merged changes from the combining_dfs.py file from branch 'embb_dev'
This commit is contained in:
commit
46e2c93885
1 changed files with 60 additions and 26 deletions
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@ -59,7 +59,7 @@ os.getcwd()
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# FIXME: local imports
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#from combining import combine_dfs_with_checks
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from combining_FIXME import detect_common_cols
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from reference_dict import oneletter_aa_dict
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from reference_dict import oneletter_aa_dict
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from reference_dict import low_3letter_dict
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from aa_code import get_aa_3lower
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@ -114,16 +114,16 @@ if not outdir:
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#=======
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# input
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#=======
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gene_list_normal = ["pnca", "katg", "rpob", "alr"]
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gene_list_normal = ['pnca', 'katg', 'rpob', 'alr']
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#FIXME: for gid, this should be SRY as this is the drug...please check!!!!
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if gene.lower() == "gid":
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print("\nReading mCSM file for gene:", gene)
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in_filename_mcsm = gene.lower() + '_complex_mcsm_norm_SRY.csv' # was incorrectly SAM previously
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if gene.lower() == "embb":
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print("\nReading mCSM file for gene:", gene)
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#in_filename_mcsm = gene.lower() + '_complex_mcsm_norm1.csv' #798
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in_filename_mcsm = gene.lower() + '_complex_mcsm_norm2.csv' #844
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#in_filename_mcsm = gene.lower() + '_complex_mcsm_norm2.csv' #844
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in_filename_mcsm = gene.lower() + '_complex_mcsm_norm3.csv' #851
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if gene.lower() in gene_list_normal:
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print("\nReading mCSM file for gene:", gene)
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@ -172,17 +172,29 @@ mcsm_f_snps = pd.read_csv(infile_mcsm_f_snps, sep = ',', names = ['mu
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#------------------------------------------------------------------------------
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# ONLY:for gene pnca and gid: End logic should pick this up!
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geneL_dy_na = ['gid']
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if gene.lower() in geneL_dy_na :
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geneL_na = ['gid', 'rpob']
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if gene.lower() in geneL_na:
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print("\nGene:", gene.lower()
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, "\nReading mCSM_na files")
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# infilename_dynamut = gene.lower() + '_dynamut_norm.csv' # gid
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# infile_dynamut = outdir + 'dynamut_results/' + infilename_dynamut
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# dynamut_df = pd.read_csv(infile_dynamut, sep = ',')
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infilename_mcsm_na = gene.lower() + '_complex_mcsm_na_norm.csv' # gid
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infile_mcsm_na = outdir + 'mcsm_na_results/' + infilename_mcsm_na
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mcsm_na_df = pd.read_csv(infile_mcsm_na, sep = ',')
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geneL_dy = ['gid']
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if gene.lower() in geneL_dy:
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print("\nGene:", gene.lower()
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, "\nReading Dynamut and mCSM_na files")
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infilename_dynamut = gene.lower() + '_dynamut_norm.csv' # gid
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infile_dynamut = outdir + 'dynamut_results/' + infilename_dynamut
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dynamut_df = pd.read_csv(infile_dynamut, sep = ',')
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infilename_mcsm_na = gene.lower() + '_complex_mcsm_na_norm.csv' # gid
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infile_mcsm_na = outdir + 'mcsm_na_results/' + infilename_mcsm_na
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mcsm_na_df = pd.read_csv(infile_mcsm_na, sep = ',')
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# infilename_mcsm_na = gene.lower() + '_complex_mcsm_na_norm.csv' # gid
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# infile_mcsm_na = outdir + 'mcsm_na_results/' + infilename_mcsm_na
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# mcsm_na_df = pd.read_csv(infile_mcsm_na, sep = ',')
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# ONLY:for gene embb and alr: End logic should pick this up!
