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)