def _redistribute(database, level, outfile, redist_inf, relative_abundance=False):
logger.debug("Beginning redistribution for file: %s" % redist_inf)
data_files = _load_metadata(database)
shear = os.path.join(database, data_files['general']['shear'])
shear_df = parse_bayes(shear)
output_files = []
output_levels = []
if level == 'all':
for l in TAXA:
df_output = redistribute_taxatable(redist_inf, shear_df, level=TAXAMAP[l])
tmp_spl = outfile.split('.')
tmp_path = '.'.join(tmp_spl[:-1] + [l] + [tmp_spl[-1]])
df_output.to_csv(tmp_path, sep='\t', float_format="%d",na_rep=0, index_label="#OTU ID")
output_files.append(tmp_path)
output_levels.append(l)
elif level == 'off':
output_files = []
else:
df_output = redistribute_taxatable(redist_inf, shear_df, level=TAXAMAP[level])
df_output.to_csv(outfile, sep='\t', float_format="%d", na_rep=0, index_label="#OTU ID")
output_files.append(outfile)
output_levels.append(level)
return output_files, output_levels
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 test_taxatable(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'))
taxatable_df_5 = redistribute_taxatable(taxatable, df_bayes, level=5)
taxatable_df_6 = redistribute_taxatable(taxatable, df_bayes, level=6)
taxatable_df_7 = redistribute_taxatable(taxatable, df_bayes, level=7)
taxatable_df_8 = redistribute_taxatable(taxatable, df_bayes, level=8)
taxatable_df_8.head()
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)
def test_read_bayes(self):
bayes = pkg_resources.resource_filename(
'shogun.tests', os.path.join('data', 'sheared_bayes.100.txt'))
df = parse_bayes(bayes)
