14 print "peakstoregion: version 1.1"
21 print "usage: python %s peakfile outfile [radius] [chromField] [posField] [labelField] [datafield]" % sys.argv[0]
29 except (IndexError, ValueError):
33 chromField = int(argv[4])
34 except (IndexError, ValueError):
38 posField = int(argv[5])
39 except (IndexError, ValueError):
43 labelField = int(argv[6])
44 except (IndexError, ValueError):
48 dataField = int(argv[7])
49 except (IndexError, ValueError):
52 peakstoregion(peakfile, outfile, radius, chromField, posField, labelField, dataField)
55 def peakstoregion(peakfilename, outfilename, radius=500, chromField=2, posField=3, labelField=1, dataField=-1):
56 peakfile = open(peakfilename)
57 outfile = open(outfilename, "w")
60 fields = line.strip().split()
63 label = fields[labelField]
67 start = int(fields[posField]) - radius
68 stop = int(fields[posField]) + radius
69 outfile.write("%s\t%s\t%d\t%d\t%s\n" % (label, fields[chromField], start, stop, fields[dataField]))
74 if __name__ == "__main__":