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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 # calcfreq.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,os,sys
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24 from decimal import Decimal,getcontext
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25 from LocationFile import LocationFile
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26
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27 #method to rank the the pthways by mut. freq.
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28 def rankd(ltfreqs):
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29 ordvals=sorted(ltfreqs)#sort and reverse freqs.
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30 #~
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31 outrnk=[]
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32 tmpFreq0,tmpCount,tmpPthw=ordvals.pop()#the highest possible value
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33 crank=1
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34 outrnk.append('\t'.join([str(tmpCount),str(tmpFreq0),str(crank),tmpPthw]))
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35 totalnvals=len(ordvals)
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36 cnt=0
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37 while totalnvals>cnt:
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38 cnt+=1
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39 tmpFreq,tmpCount,tmpPthw=ordvals.pop()
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40 if tmpFreq!=tmpFreq0:
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41 crank=len(outrnk)+1
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42 tmpFreq0=tmpFreq
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43 outrnk.append('\t'.join([str(tmpCount),str(tmpFreq),str(crank),tmpPthw]))
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44 return outrnk
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45
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46
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47 def main():
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48 parser = argparse.ArgumentParser(description='Obtain KEGG images from a list of genes.')
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49 parser.add_argument('--input',metavar='input TXT file',type=str,help='the input file with the table in txt format')
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50 parser.add_argument('--output',metavar='output TXT file',type=str,help='the output file with the table in txt format. Column 1 is the count of genes in the list, Column 2 is the percentage of the pathway genes present on the list. Column 3 is the rank based on column 2')
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51 parser.add_argument('--posKEGGclmn',metavar='column number',type=int,help='the column with the KEGG pathway code/name')
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52 parser.add_argument('--KEGGgeneposcolmn',metavar='column number',type=int,help='column with the KEGG gene code')
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53 parser.add_argument('--loc_file',metavar='location file',type=str,help='location file')
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54 parser.add_argument('--species',metavar='species',type=str,help='species')
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55 #~Open arguments
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56 class C(object):
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57 pass
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58 fulargs=C()
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59 parser.parse_args(sys.argv[1:],namespace=fulargs)
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60 #test input vars
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61 inputf,outputf,posKEGGclmn,Kgeneposcolmn=fulargs.input,fulargs.output,fulargs.posKEGGclmn,fulargs.KEGGgeneposcolmn
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62 locf,species=fulargs.loc_file,fulargs.species
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63 #make a dictionary of valid genes
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64 posKEGGclmn-=1
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65 Kgeneposcolmn-=1
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66 dKEGGcPthws=dict([(x.split('\t')[Kgeneposcolmn],set(x.split('\t')[posKEGGclmn].split('.'))) for x in open(inputf).read().splitlines()[1:] if x.strip()])
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67 sdGenes=set([x for x in dKEGGcPthws.keys() if x.find('.')>-1])
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68 while True:#to correct names with more than one gene
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69 try:
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70 mgenes=sdGenes.pop()
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71 pthwsAssotd=dKEGGcPthws.pop(mgenes)
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72 mgenes=mgenes.split('.')
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73 for eachg in mgenes:
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74 dKEGGcPthws[eachg]=pthwsAssotd
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75 except:
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76 break
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77 #~ Count genes
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78 getcontext().prec=2#set 2 decimal places
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79
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80 location_file = LocationFile(locf)
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81 prefix, kxml_dir_path, dict_file = location_file.get_values(species)
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82 dPthContsTotls = {}
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83 try:
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84 with open(dict_file) as fh:
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85 for line in fh:
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86 line = line.rstrip('\r\n')
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87 value, key = line.split('\t')
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88 dPthContsTotls[key] = int(value)
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89 except IOError, err:
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90 print >> sys.stderr, 'Error opening dict file {0}: {1}'.format(dict_file, err.strerror)
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91 sys.exit(1)
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92
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93 dPthContsTmp=dict([(x,0) for x in dPthContsTotls.keys()])#create a list of genes
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94 sdGenes=set([x for x in dKEGGcPthws.keys()])#list of all genes
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95 cntGens=0
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96 ltGens=len(sdGenes)
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97 while cntGens<ltGens:
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98 cGen=sdGenes.pop()
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99 sKEGGcPthws=dKEGGcPthws.pop(cGen)
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100 for eachP in sKEGGcPthws:
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101 if eachP!='N':
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102 dPthContsTmp[eachP]+=1
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103 cntGens+=1
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104 #~ Calculate Freqs.
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105 ltfreqs=[((Decimal(dPthContsTmp[x])/Decimal(dPthContsTotls[x])),Decimal(dPthContsTmp[x]),x) for x in dPthContsTotls]
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106 tabllfreqs='\n'.join(rankd(ltfreqs))
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107 salef=open(outputf,'w')
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108 salef.write(tabllfreqs)
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109 salef.close()
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110 return 0
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111
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112
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113 if __name__ == '__main__':
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114 main()
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