ran struc param analysis

scripts/combine_dfs.py

@@ -46,10 +46,8 @@ os.getcwd()
 #=======================================================================
 #%% command line args
 arg_parser = argparse.ArgumentParser()
-arg_parser.add_argument('-d', '--drug', help='drug name', default = 'pyrazinamide')
+arg_parser.add_argument('-d', '--drug', help='drug name', default = None)
-arg_parser.add_argument('-g', '--gene', help='gene name', default = 'pncA') # case sensitive
+arg_parser.add_argument('-g', '--gene', help='gene name', default = None) # 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 
@@ -288,8 +286,7 @@ def main():
         , 'output csv:', out_filename)
     combine_dfs(infile1, infile2, infile3, infile4, outfile)
     print('Finished Writing file:'
-		, '\nFilename:', out_filename
+        , '\nFilename:', outfile
-		, '\nPath:',  outdir
 ##        , '\nNo. of rows:', ''
 ##        , '\nNo. of cols:', ''
         , '\n===========================================================')

scripts/data_extraction.py

@@ -57,8 +57,8 @@ args = arg_parser.parse_args()
 
 drug = args.drug
 gene = args.gene
-
 gene_match = gene + '_p.'
+
 # building cols to extract
 dr_muts_col = 'dr_mutations_' + drug
 other_muts_col = 'other_mutations_' + drug
@@ -80,8 +80,8 @@ datadir = homedir + '/' + 'git/Data'
 #=======
 # input
 #=======
-#in_filename  = 'original_tanushree_data_v2.csv'
+in_filename  = 'original_tanushree_data_v2.csv'
-in_filename  = 'mtb_gwas_v3.csv'
+#in_filename  = 'mtb_gwas_v3.csv'
 infile = datadir + '/' + in_filename
 print('Input file: ', infile
       , '\n============================================================')
@@ -1028,25 +1028,25 @@ del(k, v, wt, mut, lookup_dict)
 
 ########
 # combine the wild_type+poistion+mutant_type columns to generate 
-# Mutationinformation (matches mCSM output field)
+# mutationinformation (matches mCSM output field)
 # Remember to use .map(str) for int col types to allow string concatenation
 #########
-gene_LF1['Mutationinformation'] = gene_LF1['wild_type'] + gene_LF1.position.map(str) + gene_LF1['mutant_type']
+gene_LF1['mutationinformation'] = gene_LF1['wild_type'] + gene_LF1.position.map(str) + gene_LF1['mutant_type']
-print('Created column: Mutationinformation'
+print('Created column: mutationinformation'
 	, '\n====================================================================='
-    , gene_LF1.Mutationinformation.head(10))
+    , gene_LF1.mutationinformation.head(10))
 
 #%% Write file: mCSM muts
-snps_only = pd.DataFrame(gene_LF1['Mutationinformation'].unique())
+snps_only = pd.DataFrame(gene_LF1['mutationinformation'].unique())
 snps_only.head()
 # assign column name
-snps_only.columns = ['Mutationinformation']
+snps_only.columns = ['mutationinformation']
 
 # count how many positions this corresponds to
 pos_only = pd.DataFrame(gene_LF1['position'].unique()) 
 
 print('Checking NA in snps...')# should be 0
-if snps_only.Mutationinformation.isna().sum() == 0:
+if snps_only.mutationinformation.isna().sum() == 0:
     print ('PASS: NO NAs/missing entries for SNPs'
     , '\n===============================================================')
 else:
@@ -1090,27 +1090,27 @@ print('Finished writing:', out_filename3
 del(out_filename3)
 
 #%% write file: mCSM style but with repitions for MSA and logo plots
-all_muts_msa = pd.DataFrame(gene_LF1['Mutationinformation']) 
+all_muts_msa = pd.DataFrame(gene_LF1['mutationinformation']) 
 all_muts_msa.head()
 # assign column name
-all_muts_msa.columns = ['Mutationinformation']
+all_muts_msa.columns = ['mutationinformation']
 
 # make sure it is string
 all_muts_msa.columns.dtype
 
 # sort the column
-all_muts_msa_sorted = all_muts_msa.sort_values(by = 'Mutationinformation')
+all_muts_msa_sorted = all_muts_msa.sort_values(by = 'mutationinformation')
 
