diff --git a/meta_data_analysis/pnca_data_extraction.py b/meta_data_analysis/pnca_data_extraction.py index e05c39d..2a030f9 100755 --- a/meta_data_analysis/pnca_data_extraction.py +++ b/meta_data_analysis/pnca_data_extraction.py @@ -88,10 +88,10 @@ meta_data = meta_data[['id' , 'pyrazinamide' , 'dr_mutations_pyrazinamide' , 'other_mutations_pyrazinamide' - ]] #19265, 67 + ]] # checks -total_samples = meta_data['id'].nunique() # 19265 +total_samples = meta_data['id'].nunique() # counts NA per column meta_data.isna().sum() @@ -101,9 +101,7 @@ meta_data.head() # equivalent of table in R # pyrazinamide counts -meta_data.pyrazinamide.value_counts() #12511 -#0.0 10565 -#1.0 1946 {RESULT: No. of Resistant and Susceptible samples} +meta_data.pyrazinamide.value_counts() clear variables #del(basedir, datadir, inpath, infile) @@ -160,7 +158,7 @@ del(meta_pnca_other) # Now extract "all" mutations meta_pnca_all = meta_data_pnca.loc[meta_data_pnca.dr_mutations_pyrazinamide.str.contains('pncA_p.*') | meta_data_pnca.other_mutations_pyrazinamide.str.contains('pncA_p.*') ] -#2665, 8 + meta_pnca_all['id'].nunique() {#RESULT: pnca mutations in ALL samples} pnca_samples = len(meta_pnca_all)