minor tweaks

scripts/combine_dfs.py

@@ -7,29 +7,29 @@ Created on Tue Aug  6 12:56:03 2019
 '''
 # FIXME: change filename 4 (mcsm normalised data)
 # to be consistent like (pnca_complex_mcsm_norm.csv) : changed manually, but ensure this is done in the mcsm pipeline
-#=============================================================================
+#=======================================================================
 # Task: combine 4 dfs with aa position as linking column
 # This is done in 2 steps:
 # merge 1: of 3 dfs (filenames in lowercase)
 #   <gene.lower()>_dssp.csv
 #   <gene.lower()>_kd.csv
-#   <gene.lower()>_pnca_rd.csv
+#   <gene.lower()>_rd.csv
 
 # merge 2: of 2 dfs
-#    pnca_complex_mcsm_norm.csv (!fix name)
+#    gene.lower() + '_complex_mcsm_norm.csv' (!fix name)
 #    output df from merge1
 
 # Input: 3 dfs
 #   <gene.lower()>_dssp.csv
 #   <gene.lower()>_kd.csv
-#   <gene.lower()>_pnca_rd.csv
-# pnca_complex_mcsm_norm.csv (!fix name)
+#   <gene.lower()>_rd.csv
+# gene.lower() + '_complex_mcsm_norm.csv' (!fix name)
 
 # Output: .csv of all 4 dfs combined
 
 # useful link
 # https://stackoverflow.com/questions/23668427/pandas-three-way-joining-multiple-dataframes-on-columns
-#=============================================================================
+#=======================================================================
 #%% load packages
 import sys, os
 import pandas as pd
@@ -46,10 +46,10 @@ os.getcwd()
 #=======================================================================
 #%% command line args
 arg_parser = argparse.ArgumentParser()
-#arg_parser.add_argument('-d', '--drug', help='drug name', default = 'pyrazinamide')
-#arg_parser.add_argument('-g', '--gene', help='gene name', default = 'pncA') # case sensitive
-arg_parser.add_argument('-d', '--drug', help='drug name', default = 'pyrazin')
-arg_parser.add_argument('-g', '--gene', help='gene name', default = 'pn') # case sensitive
+arg_parser.add_argument('-d', '--drug', help='drug name', default = 'pyrazinamide')
+arg_parser.add_argument('-g', '--gene', help='gene name', default = 'pncA') # case sensitive
+#arg_parser.add_argument('-d', '--drug', help='drug name', default = 'TESTDRUG')
+#arg_parser.add_argument('-g', '--gene', help='gene name (case sensitive)', default = 'testGene') # case sensitive
 args = arg_parser.parse_args()
 #=======================================================================
 #%% variable assignment: input and output 
@@ -68,11 +68,11 @@ datadir = homedir + '/' + 'git/Data'
 # input
 #=======
 indir = datadir + '/' + drug + '/' + 'output'
-in_filename1 = 'pnca_dssp.csv'
-in_filename2 = 'pnca_kd.csv'
-in_filename3 = 'pnca_rd.csv'
+in_filename1 = gene.lower() + '_dssp.csv'
+in_filename2 = gene.lower() + '_kd.csv'
+in_filename3 = gene.lower() + '_rd.csv'
 #in_filename4 = 'mcsm_complex1_normalised.csv' # FIXNAME
-in_filename4 = 'pnca_complex_mcsm_norm.csv' 
+in_filename4 = gene.lower() + '_complex_mcsm_norm.csv' 
 
 infile1 = indir + '/' + in_filename1
 infile2 = indir + '/' + in_filename2

scripts/data_extraction.py

@@ -47,8 +47,10 @@ from reference_dict import my_aa_dict # CHECK DIR STRUC THERE!
 #=======================================================================
 #%% command line args
 arg_parser = argparse.ArgumentParser()
-arg_parser.add_argument('-d', '--drug', help='drug name', default = 'pyrazinamide')
-arg_parser.add_argument('-g', '--gene', help='gene name', default = 'pncA') # case sensitive
+#arg_parser.add_argument('-d', '--drug', help='drug name', default = 'pyrazinamide')
+#arg_parser.add_argument('-g', '--gene', help='gene name', default = 'pncA') # case sensitive
+arg_parser.add_argument('-d', '--drug', help='drug name', default = 'TESTDRUG')
+arg_parser.add_argument('-g', '--gene', help='gene name (case sensitive)', default = 'testGene') # case sensitive
 args = arg_parser.parse_args()
 #=======================================================================
 #%% variable assignment: input and output paths & filenames
@@ -346,7 +348,7 @@ print('expected no. of gene samples:', expected_gene_samples)
 print('=================================================================')
 #%% write file
 #print(outdir)
-out_filename0 = gene.lower() + '_' + 'common_ids.csv'
+out_filename0 = gene.lower() + '_common_ids.csv'
 outfile0 =  outdir + '/' + out_filename0
 
