intersects.py

   1 #
   2 #  intersects.py
   3 #  ENRAGE
   4 #
   5
   6 import sys
   7 import optparse
   8 from commoncode import getConfigParser, getConfigOption, getConfigBoolOption, getConfigIntOption
   9
  10 print "intersects: version 2.1"
  11
  12 def main(argv=None):
  13     if not argv:
  14         argv = sys.argv
  15
  16     usage = "usage: python %prog infile1 infile2 outfile [options]"
  17
  18     parser = getParser(usage)
  19     (options, args) = parser.parse_args(argv[1:])
  20
  21     if len(args) < 3:
  22         print usage
  23         sys.exit(1)
  24
  25     infile1 = args[0]
  26     infile2 = args[1]
  27     outfile = args[2]
  28
  29     intersects(infile1, infile2, outfile, options.delimiter, options.infile3,
  30                options.matchField1, options.matchField2, options.matchField3,
  31                options.rejectFileName, options.trackGID)
  32
  33
  34 def getParser(usage):
  35     parser = optparse.OptionParser(usage=usage)
  36     parser.add_option("-d", dest="delimiter")
  37     parser.add_option("--file3", dest="infile3")
  38     parser.add_option("-1", type="int", dest="matchfield1")
  39     parser.add_option("-2", type="int", dest="matchfield2")
  40     parser.add_option("-3", type="int", dest="matchfield3")
  41     parser.add_option("-reject1", dest="reject1file")
  42     parser.add_option("-trackGID", action="store_true", dest="trackGID")
  43
  44     configParser = getConfigParser()
  45     section = "geneMrnaCountsWeighted"
  46     delimiter = getConfigOption(configParser, section, "delimiter", "\t")
  47     infile3 = getConfigOption(configParser, section, "infile3", None)
  48     matchField1 = getConfigIntOption(configParser, section, "matchField1", 0)
  49     matchField2 = getConfigIntOption(configParser, section, "matchField2", 0)
  50     matchField3 = getConfigIntOption(configParser, section, "matchField3", 0)
  51     rejectFileName = getConfigOption(configParser, section, "rejectFileName", "\t")
  52     trackGID = getConfigBoolOption(configParser, section, "trackGID", False)
  53
  54     parser.set_defaults(delimiter=delimiter, infile3=infile3, matchField1=matchField1, matchField2=matchField2,
  55                         matchField3=matchField3, rejectFileName=rejectFileName, trackGID=trackGID)
  56
  57     return parser
  58
  59
  60 def intersects(infile1Name, infile2Name, outfileName, delimiter="\t", infile3Name=None,
  61                matchField1=0, matchField2=0, matchField3=0, rejectFileName="", trackGID=False):
  62
  63     if rejectFileName:
  64         doReject1 = True
  65         reject1file = open(rejectFileName)
  66     else:
  67         doReject1 = False
  68
  69     if infile3Name is not None:
  70         doFile3 = True
  71     else:
  72         doFile3 = False
  73
  74     matchedList = []
  75     matchedList12 = []
  76     matchedList13 = []
  77     matchedList23 = []
  78     gidDict = {}
  79
  80     if trackGID:
  81         gidKeys = gidDict.keys()
  82         list1, fileGIDDict = getCandidatesAndGIDFromFile(infile1Name, delimiter, matchField1, gidKeys)
  83         for entry in fileGIDDict.keys():
  84             gidDict[entry] = fileGIDDict[entry]
  85
  86         gidKeys = gidDict.keys()
  87         list2, fileGIDDict = getCandidatesAndGIDFromFile(infile2Name, delimiter, matchField2, gidKeys)
  88         for entry in fileGIDDict.keys():
  89             gidDict[entry] = fileGIDDict[entry]
  90
  91         if doFile3:
  92             gidKeys = gidDict.keys()
  93             list3, fileGIDDict = getCandidatesAndGIDFromFile(infile3Name, delimiter, matchField3, gidKeys)
  94             for entry in fileGIDDict.keys():
  95                 gidDict[entry] = fileGIDDict[entry]
  96     else:
  97         list1 = getCandidateListFromFile(infile1Name, delimiter, matchField1)
  98         list2 = getCandidateListFromFile(infile2Name, delimiter, matchField2)
  99         if doFile3:
 100             list3 = getCandidateListFromFile(infile3Name, delimiter, matchField3)
 101
 102     for candidate in list1:
 103         if doFile3 and candidate in list2 and candidate in list3:
 104             matchedList.append(candidate)
 105         elif doFile3 and candidate in list3:
 106             matchedList13.append(candidate)
 107         elif doFile3 and candidate in list2:
 108             matchedList12.append(candidate)
 109         elif not doFile3 and candidate in list2:
 110             matchedList.append(candidate)
 111         elif doReject1:
 112             if trackGID:
 113                 reject1file.write("%s%s%s\n" % (candidate, delimiter, gidDict[candidate]))
 114             else:
 115                 reject1file.write("%s\n" % candidate)
 116
 117     if doFile3:
 118         for candidate in list2:
 119             if candidate not in list1 and candidate in list3:
 120                 matchedList23.append(candidate)
 121
 122     print len(list1), len(list2), len(list3)
 123     if doFile3:
 124         print len(matchedList12), len(matchedList13), len(matchedList23)
 125     print len(matchedList)
 126
 127     outfile = open(outfileName, "w")
 128     for match in matchedList:
 129         if trackGID:
 130             outfile.write("%s%s%s\n" % (match, delimiter, gidDict[match]))
 131         else:
 132             outfile.write("%s\n" % match)
 133
 134     outfile.close()
 135
 136
 137 def getCandidatesFromFile(filename, delimiter, matchField, trackGID=False, gidList=[]):
 138     infile = open(filename)
 139     candidateList = []
 140     gidDict = {}
 141
 142     for line in infile:
 143         if line[0] == "#":
 144             continue
 145
 146         fields = line.strip().split(delimiter)
 147         candidate = fields[matchField]
 148         if candidate not in candidateList:
 149             candidateList.append(candidate)
 150
 151         if trackGID and candidate not in gidList:
 152             gidDict[candidate] = fields[matchField + 1]
 153
 154     infile.close()
 155     return candidateList, gidDict
 156
 157
 158 def getCandidatesAndGIDFromFile(filename, delimiter, matchField, gidList=[]):
 159     return getCandidatesFromFile(filename, delimiter, matchField, trackGID=True, gidList=[])
 160
 161
 162 def getCandidateListFromFile(filename, delimiter, matchField):
 163     candidateList, gidDict = getCandidatesFromFile(filename, delimiter, matchField)
 164     return candidateList
 165
 166
 167 if __name__ == "__main__":
 168     main(sys.argv)