--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rtrnKEGGpthwfENSEMBLTc.py	Wed Sep 12 17:10:26 2012 -0400
@@ -0,0 +1,78 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+#       calclenchange.py
+#       
+#       Copyright 2011 Oscar Bedoya-Reina <oscar@niska.bx.psu.edu>
+#       
+#       This program is free software; you can redistribute it and/or modify
+#       it under the terms of the GNU General Public License as published by
+#       the Free Software Foundation; either version 2 of the License, or
+#       (at your option) any later version.
+#       
+#       This program is distributed in the hope that it will be useful,
+#       but WITHOUT ANY WARRANTY; without even the implied warranty of
+#       MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#       GNU General Public License for more details.
+#       
+#       You should have received a copy of the GNU General Public License
+#       along with this program; if not, write to the Free Software
+#       Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+#       MA 02110-1301, USA.
+
+import argparse,os,sys
+
+
+def main():
+	parser = argparse.ArgumentParser(description='Adds the fields KEGG gene codes and KEGG pathways to an input table of ENSEMBL transcript codes.')
+	parser.add_argument('--loc_file',metavar='correlational database',type=str,help='correlational database')
+	parser.add_argument('--species',metavar='species name',type=str,help='the species of interest in loc_file')
+	parser.add_argument('--output',metavar='output TXT file',type=str,help='the output file with the table in txt format. The output will have two more fields: KEGG gene codes and KEGG pathways of each ENSEMBL code' )
+	parser.add_argument('--posENSEMBLclmn',metavar='column number',type=int,help='the column with the ENSEMBLE transcript code')
+	parser.add_argument('--input',metavar='input TXT file',type=str,help='the input file with the table in txt format')
+	#~ 
+	#~Open arguments 
+	class C(object):
+		pass
+	fulargs=C()
+	parser.parse_args(sys.argv[1:],namespace=fulargs)
+	#test input vars
+	inputf,loc_file,species,output,posENSEMBLclmn=fulargs.input,fulargs.loc_file,fulargs.species,fulargs.output,fulargs.posENSEMBLclmn
+	posENSEMBLclmn-=1#correct pos
+	#~ Get the extra variables
+	crDB=[x.split() for x in open(loc_file).read().splitlines() if x.split()[0]==species][0]
+	sppPrefx,dinput=crDB[0],crDB[1]#X should be replaced by the position in which the Conversion Dictionary File (CDF) is placed
+	#make a dictionary of the input CDF
+	dKEGGcPthws=dict([(x.split('\t')[0],'\t'.join(x.split('\t')[1:])) for x in open(dinput).read().splitlines() if x.strip()])
+	#~ add the two new columns
+	sall=[]
+	#lENSEMBLTc=[x.split('\t') for x in open(inputf).read().splitlines() if x.strip()]
+	lENSEMBLTc = []
+	with open(inputf) as fh:
+	    for line in fh:
+	        if line.startswith('#'):
+	            continue
+	        lENSEMBLTc.append(line.rstrip('\r\n').split('\t'))
+	nLines=len(lENSEMBLTc)
+	cLines=0
+	sall=[]#the output list for with additional fields
+	#~ 
+	while cLines<nLines:
+		cLines+=1
+		lENSEMBLTcKEGGgKEGGpth=lENSEMBLTc.pop(0)
+		ENSEMBLTc=lENSEMBLTcKEGGgKEGGpth[posENSEMBLclmn]
+		try:
+			KEGGgKEGGpth=dKEGGcPthws[ENSEMBLTc]
+		except:
+			KEGGgKEGGpth='\t'.join(['U','N'])
+		sall.append('\t'.join(['\t'.join(lENSEMBLTcKEGGgKEGGpth),KEGGgKEGGpth]))
+	#~ 
+	salef=open(output,'w')
+	salef.write('\n'.join(sall))
+	salef.close()
+	return 0
+	
+
+if __name__ == '__main__':
+	main()
+