diff mkpthwpng.py @ 0:c3ba43704319 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mkpthwpng.py	Wed Sep 12 14:35:13 2012 -0400
@@ -0,0 +1,92 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+#       mkpthwpng.py
+#       
+#       Copyright 2011 Oscar Bedoya-Reina <[e-mail]>
+#       
+#       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,mechanize,os,sys
+
+#this return an image made up from a list of genes and pathway code
+def rtnHTMLformat(tmpddGenrcgenPresent,sppPrefx,pthwcod,ouPthwpng):
+	inpx='\n'.join(tmpddGenrcgenPresent)#inpx="ALDH2 color \nALDH3A1	color"
+	request=mechanize.Request("http://www.genome.jp/kegg/tool/map_pathway2.html")
+	response = mechanize.urlopen(request)
+	forms = mechanize.ParseResponse(response, backwards_compat=False)
+	form=forms[0]
+	form["unclassified"]=inpx
+	form["org_name"]=[sppPrefx]
+	request2 = form.click()
+	response2 = mechanize.urlopen(request2)
+	a=str(response2.read()).split('href="/kegg-bin/show_pathway?')[1]
+	code=a.split('/')[0]#response2.read()
+	request=mechanize.Request("http://www.genome.jp/kegg-bin/show_pathway?%s/%s.args"%(code,pthwcod))#request=mechanize.Request("http://www.genome.jp/kegg-bin/show_pathway?%s/%s.args"%('13171478854246','hsa00410'))
+	response = mechanize.urlopen(request)
+	forms = mechanize.ParseResponse(response, backwards_compat=False)
+	form=forms[1]
+	status=' NOT '
+	try:
+		imgf=str(forms[1]).split('/mark_pathway')[1].split('/')[0]
+		os.system("wget --quiet http://www.genome.jp/tmp/mark_pathway%s/%s.png -O %s"%(imgf,pthwcod,ouPthwpng))
+		status=' '
+	except:
+		pass
+	return 'A pathway image was%ssuccefully produced...'%status
+
+
+def main():
+	parser = argparse.ArgumentParser(description='Obtain KEGG images from a list of genes.')
+	parser.add_argument('--input',metavar='input TXT file',type=str,help='the input file with the table in txt format')
+	parser.add_argument('--output',metavar='output PNG image',type=str,help='the output image file in png format')
+	parser.add_argument('--KEGGpath',metavar='KEGG pathway code (i.e. cfa00230)',type=str,help='the code of the pathway of interest')
+	parser.add_argument('--posKEGGclmn',metavar='column number',type=int,help='the column with the KEGG pathway code/name')
+	parser.add_argument('--KEGGgeneposcolmn',metavar='column number',type=int,help='column with the KEGG gene code')
+	#~Open arguments 
+	class C(object):
+		pass
+	fulargs=C()
+	parser.parse_args(sys.argv[1:],namespace=fulargs)
+	#test input vars
+	inputf,outputf,KEGGpathw,posKEGGclmn,Kgeneposcolmn=fulargs.input,fulargs.output,fulargs.KEGGpath,fulargs.posKEGGclmn,fulargs.KEGGgeneposcolmn
+    # make posKEGGclmn, Kgeneposcolmn 0-based
+	sppPrefx= KEGGpathw[:3]
+	posKEGGclmn -= 1
+	Kgeneposcolmn -= 1
+	#make a dictionary of valid genes
+	dKEGGcPthws=dict([(x.split('\t')[Kgeneposcolmn],set([y.split('=')[0] for y in x.split('\t')[posKEGGclmn].split('.')])) for x in open(inputf).read().splitlines()[1:] if x.strip()])
+	for mt1gene in [x for x in dKEGGcPthws.keys() if x.find('.')>-1]:#to crrect names with more than one gene
+		pthwsAssotd=dKEGGcPthws.pop(mt1gene)
+		for eachg in mt1gene.split('.'):
+			dKEGGcPthws[eachg]=pthwsAssotd
+	tmpddGenrcgenPresent=set()
+	sKEGGc=dKEGGcPthws.keys()
+	lsKEGGc=len(sKEGGc)
+	ctPthw=0
+	while ctPthw < lsKEGGc:#to save memory
+		eachK=sKEGGc.pop()
+		alPthws=dKEGGcPthws[eachK]
+		if KEGGpathw in alPthws:
+			tmpddGenrcgenPresent.add('\t'.join([eachK,'red']))
+		ctPthw+=1
+	#run the program
+	rtnHTMLformat(tmpddGenrcgenPresent,sppPrefx,KEGGpathw,outputf)
+	return 0
+	
+
+if __name__ == '__main__':
+	main()