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annotate cluster_onConnctdComps.py @ 32:03c22b722882

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remove BeautifulSoup dependency
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 20 Sep 2013 13:54:23 -0400
parents a631c2f6d913
children
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31
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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 # Cluster_GOKEGG.py
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5 #
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6 # Copyright 2013 Oscar 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
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24 import os
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25 from networkx import connected_components,Graph,clustering
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26 from numpy import percentile
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27 from decimal import Decimal,getcontext
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28 from itertools import permutations,combinations
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29 import sys
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30
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31 def rtrnClustrsOnCltrCoff(dNodesWeightMin,threshold,perctile=True):
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32 """
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33 From a file with three columns: nodeA, nodeB and a score, it returns
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34 the strong and weak connected components produced when the edges
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35 below the percentage threshold (or value) are excluded.
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36 """
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37 #~
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38 Gmin = Graph()
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39 for nodeA,nodeB in dNodesWeightMin:
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40 wMin=dNodesWeightMin[nodeA,nodeB]
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41 Gmin.add_edge(nodeA,nodeB,weight=wMin)
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42 #~
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43 clstrCoffcMin=clustering(Gmin,weight='weight')
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44 #~
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45 if perctile:
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46 umbralMin=percentile(clstrCoffcMin.values(),threshold)
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47 else:
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48 umbralMin=threshold
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49 #~
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50 GminNdsRmv=[x for x in clstrCoffcMin if clstrCoffcMin[x]<umbralMin]
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51 #~
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52 Gmin.remove_nodes_from(GminNdsRmv)
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53 #~
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54 dTermCmptNumbWkMin=rtrndata(Gmin)
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55 #~
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56 salelClustr=[]
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57 srtdterms=sorted(dTermCmptNumbWkMin.keys())
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58 for echTerm in srtdterms:
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59 try:
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60 MinT=dTermCmptNumbWkMin[echTerm]
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61 except:
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62 MinT='-'
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63 salelClustr.append('\t'.join([echTerm,MinT]))
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64 #~
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65 return salelClustr
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66
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67 def rtrndata(G):
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68 """
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69 returna list of terms and its clustering, as well as clusters from
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70 a networkx formatted file.
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71 """
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72 #~
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73 cntCompnts=0
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74 dTermCmptNumbWk={}
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75 for echCompnt in connected_components(G):
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76 cntCompnts+=1
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77 #print '.'.join(echCompnt)
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78 for echTerm in echCompnt:
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79 dTermCmptNumbWk[echTerm]=str(cntCompnts)
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80 #~
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81 return dTermCmptNumbWk
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82
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83 def rtrnCATcENSEMBLc(inCATfile,classClmns,ENSEMBLTcolmn,nonHdr=True):
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84 """
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85 return a dictionary of all the categories in an input file with
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86 a set of genes. Takes as input a file with categories an genes.
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87 """
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88 dCAT={}
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89 dENSEMBLTCAT={}
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90 for eachl in open(inCATfile,'r'):
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91 if nonHdr and eachl.strip():
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92 ENSEMBLT=eachl.splitlines()[0].split('\t')[ENSEMBLTcolmn]
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93 sCAT=set()
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94 for CATcolmn in classClmns:
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95 sCAT.update(set([x for x in eachl.splitlines()[0].split('\t')[CATcolmn].split('.')]))
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96 sCAT=sCAT.difference(set(['','U','N']))
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97 if len(sCAT)>0:
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98 dENSEMBLTCAT[ENSEMBLT]=sCAT
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99 for CAT in sCAT:
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100 try:
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101 dCAT[CAT].add(ENSEMBLT)
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102 except:
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103 dCAT[CAT]=set([ENSEMBLT])
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104 nonHdr=True
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105 #~
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106 dCAT=dict([(x,len(dCAT[x])) for x in dCAT.keys()])
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107 #~
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108 return dCAT,dENSEMBLTCAT
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109
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110
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111 def calcDistance(sCAT1,sCAT2):
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112 """
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113 takes as input two set of genesin different categories and returns
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114 a value 1-percentage of gene shared cat1->cat2, and cat2->cat1.
