added af_or to add to combining_dfs.py
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8a301e8bb1
commit
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1 changed files with 78 additions and 9 deletions
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@ -40,7 +40,6 @@ import sys, os
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import pandas as pd
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from pandas import DataFrame
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import numpy as np
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#from varname import nameof
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import argparse
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#=======================================================================
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#%% specify input and curr dir
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@ -132,7 +131,7 @@ in_filename_kd = gene.lower() + '_kd.csv'
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in_filename_rd = gene.lower() + '_rd.csv'
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#in_filename_snpinfo = 'ns' + gene.lower() + '_snp_info_f.csv' # gwas f info
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#in_filename_afor = gene.lower() + '_af_or.csv'
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in_filename_afor = gene.lower() + '_af_or.csv'
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#in_filename_afor_kin = gene.lower() + '_af_or_kinship.csv'
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infile_mcsm = outdir + in_filename_mcsm
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@ -144,7 +143,7 @@ infile_kd = outdir + in_filename_kd
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infile_rd = outdir + in_filename_rd
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#infile_snpinfo = outdir + '/' + in_filename_snpinfo
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#infile_afor = outdir + '/' + in_filename_afor
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infile_afor = outdir + '/' + in_filename_afor
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#infile_afor_kin = outdir + '/' + in_filename_afor_kin
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print('\nInput path:', indir
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@ -157,7 +156,7 @@ print('\nInput path:', indir
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, '\nInput filename rd', infile_rd
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#, '\nInput filename snp info:', infile_snpinfo, '\n'
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#, '\nInput filename af or:', infile_afor
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, '\nInput filename af or:', infile_afor
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#, '\nInput filename afor kinship:', infile_afor_kin
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, '\n============================================================')
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@ -216,7 +215,7 @@ mcsm_foldx_deepddg_dfs['deepddg_outcome'].value_counts()
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ncols_deepddg_merge = len(mcsm_foldx_deepddg_dfs.columns)
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#%%============================================================================
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print('==================================='
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, '\nSecond merge: dssp + kd'
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, '\Third merge: dssp + kd'
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, '\n===================================')
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dssp_df = pd.read_csv(infile_dssp, sep = ',')
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@ -227,11 +226,11 @@ rd_df = pd.read_csv(infile_rd, sep = ',')
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merging_cols_m2 = detect_common_cols(dssp_df, kd_df)
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dssp_kd_dfs = pd.merge(dssp_df, kd_df, on = merging_cols_m2, how = o_join)
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print('\n\nResult of second merge:', dssp_kd_dfs.shape
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print('\n\nResult of third merge:', dssp_kd_dfs.shape
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, '\n===================================================================')
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#%%============================================================================
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print('==================================='
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, '\nThird merge: second merge + rd_df'
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, '\nFourth merge: third merge + rd_df'
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, '\ndssp_kd_dfs + rd_df'
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, '\n===================================')
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#dssp_kd_rd_dfs = combine_dfs_with_checks(dssp_kd_dfs, rd_df, my_join = o_join)
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@ -247,7 +246,7 @@ dssp_kd_rd_dfs[merging_cols_m3].apply(len)
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dssp_kd_rd_dfs[merging_cols_m3].apply(len) == len(dssp_kd_rd_dfs)
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#%%============================================================================
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print('======================================='
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, '\nFourth merge: First merge + Third merge'
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, '\nFifth merge: Second merge + fourth merge'
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, '\nmcsm_foldx_dfs + dssp_kd_rd_dfs'
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, '\n=======================================')
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#combined_df = combine_dfs_with_checks(mcsm_foldx_dfs, dssp_kd_rd_dfs, my_join = i_join)
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@ -270,6 +269,7 @@ else:
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print('\nResult of Fourth merge:', combined_df.shape
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, '\n===================================================================')
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combined_df[merging_cols_m4].apply(len)
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combined_df[merging_cols_m4].apply(len) == len(combined_df)
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#%%============================================================================
