def test_generate_rtax_commands(self): """Functions correctly using standard valid input data.""" exp = [[('Assigning taxonomy (RTAX, single-end)', 'assign_taxonomy.py -i /foo/bar/rep_set.fna -o /foo/bar/rtax_single ' '-m rtax -r /baz/reference_seqs.fasta -t /baz/id_to_taxonomy.txt ' '--read_1_seqs_fp /foo/bar/read_1_seqs.fna')], [('Adding taxa (RTAX, single-end)', 'add_taxa.py -i /foo/bar/otu_table.biom ' '-o /foo/bar/rtax_single/otu_table_w_taxa.biom ' '-t /foo/bar/rtax_single/rep_set_tax_assignments.txt')], [('Summarizing taxa (RTAX, single-end)', 'summarize_taxa.py -i /foo/bar/rtax_single/otu_table_w_taxa.biom ' '-o /foo/bar/rtax_single')], [('Assigning taxonomy (RTAX, paired-end)', 'assign_taxonomy.py -i /foo/bar/rep_set.fna -o /foo/bar/rtax_paired ' '-m rtax -r /baz/reference_seqs.fasta -t /baz/id_to_taxonomy.txt ' '--read_1_seqs_fp /foo/bar/read_1_seqs.fna ' '--read_2_seqs_fp /foo/bar/read_2_seqs.fna')], [('Adding taxa (RTAX, paired-end)', 'add_taxa.py -i /foo/bar/otu_table.biom ' '-o /foo/bar/rtax_paired/otu_table_w_taxa.biom ' '-t /foo/bar/rtax_paired/rep_set_tax_assignments.txt')], [('Summarizing taxa (RTAX, paired-end)', 'summarize_taxa.py -i /foo/bar/rtax_paired/otu_table_w_taxa.biom ' '-o /foo/bar/rtax_single')]] obs = _generate_rtax_commands('/foo/bar', '/foo/bar/rep_set.fna', '/baz/reference_seqs.fasta', '/baz/id_to_taxonomy.txt', '/foo/bar/otu_table.biom', '/foo/bar/read_1_seqs.fna', read_2_seqs_fp='/foo/bar/read_2_seqs.fna')
def test_generate_rtax_commands_custom_regexes(self): """Correctly passes custom regexes through to RTAX.""" exp = [[('Assigning taxonomy (RTAX, mode: single)', 'assign_taxonomy.py -i /foo/bar/rep_set.fna -o /foo/bar/rtax_single.tmp -m rtax -r /baz/reference_seqs.fasta -t /baz/id_to_taxonomy.txt --read_1_seqs_fp /foo/bar/read_1_seqs.fna --read_id_regex \'f*\' --amplicon_id_regex \'*b\' --header_id_regex \'b(*)z\'')], [('Assigning taxonomy (RTAX, mode: paired)', 'assign_taxonomy.py -i /foo/bar/rep_set.fna -o /foo/bar/rtax_paired.tmp ' '-m rtax -r /baz/reference_seqs.fasta -t /baz/id_to_taxonomy.txt ' '--read_1_seqs_fp /foo/bar/read_1_seqs.fna ' '--read_2_seqs_fp /foo/bar/read_2_seqs.fna --read_id_regex \'f*\' --amplicon_id_regex \'*b\' --header_id_regex \'b(*)z\' --single_ok')]] obs = _generate_rtax_commands('/foo/bar', '/foo/bar/rep_set.fna', '/baz/reference_seqs.fasta', '/baz/id_to_taxonomy.txt', '/foo/bar/otu_table.biom', ['single', 'paired'], '/foo/bar/read_1_seqs.fna', '/foo/bar/read_2_seqs.fna', 'f*', '*b', 'b(*)z') self.assertEqual(len(obs), 8) self.assertEqual(obs[0], exp[0]) self.assertEqual(obs[4], exp[1])