 #FIXME: CHECK line len(common_ids)
@@ -741,7 +743,7 @@ del(c1, c2, col_to_split1, col_to_split2, comp_gene_samples, dr_WF0, dr_df, dr_m
 #dr_muts.to_csv('dr_muts.csv', header = True)
 #other_muts.to_csv('other_muts.csv', header = True)
 
-out_filename1 = gene.lower() + '_' + 'ambiguous_muts.csv'
+out_filename1 = gene.lower() + '_ambiguous_muts.csv'
 outfile1 = outdir + '/' + out_filename1
 print('Writing file: ambiguous muts',
       '\nFilename:', out_filename1,
@@ -1053,7 +1055,7 @@ else:
           , '\nDebug please!'
           , '\n=========================================================')
 
-out_filename2 = gene.lower() + '_' + 'mcsm_snps.csv'
+out_filename2 = gene.lower() + '_mcsm_snps.csv'
 outfile2 = outdir + '/' + out_filename2
 
 print('Writing file: mCSM style muts'
@@ -1074,7 +1076,7 @@ del(out_filename2)
 
 #%% Write file: gene_metadata (i.e gene_LF1)
 # where each row has UNIQUE mutations NOT unique sample ids
-out_filename3 = gene.lower() + '_' + 'metadata.csv'
+out_filename3 = gene.lower() + '_metadata.csv'
 outfile3 = outdir + '/' + out_filename3
 print('Writing file: LF formatted data'
       , '\nFilename:', out_filename3
@@ -1117,7 +1119,7 @@ else:
           , '\nDebug please!'
           , '\n=========================================================')
 
-out_filename4 = gene.lower() + '_' + 'all_muts_msa.csv'
+out_filename4 = gene.lower() +'_all_muts_msa.csv'
 outfile4 = outdir + '/' + out_filename4
 
 print('Writing file: mCSM style muts for msa',
@@ -1149,7 +1151,7 @@ pos_only.position.dtype
 # sort by position value
 pos_only_sorted = pos_only.sort_values(by = 'position', ascending = True)
 
-out_filename5 = gene.lower() + '_' + 'mutational_positons.csv'
+out_filename5 = gene.lower() + '_mutational_positons.csv'
 outfile5 = outdir + '/' + out_filename5
 
 print('Writing file: mutational positions'

scripts/dssp_df.py

@@ -30,8 +30,10 @@ os.getcwd()
 #=======================================================================
 #%% command line args
 arg_parser = argparse.ArgumentParser()
-arg_parser.add_argument('-d', '--drug', help='drug name', default = 'pyrazinamide')
-arg_parser.add_argument('-g', '--gene', help='gene name', default = 'pncA') # case sensitive
+#arg_parser.add_argument('-d', '--drug', help='drug name', default = 'pyrazinamide')
+#arg_parser.add_argument('-g', '--gene', help='gene name', default = 'pncA') # case sensitive
+arg_parser.add_argument('-d', '--drug', help='drug name', default = 'TESTDRUG')
+arg_parser.add_argument('-g', '--gene', help='gene name (case sensitive)', default = 'testGene') # case sensitive
 args = arg_parser.parse_args()
 #=======================================================================
 #%% variable assignment: input and output 

scripts/rd_df.py

@@ -33,8 +33,8 @@ os.getcwd()
 arg_parser = argparse.ArgumentParser()
 #arg_parser.add_argument('-d', '--drug', help='drug name', default = 'pyrazinamide')
 #arg_parser.add_argument('-g', '--gene', help='gene name', default = 'pncA') # case sensitive
-arg_parser.add_argument('-d', '--drug', help='drug name', default = 'DRUGNAME')
-arg_parser.add_argument('-g', '--gene', help='gene name', default = 'geneName')
+arg_parser.add_argument('-d', '--drug', help='drug name', default = 'TESTDRUG')
+arg_parser.add_argument('-g', '--gene', help='gene name (case sensitive)', default = 'testGene') # case sensitive
 args = arg_parser.parse_args()
 #=======================================================================
 #%% variable assignment: input and output