 # create an extra column with protein name
 all_muts_msa_sorted = all_muts_msa_sorted.assign(fasta_name = '3PL1') 
 all_muts_msa_sorted.head()
 
 # rearrange columns so the fasta name is the first column (required for mutate.script)
-all_muts_msa_sorted = all_muts_msa_sorted[['fasta_name', 'Mutationinformation']]
+all_muts_msa_sorted = all_muts_msa_sorted[['fasta_name', 'mutationinformation']]
 all_muts_msa_sorted.head()
 
 print('Checking NA in snps...')# should be 0
-if all_muts_msa.Mutationinformation.isna().sum() == 0:
+if all_muts_msa.mutationinformation.isna().sum() == 0:
     print ('PASS: NO NAs/missing entries for SNPs'
     , '\n===============================================================')
 else:

scripts/dssp_df.py

@@ -30,10 +30,8 @@ os.getcwd()
 #=======================================================================
 #%% command line args
 arg_parser = argparse.ArgumentParser()
-#arg_parser.add_argument('-d', '--drug', help='drug name', default = 'pyrazinamide')
+arg_parser.add_argument('-d', '--drug', help='drug name', default = None)
-#arg_parser.add_argument('-g', '--gene', help='gene name', default = 'pncA') # case sensitive
+arg_parser.add_argument('-g', '--gene', help='gene name (case sensitive)', default = None) # 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 
@@ -49,6 +47,8 @@ args = arg_parser.parse_args()
 
 drug = args.drug
 gene = args.gene
+gene_match = gene + '_p.'
+
 #==========
 # data dir
 #==========
@@ -147,7 +147,7 @@ def extract_chain_dssp(inputpdbfile):
     return pdbchainlist
 #=======================================================================
 #%% write csv of processed dssp output
-def dssp_to_csv(inputdsspfile, outfile, pdbchainlist):
+def dssp_to_csv(inputdsspfile, outfile, pdbchainlist = ['A']):
     """
     Create a df from a dssp file containing ASA, RSA, SS for all chains
 

scripts/kd_df.py

@@ -39,10 +39,8 @@ os.getcwd()
 #=======================================================================
 #%% command line args
 arg_parser = argparse.ArgumentParser()
-#arg_parser.add_argument('-d', '--drug', help='drug name', default = 'pyrazinamide')
+arg_parser.add_argument('-d', '--drug', help='drug name', default = None)
-#arg_parser.add_argument('-g', '--gene', help='gene name', default = 'pncA') # case sensitive
+arg_parser.add_argument('-g', '--gene', help='gene name', default = None)
-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('-p', '--plot', help='show plot',  action='store_true')
 args = arg_parser.parse_args()
 #=======================================================================
@@ -81,7 +79,7 @@ print('Output filename:', out_filename
 #%% end of variable assignment for input and output files
 #=======================================================================
 #%% kd values from fasta file and output csv
-def kd_to_csv(inputfasta, outputkdcsv, windowsize):
+def kd_to_csv(inputfasta, outputkdcsv, windowsize = 3):
     """
     Calculate kd (hydropathy values) from input fasta file
 
@@ -223,8 +221,7 @@ def main():
         , '\noutfile:', out_filename)
     kd_to_csv(infile, outfile, 3)
     print('Finished writing file:'
-		, '\nFilename:', out_filename
+        , '\nFilename:', outfile
-		, '\nPath:',  outdir
         , '\n=============================================================')
     
 if __name__ == '__main__':

scripts/rd_df.py

@@ -31,10 +31,8 @@ os.getcwd()
 #=======================================================================
 #%% command line args
 arg_parser = argparse.ArgumentParser()
-#arg_parser.add_argument('-d', '--drug', help='drug name', default = 'pyrazinamide')
+arg_parser.add_argument('-d', '--drug', help='drug name', default = None)
-#arg_parser.add_argument('-g', '--gene', help='gene name', default = 'pncA') # case sensitive
+arg_parser.add_argument('-g', '--gene', help='gene name', default = None) # 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 
@@ -165,8 +163,7 @@ def main():
         , '\noutfile:', out_filename)
     rd_to_csv(infile, outfile)
     print('Finished Writing file:'
-		, '\nFilename:', out_filename
+        , '\nFilename:', outfile
-		, '\nPath:',  outdir
         , '\n=============================================================')
 
 if __name__ == '__main__':