From 811027e34d77794ccff34cfa6724cd9f202ada21 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Tue, 7 Apr 2020 17:42:06 +0100
Subject: [PATCH] tidy kd_df script

---
 scripts/kd_df.py | 40 +++++++++++++++++++++++-----------------
 1 file changed, 23 insertions(+), 17 deletions(-)

diff --git a/scripts/kd_df.py b/scripts/kd_df.py
index 904d92f..97184b0 100755
--- a/scripts/kd_df.py
+++ b/scripts/kd_df.py
@@ -78,7 +78,8 @@ print('Output filename:', out_filename
       , '\n=============================================================')
 #%% end of variable assignment for input and output files
 #=======================================================================
-def kd_to_csv(inputfasta, outputkdcsv, windowsize):
+#%% kd values from fasta file and output csv
+def kd_to_csv(inputfasta, outputkdcsv, windowsize, plot=False):
 	"""
     Calculate kd (hydropathy values) from input fasta file
 
@@ -181,17 +182,14 @@ def kd_to_csv(inputfasta, outputkdcsv, windowsize):
 	#===============
 	# writing file
 	#===============
-	print('Writing file:', out_filename
-		  , '\nFilename:', out_filename
-		  , '\nPath:',  outdir
+	print('Writing file:'
+		  , '\nFilename:', outputkdcsv
+#		  , '\nPath:',  outdir
+		  , '\nExpected no. of rows:', len(kd_df)
+		  , '\nExpected no. of cols:', len(kd_df.columns)
 		  , '\n=============================================================')
 
-	kd_df.to_csv(outfile, header = True, index = True)
-
-	print('Finished writing:', out_filename
-		  , '\nNo. of rows:', len(kd_df)
-		  , '\nNo. of cols:', len(kd_df.columns)
-		  , '\n=============================================================')
+	kd_df.to_csv(outputkdcsv, header = True, index = True)
 		  
 	#===============
 	# plot: optional!
@@ -201,12 +199,14 @@ def kd_to_csv(inputfasta, outputkdcsv, windowsize):
 	# 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)
-	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 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()
+		
 #%% end of function
 #=======================================================================
 #%% call function
@@ -214,7 +214,13 @@ def kd_to_csv(inputfasta, outputkdcsv, windowsize):
 #=======================================================================
 def main():
 	print('Running hydropathy calcs', in_filename, 'output csv:', out_filename)
-	kd_to_csv(infile, outfile, windowsize = 3)
+	kd_to_csv(infile, outfile, 3)
+	print('Finished writing file:'
+		  , '\nFilename:', outfile
+		  , '\nPath:',  outdir
+#		  , '\nNo. of rows:', ''
+#		  , '\nNo. of cols:', ''
+		  , '\n=============================================================')
 	
 if __name__ == '__main__':
 	main()