Region.py

   1 import string
   2
   3 class Region(object):
   4     """
   5         Region description
   6     """
   7
   8
   9     def __init__(self, start, stop, label="", index=0, chrom="", numReads=0., foldRatio=0., multiP=0., peakDescription="", shift=0, peakPos=0, peakHeight=0):
  10         self.label = label
  11         self.index = index
  12         self.chrom = chrom
  13         self.start = start
  14         self.stop = stop
  15         self.numReads = numReads
  16         self.foldRatio = foldRatio
  17         self.multiP = multiP
  18         self.peakDescription = peakDescription
  19         self.shift = shift
  20         self.length = abs(self.stop - self.start)
  21         self.peakPos = peakPos
  22         self.peakHeight = peakHeight
  23
  24
  25     def printRegion(self, delimiter="\t"):
  26         fields = ["%s%d" % (self.label, self.index),
  27                   "%s" % self.chrom,
  28                   "%d" % self.start,
  29                   "%d" % self.stop,
  30                   "%.1f" % self.numReads,
  31                   "%.1f" % self.foldRatio,
  32                   "%.1f" % self.multiP,
  33                   "%s" % self.peakDescription
  34         ]
  35
  36         return string.join(fields, delimiter)
  37
  38
  39     def printRegionWithShift(self, delimiter="\t"):
  40         fields = [self.printRegion(delimiter)]
  41         fields.append("%d" % self.shift)
  42
  43         return string.join(fields, delimiter)
  44
  45
  46 class DirectionalRegion(Region):
  47     """
  48         Region with percentage of plus reads.
  49     """
  50
  51     def __init__(self, start, stop, label="", index=0, chrom="", numReads=0, foldRatio=0., multiP=0., plusP=0., leftP=0., peakDescription="", shift=0):
  52         Region.__init__(self, start, stop, label, index, chrom, numReads, foldRatio, multiP, peakDescription, shift)
  53         self.plusP = plusP
  54         self.leftP = leftP
  55
  56
  57     def printRegion(self, delimiter="\t"):
  58         fields = ["%s%d" % (self.label, self.index),
  59                   "%s" % self.chrom,
  60                   "%d" % self.start,
  61                   "%d" % self.stop,
  62                   "%.1f" % self.numReads,
  63                   "%.1f" % self.foldRatio,
  64                   "%.1f" % self.multiP,
  65                   "%.1f" % self.plusP,
  66                   "%.1f" % self.leftP,
  67                   "%s" % self.peakDescription
  68         ]
  69
  70         return string.join(fields, delimiter)