGCTACAATGGCTG GTACAGAGAGTGGCGAGCCTGTGAGGGTGAGCGAATCTCGGAAAGCCGGTCTCAGTTCGGATTGGGGTCTGCAACTCGAC CTCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGGCT >508050 ATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGTAACAGGTCTTCGGATGCTGACGAGTGGCGAACGGGTG AGTAATACATCGGAACGTGCCCGATCGTGGGGGATAACGAGGCGAAAGCTTTGCTAATACCGCATACGATCTACGGATGA AAGCGGGGGATCTTCGGACCTCGCGCGGACGGAGCGGCCGATGGCAGATTAGGTAGTTGGTGGGATAAAAGCTTACCAAG CCGACGATCTGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGC AGTGGGGAATTTTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGCAGGATGAAGGCCTTCGGGTTGTAAACTG CTTTTGTACGGAACGAAAAGCCTCTTTCTAATAAAGAGGGGTCATGACGGTACCGTAAGAATAAGCACCGGCTAACTACG TGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTTGTA AGACAGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTTTGTGACTGCAAGGCTGGAGTGCGGCAGAGGGGGATGGA ATTCCGCGTGTAGCAGTGAAATGCGTAGATATGCGGAGGAACACCGATGGCGAAGGCAATCCCCTGGGCCTGCACTGACG CTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAACTGGTTGTTG GGTCTTCACTGACTCAGTAACGAAGCTAACGCGTGAAGTTGACCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAAG GAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGTTTAATTCGATGCAACGCGAAAAACCTTACCCACCTTTGACA TGGCAGGAAGTTTCCAGAGATGGATTCGTGCCCGAAAGGGAACCTGCACACAGGTGCTGCATGGCTGTCGTCAGCTCGTG TCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGCCATTAGTTGCTACGAAAGGGCACTCTAATGGGACTG CCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATAGGTGGGGCTACACACGTCATACAAT GGCTGGTACAGAGGGTTGCCAACCCGCGAGGGGGAGCTAATCCCATAAAGCCAGTCGTAGTCCGGATCGCAGTCTGCAAC TCGACTGCGTGAAGTCGGAATCGCTAGTAATCGCGGATCAGAATGTCGCGGTGAATACGTTCCCGGGTCT >502492 ATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGTAACGGGTCCTTCGGGATGCCGACGAGTGGCGAACGGG TGAGTAATATATCGGAACGTGCCCAGTAGTGGGGGATAACTGCTCGAAAGAGCAGCTAATACCGCATACGACCTGAGGGT GAAAGGGGGGGATCGCAAGACCTCTCGCTATTGGAGCGGCCGATATCAGATTAGCTAGTTGGTGGGGTAAAGGCCTACCA AGGCAACGATCTGTAGTTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCA GCAGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCAATGCCGCGTGCAGGAAGAAGGCCTTCGGGTTGTAAAC TGCTTTTGTCAGGGAAGAAATCTTCTGGGCTAATACCCCGGGAGGATGACGGTACCTGAAGAATAAGCACCGGCTAACTA CGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGCTTTG CAAGACAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTTGTGACTGCAAGGCTAGAGTACGGCAGAGGGGGATG GAATTCCGCGTGTAGCAGTGAAATGCGTAGATATGCGGAGGAACACCAATGGCGAAGGCAATCCCCTGGGCCTGTACTGA CGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAACTGGTTGT TGGACGGCTTGCTGTTCAGTAACGAAGCTAACGCGTGAAGTTGACCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAA AGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGTTTAATTCGATGCAACGCGAAAAACCTTACCTACCCTTGA CATGTCAAGAATTCTGCAGAGATGTGGAAGTGCTCGAAAGAGAACTTGAACACAGGTGCTGCATGGCCGTCGTCAGCTCG TGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCATTAGTTGCTACGCAAGAGCACTCTAATGAGAC TGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAGGTCCTCATGGCCCTTATGGGTAGGGCTACACACGTCATACA ATGGCCGGTACAGAGGGCTGCCAACCCGCGAGGGGGAGCCAATCCCAGAAAACCGGTCGTAGTCCGGATCGTAGTCTGCA ACTCGACTGCGTGAAGTCGGAATCGCTAGTAATCGCGGATCAGCTTGCCGCGGTGAATACGTTCCCGGGTCT """ rtax_test_repset_fasta = """>clusterIdA splitRead1IdA ACCAAGGCTTTGACGGGTAGCCGGCCTGAGTGGGTGACCGGCCACATTGGGACTGAGATACGGCCCAGACTCCTACGGGA >clusterIdB splitRead1IdB CCGACGATCTGTAGCTGGTCTGAGAGGATGTTCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGC >clusterIdC splitRead1IdC AGGCAACGATCTGTAGTTGGTCTGAGAGGAGGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCA >clusterIdD splitRead1IdD AGGCAACGATCTGTAGTTGGTCTGAGAGGAGGACCAGCCACACTGGGACGGGGGGGGGGCCCAGACTCCTACGGGAGGCA """ # these reads are the 4th and 14th lines from the reference seqs #rtax_test_read1_fasta = """>splitRead1IdA ampliconId_34563456/1 #ACCAAGGCTTTGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACATTGGGACTGAGATACGGCCCAGACTCCTACGGGA #>splitRead1IdB ampliconId_ #CCGACGATCTGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGC #>splitRead1IdC ampliconId_ #AGGCAACGATCTGTAGTTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCA #""" # #rtax_test_read2_fasta = """>splitRead2IdA ampliconId_34563456/3 #GGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTCACTGTTGCCAGCACGTTATGGTGGGGACTCAGTGGAGACCGCCGGG #>splitRead2IdB ampliconId_ #TCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGCCATTAGTTGCTACGAAAGGGCACTCTAATGGGACTG #>splitRead2IdC ampliconId_ #TGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCATTAGTTGCTACGCAAGAGCACTCTAATGAGAC #""" # these reads are the 4th and 14th lines from the reference seqs, with one nucleotide changed each # except D and E, which are unique to one read or the other # and F and G, which are just decoys rtax_test_read1_fasta = """>splitRead1IdA ampliconId_34563456/1 ACCAAGGCTTTGACGGGTAGCCGGCCTGAGTGGGTGACCGGCCACATTGGGACTGAGATACGGCCCAGACTCCTACGGGA >splitRead1IdB ampliconId_12341234/1 CCGACGATCTGTAGCTGGTCTGAGAGGATGTTCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGC >splitRead1IdC ampliconId_23452345/1 AGGCAACGATCTGTAGTTGGTCTGAGAGGAGGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCA >splitRead1IdD ampliconId_45674567/1 AGGCAACGATCTGTAGTTGGTCTGAGAGGAGGACCAAAAAAAAAAAGACTGAGACACGGCCCAGACTCCTACGGGAGGCA >splitRead1IdF ampliconId_56785678/1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA """ rtax_test_read2_fasta = """>splitRead2IdA ampliconId_34563456/3 GGGTTAAGTCCCGCAACGAGCGCAACCCTTATTCACTGTTGCCAGCACGTTATGGTGGGGACTCAGTGGAGACCGCCGGG >splitRead2IdB ampliconId_12341234/3 TCGTGAGATGTTGGGTTAAGTCCCGCAACGTGCGCAACCCTTGCCATTAGTTGCTACGAAAGGGCACTCTAATGGGACTG >splitRead2IdC ampliconId_23452345/3 TGTCGTGAGATGTTGGGTTAAGTCCCGCAAAGAGCGCAACCCTTGTCATTAGTTGCTACGCAAGAGCACTCTAATGAGAC >splitRead2IdE ampliconId_67896789/3 TGTCGTGAGATGTTGGGTTAAAAAAAAAAAAAAACGCAACCCTTGTCATTAGTTGCTACGCAAGAGCACTCTAATGAGAC >splitRead2IdG ampliconId_78907890/3 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT """ rtax_expected_result_paired = { 'clusterIdA splitRead1IdA': ('k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Propionibacteriaceae; g__Propionibacterium; s__Propionibacterium acnes', 1.0), 'clusterIdB splitRead1IdB': ('k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Comamonadaceae; g__Diaphorobacter; s__', 1.0), 'clusterIdC splitRead1IdC': ('k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__; g__Aquabacterium; s__', 1.0), } rtax_expected_result_paired_with_fallback = { 'clusterIdA splitRead1IdA': ('k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Propionibacteriaceae; g__Propionibacterium; s__Propionibacterium acnes', 1.0), 'clusterIdB splitRead1IdB': ('k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Comamonadaceae; g__Diaphorobacter; s__', 1.0), 'clusterIdC splitRead1IdC': ('k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__; g__Aquabacterium; s__', 1.0), 'clusterIdD splitRead1IdD': ('k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__; g__Aquabacterium; s__', 1.0), } rtax_expected_result_single = { 'clusterIdA splitRead1IdA': ('k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Propionibacteriaceae; g__Propionibacterium; s__Propionibacterium acnes', 1.0), 'clusterIdB splitRead1IdB': ('k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Comamonadaceae; g__Diaphorobacter; s__', 1.0), 'clusterIdC splitRead1IdC': ('k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__; g__Aquabacterium; s__', 1.0), 'clusterIdD splitRead1IdD': ('k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__; g__Aquabacterium; s__', 1.0), } if __name__ == "__main__": main()