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added FIXME and TODO related to alr in combinig_dfs.py

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Tanushree Tunstall 2021-11-09 13:23:50 +00:00
parent 246cd636a1
commit 34ee2519d3
1 changed files with 5 additions and 1 deletions
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6
scripts/combining_dfs.py
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@ -116,6 +116,7 @@ if not outdir:
#======= #=======
gene_list_normal = ["pnca", "katg", "rpob", "alr"] gene_list_normal = ["pnca", "katg", "rpob", "alr"]
#FIXME: for gid, this should be SRY as this is the drug...please check!!!!
if gene.lower() == "gid": if gene.lower() == "gid":
print("\nReading mCSM file for gene:", gene) print("\nReading mCSM file for gene:", gene)
in_filename_mcsm = gene.lower() + '_complex_mcsm_norm_SAM.csv' in_filename_mcsm = gene.lower() + '_complex_mcsm_norm_SAM.csv'
@ -178,6 +179,8 @@ if gene.lower() in geneL_dy_na :
infile_mcsm_na = outdir + 'mcsm_na_results/' + infilename_mcsm_na infile_mcsm_na = outdir + 'mcsm_na_results/' + infilename_mcsm_na
mcsm_na_df = pd.read_csv(infile_mcsm_na, sep = ',') mcsm_na_df = pd.read_csv(infile_mcsm_na, sep = ',')
# FIXME: ppi2, not extracted as expected for alr
# TODO: get mcsm_ppi2 data for alr
# ONLY:for gene embb and alr: End logic should pick this up! # ONLY:for gene embb and alr: End logic should pick this up!
geneL_ppi2 = ["embb", "alr"] geneL_ppi2 = ["embb", "alr"]
#if gene.lower() == "embb" or "alr": #if gene.lower() == "embb" or "alr":
@ -336,6 +339,7 @@ if len(deepddg_df.loc[:,'chain_id'].value_counts()) > 1:
, "\nChains:", deepddg_df.loc[:,'chain_id'].value_counts().index) , "\nChains:", deepddg_df.loc[:,'chain_id'].value_counts().index)
#-------------------------- #--------------------------
# FIXME: This needs to happen BEFORE scaling as it will vary
# subset chain # subset chain
#-------------------------- #--------------------------
if gene.lower() == "embb": if gene.lower() == "embb":
@ -709,4 +713,4 @@ combined_all_params.to_csv(outfile_comb, index = False)
print('\nFinished writing file:' print('\nFinished writing file:'
, '\nNo. of rows:', combined_all_params.shape[0] , '\nNo. of rows:', combined_all_params.shape[0]
, '\nNo. of cols:', combined_all_params.shape[1]) , '\nNo. of cols:', combined_all_params.shape[1])
#%% end of script #%% end of script