def test_generate_rtax_single_commands(self): """Functions correctly using standard valid input data.""" exp = [ [('Assigning taxonomy (RTAX, single-end)', 'assign_taxonomy.py -i /foo/bar/rep_set.fna -o /foo/bar/rtax_single ' '-m rtax -r /baz/reference_seqs.fasta -t /baz/id_to_taxonomy.txt ' '--read_1_seqs_fp /foo/bar/read_1_seqs.fna')], [('Adding taxa (RTAX, single-end)', 'add_taxa.py -i /foo/bar/otu_table.biom ' '-o /foo/bar/rtax_single/otu_table_w_taxa.biom ' '-t /foo/bar/rtax_single/rep_set_tax_assignments.txt')], [('Summarizing taxa (RTAX, single-end)', 'summarize_taxa.py -i /foo/bar/rtax_single/otu_table_w_taxa.biom ' '-o /foo/bar/rtax_single')] ] obs = _generate_rtax_commands('/foo/bar', '/foo/bar/rep_set.fna', '/baz/reference_seqs.fasta', '/baz/id_to_taxonomy.txt', '/foo/bar/otu_table.biom', '/foo/bar/read_1_seqs.fna')
def test_generate_rtax_commands(self): """Functions correctly using standard valid input data.""" exp = [[('Assigning taxonomy (RTAX, mode: single)', 'assign_taxonomy.py -i /foo/bar/rep_set.fna -o /foo/bar/rtax_single.tmp ' '-m rtax -r /baz/reference_seqs.fasta -t /baz/id_to_taxonomy.txt ' '--read_1_seqs_fp /foo/bar/read_1_seqs.fna')], [('Adding metadata (RTAX, mode: single)', 'biom add-metadata -i /foo/bar/otu_table.biom -o ' '/foo/bar/rtax_single.tmp/otu_table_w_taxa.biom ' '--observation-metadata-fp ' '/foo/bar/rtax_single.tmp/rep_set_tax_assignments.txt ' '--sc-separated taxonomy --observation-header OTUID,taxonomy')], [('Summarizing taxa (RTAX, mode: single)', 'summarize_taxa.py -i /foo/bar/rtax_single.tmp/otu_table_w_taxa.biom ' '-o /foo/bar/rtax_single.tmp')], [('Renaming output directory (RTAX, mode: single)', 'mv /foo/bar/rtax_single.tmp /foo/bar/rtax_single')], [('Assigning taxonomy (RTAX, mode: paired)', 'assign_taxonomy.py -i /foo/bar/rep_set.fna -o /foo/bar/rtax_paired.tmp ' '-m rtax -r /baz/reference_seqs.fasta -t /baz/id_to_taxonomy.txt ' '--read_1_seqs_fp /foo/bar/read_1_seqs.fna ' '--read_2_seqs_fp /foo/bar/read_2_seqs.fna --single_ok')], [('Adding metadata (RTAX, mode: paired)', 'biom add-metadata -i /foo/bar/otu_table.biom -o ' '/foo/bar/rtax_paired.tmp/otu_table_w_taxa.biom ' '--observation-metadata-fp ' '/foo/bar/rtax_paired.tmp/rep_set_tax_assignments.txt ' '--sc-separated taxonomy --observation-header OTUID,taxonomy')], [('Summarizing taxa (RTAX, mode: paired)', 'summarize_taxa.py -i /foo/bar/rtax_paired.tmp/otu_table_w_taxa.biom ' '-o /foo/bar/rtax_paired.tmp')], [('Renaming output directory (RTAX, mode: paired)', 'mv /foo/bar/rtax_paired.tmp /foo/bar/rtax_paired')]] obs = _generate_rtax_commands('/foo/bar', '/foo/bar/rep_set.fna', '/baz/reference_seqs.fasta', '/baz/id_to_taxonomy.txt', '/foo/bar/otu_table.biom', ['single', 'paired'], '/foo/bar/read_1_seqs.fna', '/foo/bar/read_2_seqs.fna') self.assertEqual(obs, exp)