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115 """
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116 getcontext().prec=5
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117 lgensS1=Decimal(len(sCAT1))
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118 lgensS2=Decimal(len(sCAT2))
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119 shrdGns=sCAT1.intersection(sCAT2)
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120 lenshrdGns=len(shrdGns)
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121 #~
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parents:
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122 dC1C2=1-(lenshrdGns/lgensS1)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
123 dC2C1=1-(lenshrdGns/lgensS2)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
124 #~
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
125 return dC1C2,dC2C1
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
126
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
127 def rtnPrwsdtncs(dCAT,dENSEMBLTCAT):
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
128 """
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
129 return a mcl formated pairwise distances from a list of categories
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
130 """
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
131 #~
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
132 getcontext().prec=5
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
133 dCATdst={}
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
134 lENSEMBL=dENSEMBLTCAT.keys()
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
135 l=len(lENSEMBL)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
136 c=0
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
137 for ENSEMBL in lENSEMBL:
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
138 c+=1
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
139 lCAT=dENSEMBLTCAT.pop(ENSEMBL)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
140 for CAT1,CAT2 in combinations(lCAT, 2):
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
141 try:
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
142 dCATdst[CAT1,CAT2]+=1
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
143 except:
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
144 dCATdst[CAT1,CAT2]=1
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
145 try:
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
146 dCATdst[CAT2,CAT1]+=1
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
147 except:
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
148 dCATdst[CAT2,CAT1]=1
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
149 #~
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
150 dNodesWeightMin={}
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
151 l=len(dCATdst)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
152 for CAT1,CAT2 in dCATdst.keys():
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
153 shrdGns=dCATdst.pop((CAT1,CAT2))
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
154 dC1C2=float(shrdGns)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
155 nodeA,nodeB=sorted([CAT1,CAT2])
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
156 try:
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
157 cscor=dNodesWeightMin[nodeA,nodeB]
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
158 if cscor>=dC1C2:
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
159 dNodesWeightMin[nodeA,nodeB]=dC1C2
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
160 except:
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
161 dNodesWeightMin[nodeA,nodeB]=dC1C2
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
162 #
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
163 return dNodesWeightMin
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
164
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
165 def parse_class_columns(val, max_col):
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
166 int_list = []
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
167
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
168 for elem in [x.strip() for x in val.split(',')]:
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
169 if elem[0].lower() != 'c':
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
170 print >> sys.stderr, "bad column format:", elem
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
171 sys.exit(1)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
172
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
173 int_val = as_int(elem[1:])
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
174
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
175 if int_val is None:
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
176 print >> sys.stderr, "bad column format:", elem
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
177 sys.exit(1)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
178 elif not 1 <= int_val <= max_col:
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
179 print >> sys.stderr, "column out of range:", elem
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
180 sys.exit(1)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
181
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
182 int_list.append(int_val - 1)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
183
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
184 return int_list
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
185
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
186 def as_int(val):
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
187 try:
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
188 return int(val)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
189 except ValueError:
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
190 return None
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
191 else:
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
192 raise
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
193
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
194 def main():
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
195 """
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
196 """
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
197 #~ bpython cluster_onConnctdComps.py --input=../conctFinal_CEU.tsv --outfile=../borrar.txt --threshold=90 --ENSEMBLTcolmn=1 --classClmns='20 22'
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
198 parser = argparse.ArgumentParser(description='Returns the count of genes in ...')
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
199 parser.add_argument('--input',metavar='input TXT file',type=str,help='the input file with the table in txt format.',required=True)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
200 parser.add_argument('--input_columns',metavar='input INT value',type=int,help='the number of columns in the input file.',required=True)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
201 parser.add_argument('--outfile',metavar='input TXT file',type=str,help='the output file with the connected components.',required=True)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
202 parser.add_argument('--threshold',metavar='input FLOAT value',type=float,help='the threshold to disconnect the nodes.',required=True)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
203 parser.add_argument('--ENSEMBLTcolmn',metavar='input INT file',type=int,help='the column with the ENSEMBLE code in the input.',required=True)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
204 parser.add_argument('--classClmns',metavar='input STR value',type=str,help='the list of columns with the gene categories separated by space.',required=True)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
205 args = parser.parse_args()
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
206 infile = args.input
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
207 threshold = args.threshold
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
208 outfile = args.outfile
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
209 ENSEMBLTcolmn = args.ENSEMBLTcolmn
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
210 classClmns = parse_class_columns(args.classClmns, args.input_columns)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
211 #~
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
212 dCAT,dENSEMBLTCAT=rtrnCATcENSEMBLc(infile,classClmns,ENSEMBLTcolmn)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
213 dNodesWeightMin=rtnPrwsdtncs(dCAT,dENSEMBLTCAT)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
214 salelClustr=rtrnClustrsOnCltrCoff(dNodesWeightMin,threshold)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
215 #~
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
216 with open(outfile, 'w') as salef:
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
217 print >> salef, '\n'.join(salelClustr)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
218 #~
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
219 #~
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
220
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
221 if __name__ == '__main__':
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
222 main()
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
223