saving work for today

scripts/kd_df.py

@@ -43,6 +43,7 @@ arg_parser = argparse.ArgumentParser()
 #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('-p', '--plot', help='show plot',  action='store_true')
 args = arg_parser.parse_args()
 #=======================================================================
 #%% variable assignment: input and output 
@@ -50,6 +51,7 @@ args = arg_parser.parse_args()
 #gene = 'pncA'
 drug = args.drug
 gene = args.gene
+#plot = args.plot
 gene_match = gene + '_p.'
 
 #==========
@@ -79,7 +81,7 @@ 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, plot=False):
+def kd_to_csv(inputfasta, outputkdcsv, windowsize):
 	"""
     Calculate kd (hydropathy values) from input fasta file
 
@@ -199,13 +201,13 @@ def kd_to_csv(inputfasta, outputkdcsv, windowsize, plot=False):
 	# FIXME: save fig
 	# extract just pdb if from 'id' to pass to title of plot
 	# foo = re.match(r'(^[0-9]{1}\w{3})', id).groups(1)
-	if plot:
-		plot(kd_values, linewidth = 1.0)
-		#axis(xmin = 1, xmax = num_residues)
-		xlabel('Residue Number')
-		ylabel('Hydrophobicity')
-		title('K&D Hydrophobicity for ' + id)
-		show()
+#	if doplot:
+	plot(kd_values, linewidth = 1.0)
+	#axis(xmin = 1, xmax = num_residues)
+	xlabel('Residue Number')
+	ylabel('Hydrophobicity')
+	title('K&D Hydrophobicity for ' + id)
+	show()
 		
 #%% end of function
 #=======================================================================