def test_no_column_library():
try:
os.mkdir("output_plots")
except:
pass
try:
os.mkdir("output_summary_library")
except:
pass
libraryidentifications_df = pd.read_csv(
"reference_stats/librarysearch.tsv", sep=None, error_bad_lines=False)
libraryidentifications_df = libraryidentifications_df[[
"#Scan#", "Compound_Name", "Smiles", "INCHI"
]]
libraryidentifications_df = libraryidentifications_df.rename(
columns={
"Compound_Name": "featurecompoundname",
"Smiles": "featuresmiles",
"INCHI": "featureinchi"
})
calculate_stats.calculate_statistics(
"reference_stats/feature_table.csv",
"reference_stats/metadata.tsv",
"output_summary_library",
output_plots_folder="output_plots",
libraryidentifications_df=libraryidentifications_df)
def test_no_column():
try:
os.mkdir("output_plots")
except:
pass
try:
os.mkdir("output_summary")
except:
pass
calculate_stats.calculate_statistics("reference_stats/feature_table.csv",
"reference_stats/metadata.tsv",
"output_summary",
output_plots_folder="output_plots")
def test_column():
try:
os.mkdir("output_plots_chosen")
except:
pass
try:
os.mkdir("output_summary")
except:
pass
calculate_stats.calculate_statistics("reference_stats/feature_table.csv",
"reference_stats/metadata.tsv",
None,
"output_summary",
output_plots_folder="output_plots_chosen",
metadata_column="ATTRIBUTE_sample_type",
condition_first="urine",
condition_second="unknown")
def test_facet_column():
try:
os.mkdir("output_plots_facet")
except:
pass
try:
os.mkdir("output_summary")
except:
pass
calculate_stats.calculate_statistics("reference_stats/feature_table.csv",
"reference_stats/metadata.tsv",
None,
"output_summary",
output_plots_folder="output_plots_facet",
metadata_column="ATTRIBUTE_sex",
condition_first="male",
condition_second="female",
metadata_facet_column="ATTRIBUTE_disease_stage")