annotate mkpthwpng.py @ 28:184d14e4270d

Update to Miller Lab devshed revision 4ede22dd5500
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 17 Jul 2013 12:46:46 -0400
parents 66a183c44dd5
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1 #!/usr/bin/env python
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2 # -*- coding: utf-8 -*-
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3 #
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4 # mkpthwpng.py
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5 #
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6 # Copyright 2011 Oscar Bedoya-Reina <oscar@niska.bx.psu.edu>
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7 #
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8 # This program is free software; you can redistribute it and/or modify
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9 # it under the terms of the GNU General Public License as published by
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10 # the Free Software Foundation; either version 2 of the License, or
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11 # (at your option) any later version.
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12 #
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13 # This program is distributed in the hope that it will be useful,
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14 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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15 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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16 # GNU General Public License for more details.
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17 #
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18 # You should have received a copy of the GNU General Public License
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19 # along with this program; if not, write to the Free Software
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20 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
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21 # MA 02110-1301, USA.
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22
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23 import argparse,mechanize,os,sys
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24
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25 #this return an image made up from a list of genes and pathway code
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26 def rtnHTMLformat(tmpddGenrcgenPresent,sppPrefx,pthwcod,ouPthwpng):
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27 inpx='\n'.join(tmpddGenrcgenPresent)#inpx="ALDH2 color \nALDH3A1 color"
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28 request=mechanize.Request("http://www.genome.jp/kegg/tool/map_pathway2.html")
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29 response = mechanize.urlopen(request)
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30 forms = mechanize.ParseResponse(response, backwards_compat=False)
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31 form=forms[0]
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32 form["unclassified"]=inpx
23
66a183c44dd5 bugfix for Pathway Image tool
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33 form["org"]=sppPrefx
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34 request2 = form.click()
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35 response2 = mechanize.urlopen(request2)
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36 a=str(response2.read()).split('href="/kegg-bin/show_pathway?')[1]
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37 code=a.split('/')[0]#response2.read()
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38 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'))
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39 response = mechanize.urlopen(request)
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40 forms = mechanize.ParseResponse(response, backwards_compat=False)
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41 form=forms[1]
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42 status=' NOT '
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43 try:
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44 imgf=str(forms[1]).split('/mark_pathway')[1].split('/')[0]
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45 os.system("wget --quiet http://www.genome.jp/tmp/mark_pathway%s/%s.png -O %s"%(imgf,pthwcod,ouPthwpng))
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46 status=' '
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47 except:
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48 pass
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49 return 'A pathway image was%ssuccefully produced...'%status
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50
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51
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52 def main():
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53 parser = argparse.ArgumentParser(description='Obtain KEGG images from a list of genes.')
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54 parser.add_argument('--input',metavar='input TXT file',type=str,help='the input file with the table in txt format')
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55 parser.add_argument('--output',metavar='output PNG image',type=str,help='the output image file in png format')
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56 parser.add_argument('--KEGGpath',metavar='KEGG pathway code (i.e. cfa00230)',type=str,help='the code of the pathway of interest')
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57 parser.add_argument('--posKEGGclmn',metavar='column number',type=int,help='the column with the KEGG pathway code/name')
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58 parser.add_argument('--KEGGgeneposcolmn',metavar='column number',type=int,help='column with the KEGG gene code')
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59 #~Open arguments
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60 class C(object):
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61 pass
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62 fulargs=C()
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63 parser.parse_args(sys.argv[1:],namespace=fulargs)
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64 #test input vars
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65 inputf,outputf,KEGGpathw,posKEGGclmn,Kgeneposcolmn=fulargs.input,fulargs.output,fulargs.KEGGpath,fulargs.posKEGGclmn,fulargs.KEGGgeneposcolmn
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66 # make posKEGGclmn, Kgeneposcolmn 0-based
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67 sppPrefx= KEGGpathw[:3]
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68 posKEGGclmn -= 1
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69 Kgeneposcolmn -= 1
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70 #make a dictionary of valid genes
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71 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()])
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72 for mt1gene in [x for x in dKEGGcPthws.keys() if x.find('.')>-1]:#to crrect names with more than one gene
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73 pthwsAssotd=dKEGGcPthws.pop(mt1gene)
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74 for eachg in mt1gene.split('.'):
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75 dKEGGcPthws[eachg]=pthwsAssotd
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76 tmpddGenrcgenPresent=set()
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77 sKEGGc=dKEGGcPthws.keys()
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78 lsKEGGc=len(sKEGGc)
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79 ctPthw=0
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80 while ctPthw < lsKEGGc:#to save memory
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81 eachK=sKEGGc.pop()
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82 alPthws=dKEGGcPthws[eachK]
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83 if KEGGpathw in alPthws:
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84 tmpddGenrcgenPresent.add('\t'.join([eachK,'red']))
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85 ctPthw+=1
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86 #run the program
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87 rtnHTMLformat(tmpddGenrcgenPresent,sppPrefx,KEGGpathw,outputf)
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88 return 0
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89
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90
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91 if __name__ == '__main__':
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92 main()