annotate mkpthwpng.py @ 14:8ae67e9fb6ff

Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]

#!/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()