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geneL_ppi2 = ['embb', 'alr']
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@ -192,7 +204,6 @@ if gene.lower() in geneL_ppi2:
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infile_mcsm_ppi2 = outdir + 'mcsm_ppi2/' + infilename_mcsm_ppi2
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mcsm_ppi2_df = pd.read_csv(infile_mcsm_ppi2, sep = ',')
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if gene.lower() == "embb":
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sel_chain = "B"
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else:
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@ -227,7 +238,7 @@ foldx_df['ddg_foldx']
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# Rescale values in Foldx_change col b/w -1 and 1 so negative numbers
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# stay neg and pos numbers stay positive
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foldx_min = foldx_df['ddg_foldx'].min()
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foldx_min = foldx_df['ddg_foldx'].min()
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foldx_max = foldx_df['ddg_foldx'].max()
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foldx_min
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foldx_max
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@ -299,7 +310,13 @@ if len(deepddg_df.loc[:,'chain_id'].value_counts()) > 1:
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print('\nSelecting chain:', sel_chain, 'for gene:', gene)
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deepddg_df = deepddg_df[deepddg_df['chain_id'] == sel_chain]
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#--------------------------
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# Drop chain id col as other targets don't have it.Check for duplicates
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#--------------------------
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col_to_drop = ['chain_id']
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deepddg_df = deepddg_df.drop(col_to_drop, axis = 1)
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#--------------------------
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# Check for duplicates
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#--------------------------
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@ -312,12 +329,6 @@ if len(deepddg_df['mutationinformation'].duplicated().value_counts())> 1:
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else:
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print("\nPASS: No duplicates detected in DeepDDG infile")
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#--------------------------
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# Drop chain id col as other targets don't have it.Check for duplicates
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#--------------------------
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col_to_drop = ['chain_id']
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deepddg_df = deepddg_df.drop(col_to_drop, axis = 1)
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#-------------------------
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# scale Deepddg values
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#-------------------------
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@ -366,8 +377,7 @@ else:
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, '\nGot:', doc[0]
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, '\n======================================================')
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sys.exit()
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if deepddg_df['deepddg_scaled'].min() == -1 and deepddg_df['deepddg_scaled'].max() == 1:
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print('\nPASS: Deepddg data is scaled between -1 and 1',
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'\nproceeding with merge')
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@ -571,7 +581,7 @@ foo = combined_df[['wild_type', 'wild_type_kd', 'wt_3letter_caps', 'wt_aa_3lower
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# Drop cols
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cols_to_drop = ['chain_id', 'wild_type_kd', 'wild_type_dssp', 'wt_3letter_caps']
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combined_df_clean = combined_df.drop(cols_to_drop, axis = 1)
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combined_df_clean.columns
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del(foo)
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#%%============================================================================
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# Output columns
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@ -611,7 +621,7 @@ get_aa_1upper(df = afor_df
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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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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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@ -683,14 +693,24 @@ if gene.lower() == "embb":
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if gene.lower() == "katg":
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dfs_list = [dynamut2_df]
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if gene.lower() == "rpob":
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dfs_list = [dynamut2_df]
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dfs_list = [dynamut2_df, mcsm_na_df]
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if gene.lower() == "alr":
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dfs_list = [dynamut2_df, mcsm_ppi2_df]
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# noticed that with revised rpoB that mcsm-NA had one less position,
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# Hence this condition else the last check fails with discrepancy for expected_nrows
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if len(dfs_list) > 1:
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join_type = 'outer'
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else:
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join_type = 'inner'
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print('\nUsing join type: "', join_type, '" for the last but one merge')
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dfs_merged = reduce(lambda left,right: pd.merge(left
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, right
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, on = ['mutationinformation']
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, how = 'inner')
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#, how = 'inner')
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, how = join_type)
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, dfs_list)
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# drop excess columns
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drop_cols = detect_common_cols(dfs_merged, combined_stab_afor)
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@ -718,7 +738,21 @@ else:
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, '\nGot:', len(dfs_merged_clean.columns)
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, '\nExpected nrows:', expected_nrows
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, '\nGot:', len(dfs_merged_clean) )
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# FIXME: need to extract 'cols_to_drop' programatically
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# Drop cols
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if combined_all_params.columns.str.contains(r'_x$|_y$', regex = True).any():
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print('\nDuplicate column names detected...'
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, '\nDropping these before writing file')
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extra_cols_to_drop = list(combined_all_params.columns.str.extract(r'(.*_x$|.*_y$)', expand = True).dropna()[0])
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print('\nTotal cols:', len(combined_all_params.columns)
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,'\nDropping:', len(extra_cols_to_drop), 'columns')
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#extra_cols_to_drop = ['chain_x', 'chain_y']
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combined_all_params = combined_all_params.drop(extra_cols_to_drop, axis = 1)
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else:
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print('\nNo duplicate column names detected, just writing file'
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, '\nTotal cols:', len(combined_all_params.columns) )
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#del(foo)
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#%% Done for gid on 10/09/2021
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# write csv
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print('Writing file: all params')
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@ -727,4 +761,4 @@ combined_all_params.to_csv(outfile_comb, index = False)
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print('\nFinished writing file:'
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, '\nNo. of rows:', combined_all_params.shape[0]
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, '\nNo. of cols:', combined_all_params.shape[1])
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#%% end of script
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#%% end of script
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