Mercurial > repos > miller-lab > genome_diversity

annotate rank_pathways_pct.py @ 22:95a05c1ef5d5

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update to devshed revision aaece207bd01
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 11 Mar 2013 11:28:06 -0400
parents
children 8997f2ca8c7a
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22
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Richard Burhans <burhans@bx.psu.edu>
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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 from fisher import pvalue
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27
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28 #method to rank the the pthways by mut. freq.
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29 def rankd(ltfreqs):
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30 ordvals=sorted(ltfreqs)#sort and reverse freqs.
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31 #~
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32 outrnk=[]
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33 tmpFreq0,tmpCount,pval,tmpPthw=ordvals.pop()#the highest possible value
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34 crank=1
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35 outrnk.append('\t'.join([str(tmpCount),str(tmpFreq0),str(crank),str(pval),tmpPthw]))
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36 totalnvals=len(ordvals)
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37 cnt=0
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38 while totalnvals>cnt:
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39 cnt+=1
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40 tmpFreq,tmpCount,pval,tmpPthw=ordvals.pop()
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41 if tmpFreq!=tmpFreq0:
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42 crank=len(outrnk)+1
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43 tmpFreq0=tmpFreq
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44 outrnk.append('\t'.join([str(tmpCount),str(tmpFreq),str(crank),str(pval),tmpPthw]))
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45 return outrnk
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46
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47
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48 def main():
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49 parser = argparse.ArgumentParser(description='Obtain KEGG images from a list of genes.')
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50 parser.add_argument('--input',metavar='input TXT file',type=str,help='the input file with the table in txt format')
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51 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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52 parser.add_argument('--posKEGGclmn',metavar='column number',type=int,help='the column with the KEGG pathway code/name')
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53 parser.add_argument('--KEGGgeneposcolmn',metavar='column number',type=int,help='column with the KEGG gene code')
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54 parser.add_argument('--loc_file',metavar='location file',type=str,help='location file')
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55 parser.add_argument('--species',metavar='species',type=str,help='species')
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56 #~Open arguments
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57 class C(object):
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58 pass
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59 fulargs=C()
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60 parser.parse_args(sys.argv[1:],namespace=fulargs)
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61 #test input vars
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62 inputf,outputf,posKEGGclmn,Kgeneposcolmn=fulargs.input,fulargs.output,fulargs.posKEGGclmn,fulargs.KEGGgeneposcolmn
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63 locf,species=fulargs.loc_file,fulargs.species
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64 #make a dictionary of valid genes
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65 posKEGGclmn-=1
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66 Kgeneposcolmn-=1
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67 dKEGGcPthws=dict([(x.split('\t')[Kgeneposcolmn],set(x.split('\t')[posKEGGclmn].split('.'))) for x in open(inputf).read().splitlines()[1:] if x.split('\t')[posKEGGclmn] not in set(['U','N'])])
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68 for u in ['U','N']:
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69 try:
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70 a=dKEGGcPthws.pop(u)
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71 except:
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72 pass
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73 getcontext().prec=2#set 2 decimal places
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74 sdGenes=set([x for x in dKEGGcPthws.keys() if x.find('.')>-1])
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75 while True:#to correct names with more than one gene
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76 try:
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Richard Burhans <burhans@bx.psu.edu>
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77 mgenes=sdGenes.pop()
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78 pthwsAssotd=dKEGGcPthws.pop(mgenes)
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79 mgenes=mgenes.split('.')
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80 for eachg in mgenes:
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81 dKEGGcPthws[eachg]=pthwsAssotd
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82 except:
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83 break
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84 #~ Count genes
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85
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86 location_file = LocationFile(locf)
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87 prefix, kxml_dir_path, dict_file = location_file.get_values(species)
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88 dPthContsTotls = {}
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89 try:
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90 with open(dict_file) as fh:
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91 for line in fh:
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92 line = line.rstrip('\r\n')
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93 value, key = line.split('\t')
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94 dPthContsTotls[key] = int(value)
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95 except IOError, err:
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96 print >> sys.stderr, 'Error opening dict file {0}: {1}'.format(dict_file, err.strerror)
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97 sys.exit(1)
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98
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99 dPthContsTmp=dict([(x,0) for x in dPthContsTotls.keys()])#create a list of genes
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100 sdGenes=set(dKEGGcPthws.keys())#list of all genes
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101 cntGens=0
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102 ltGens=len(sdGenes)
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103 while cntGens<ltGens:
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104 cGen=sdGenes.pop()
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105 sKEGGcPthws=dKEGGcPthws.pop(cGen)
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106 for eachP in sKEGGcPthws:
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107 if eachP!='N':
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108 if eachP in dPthContsTmp:
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109 dPthContsTmp[eachP]+=1
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110 else:
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111 print >> sys.stderr, "Error: pathway not found in database: '{0}'".format(eachP)
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112 sys.exit(1)
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113 cntGens+=1
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114 #~ Calculate Freqs.
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115 ltfreqs=[]
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116 cntAllKEGGinGnm=sum(dPthContsTotls.values())
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117 cntListKEGGinGnm=sum(dPthContsTmp.values())
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118 cntAllKEGGNOTinGnm=cntAllKEGGinGnm-cntListKEGGinGnm
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119 for pthw in dPthContsTotls:
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120 cntAllKEGGinpthw=Decimal(dPthContsTotls[pthw])
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121 try:
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122 cntListKEGGinpthw=Decimal(dPthContsTmp[pthw])
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123 except:
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124 cntListKEGGinpthw=Decimal('0')
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125 cntAllKEGGNOTinpthw=cntAllKEGGinpthw-cntListKEGGinpthw
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126 pval=pvalue(cntListKEGGinpthw,cntAllKEGGNOTinpthw,cntListKEGGinGnm,cntAllKEGGNOTinGnm)
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127
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128 ltfreqs.append([(cntListKEGGinpthw/cntAllKEGGinpthw),cntListKEGGinpthw,Decimal(str(pval.two_tail))*1,pthw])
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129 #~ ltfreqs=[((Decimal(dPthContsTmp[x])/Decimal(dPthContsTotls[x])),Decimal(dPthContsTmp[x]),x) for x in dPthContsTotls]
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130 tabllfreqs='\n'.join(rankd(ltfreqs))
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Richard Burhans <burhans@bx.psu.edu>
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131 salef=open(outputf,'w')
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132 salef.write(tabllfreqs)
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Richard Burhans <burhans@bx.psu.edu>
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133 salef.close()
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Richard Burhans <burhans@bx.psu.edu>
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134 return 0
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135
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136
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137 if __name__ == '__main__':
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138 main()