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@ -280,6 +280,7 @@ combined_df_colnames = combined_df.columns
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combined_df['chain'].equals(combined_df['chain_id'])
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combined_df['wild_type'].equals(combined_df['wild_type_kd']) # has nan
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combined_df['wild_type'].equals(combined_df['wild_type_dssp'])
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#sanity check
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foo = combined_df[['wild_type', 'wild_type_kd', 'wt_3letter_caps', 'wt_aa_3lower', 'mut_aa_3lower']]
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@ -301,6 +302,74 @@ combined_df_clean.to_csv(outfile_stab_struc, index = False)
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print('\nFinished writing file:'
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, '\nNo. of rows:', combined_df_clean.shape[0]
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, '\nNo. of cols:', combined_df_clean.shape[1])
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#%%=====================================================================
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print('======================================='
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, '\nFifth merge:
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, '\ncombined_df_clean + afor_df '
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, '\n=======================================')
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afor_df = pd.read_csv(infile_afor, sep = ',')
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afor_cols = afor_df.columns
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# create a mapping from the gwas mutation column i.e <gene_match>_abcXXXrst
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#----------------------
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# call get_aa_upper():
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# adds 3 more cols with one letter aa code
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#----------------------
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get_aa_1upper(df = afor_df
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, gwas_mut_colname = 'mutation'
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, wt_colname = 'wild_type'
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, pos_colname = 'position'
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, mut_colname = 'mutant_type')
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afor_df['mutationinformation'] = afor_df['wild_type'] + afor_df['position'].map(str) + afor_df['mutant_type']
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afor_cols = afor_df.columns
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merging_cols_m5 = detect_common_cols(combined_df_clean, afor_df)
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# remove position so that merging can take place without dtype conflicts
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merging_cols_m5.remove('position')
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# drop position column from afor_df
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afor_df = afor_df.drop(['position'], axis = 1)
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afor_cols = afor_df.columns
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# merge
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combined_stab_afor = pd.merge(combined_df_clean, afor_df, on = merging_cols_m5, how = l_join)
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comb_afor_df_cols = combined_stab_afor.columns
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comb_afor_expected_cols = len(combined_df_clean.columns) + len(afor_df.columns) - len(merging_cols_m5)
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if len(combined_stab_afor) == len(combined_df_clean) and len(combined_stab_afor.columns) == comb_afor_expected_cols:
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print('\nPASS: successfully combined 6 dfs'
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, '\nNo. of rows combined_stab_afor:', len(combined_stab_afor)
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, '\nNo. of cols combined_stab_afor:', len(combined_stab_afor.columns))
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else:
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sys.exit('\nFAIL: check individual df merges')
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print('\n\nResult of Fourth merge:', combined_stab_afor.shape
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, '\n===================================================================')
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combined_stab_afor[merging_cols_m5].apply(len)
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combined_stab_afor[merging_cols_m5].apply(len) == len(combined_stab_afor)
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if len(combined_stab_afor) - combined_stab_afor['mutation'].isna().sum() == len(afor_df):
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print('\nPASS: Merge successful for af and or'
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, '\nNo. of nsSNPs with valid ORs: ', len(afor_df))
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else:
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sys.exit('\nFAIL: merge unsuccessful for af and or')
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#%%============================================================================
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# Output columns
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out_filename_comb_afor = gene.lower() + '_comb_afor.csv'
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outfile_comb_afor = outdir + '/' + out_filename_comb_afor
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print('Output filename:', outfile_comb_afor
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, '\n===================================================================')
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# write csv
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print('Writing file: combined stability and afor')
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combined_stab_afor.to_csv(outfile_comb_afor, index = False)
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print('\nFinished writing file:'
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, '\nNo. of rows:', combined_stab_afor.shape[0]
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, '\nNo. of cols:', combined_stab_afor.shape[1])
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#%% end of script
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