def test_coverage_report(self):
bayes = pkg_resources.resource_filename('shogun.tests', os.path.join('data', 'sheared_bayes.32.txt'))
df_bayes = parse_bayes(bayes)
taxatable = pkg_resources.resource_filename('shogun.tests', os.path.join('data', 'results', 'burst_taxatable.txt'))
infile = pkg_resources.resource_filename('shogun.tests', os.path.join('data', 'results', 'burst_results.b6'))
self.assertTrue(get_coverage_of_microbes(infile, df_bayes, 6) is not None)
self.assertTrue(get_coverage_of_microbes(infile, df_bayes, 7) is not None)
self.assertTrue(get_coverage_of_microbes(infile, df_bayes, 8) is not None)
def _coverage(input, database, output, level, taxonomy):
data_files = _load_metadata(database)
shear = os.path.join(database, data_files['general']['shear'])
if taxonomy == 'mapping':
taxatree = Taxonomy(os.path.join(database, data_files['general']['taxonomy']))
parse_taxonomy_from_row = lambda row: taxatree(row[1])
else:
parse_taxonomy_from_row = lambda row: row[-1]
shear_df = parse_bayes(shear)
outdf = get_coverage_of_microbes(input, shear_df, level, parse_taxonomy_from_row=parse_taxonomy_from_row)
outdf.to_csv(output, sep='\t', float_format="%.5f", na_rep=0)