splitterToBreakpointExt

#!/usr/bin/python

import sys
from optparse import OptionParser
import os

def splitterToBreakpoint(contigFile,splitReadSlop,localRange):
#Define whether event is inv, del, or dup (classifying translocations as if they were local intrachromosomal events)
    if contigFile == "stdin":
        contigs = sys.stdin
    else:
        contigs = open(str(contigFile))
    for line in contigs:
        split = line.split()       
        if (split[0] > split[3]) or ((split[0] == split[3]) and (int(split[1]) > int(split[4]))):
            chrom1 = split[3]
            start1 = int(split[4])
            end1 = int(split[5])
            chrom2 = split[0]
            start2 = int(split[1])
            end2 = int(split[2])
            ID = split[6]
            score = int(split[7])
            strand1 = split[9]
            strand2 = split[8]
            queryStart1 = int(split[12])
            queryEnd1 = int(split[13])
            queryStart2 = int(split[10])
            queryEnd2 = int(split[11])
            minNonOverlap = int(split[14])
            queryLength = int(split[15])
            if len(split) > 16: qualScores = split[16]
            else: qualScores = '*'

        else:
            chrom1 = split[0]
            start1 = int(split[1])
            end1 = int(split[2])
            chrom2 = split[3]
            start2 = int(split[4])
            end2 = int(split[5])
            ID = split[6]
            score = int(split[7])
            strand1 = split[8]
            strand2 = split[9]
            queryStart1 = int(split[10])
            queryEnd1 = int(split[11])
            queryStart2 = int(split[12])
            queryEnd2 = int(split[13])         
       	    minNonOverlap = int(split[14])
       	    queryLength = int(split[15])
            if len(split) > 16: qualScores = split[16]
            else: qualScores = '*'
        
        if strand1 != strand2: #Classifying Inversions
            if chrom1  == chrom2 and abs(end2 - start1) <= localRange:
                variant = "local_inversion"
            else:
                variant = "distant_inversion"
        elif ((strand1=="+" and strand2=="+" and queryStart1 < queryStart2) or (strand1=="-" and strand2=="-" and queryStart1 > queryStart2)): #Classifying Deletions
            if chrom1  == chrom2 and (end2 - start1) <= localRange:
                variant = "local_deletion"
            else:
                variant = "distant_deletion"
        elif ((strand1=="+" and strand2=="+" and queryStart1 > queryStart2) or (strand1=="-" and strand2=="-" and queryStart1 < queryStart2)): #Classifying Tandem Duplications
            if chrom1  == chrom2 and (end2 - start1) <= localRange:
                variant = "local_duplication"
            else:
                variant = "distant_duplication"
        else:
            print "ERROR: variant " + ID + " is lost in variant classification step. Contact Mitchell"
        if variant == "local_inversion" or variant == "distant_inversion":
            if ((queryStart1 < queryStart2) and (strand1 == "-") and (strand2 == "+")) or ((queryStart1 > queryStart2) and (strand1 == "+") and (strand2 == "-")):
                breakStart1 = str(start1-splitReadSlop)
                breakEnd1 = str(start1+splitReadSlop)
                breakStart2 = str(start2-splitReadSlop) 
                breakEnd2 = str(start2+splitReadSlop)
            elif ((queryStart1 < queryStart2) and (strand1 == "+") and (strand2 == "-")) or ((queryStart1 > queryStart2) and (strand1 == "-") and (strand2 == "+")):
                breakStart1 = str(end1-splitReadSlop)
                breakEnd1 = str(end1+splitReadSlop)
                breakStart2 = str(end2-splitReadSlop)
                breakEnd2 = str(end2+splitReadSlop)
        elif variant == "local_deletion" or variant == "distant_deletion":
            breakStart1 = str(end1-splitReadSlop)
            breakEnd1 = str(end1+splitReadSlop)
            breakStart2 = str(start2-splitReadSlop)
            breakEnd2 = str(start2+splitReadSlop)
        elif variant == "local_duplication" or variant == "distant_duplication":
            breakStart1 = str(start1-splitReadSlop)
            breakEnd1 = str(start1+splitReadSlop)
            breakStart2 = str(end2-splitReadSlop)
            breakEnd2 = str(end2+splitReadSlop)
        else:
            print "ERROR: " + ID + " is lost in breakpoint locus prediction step. Contact Mitchell"
        print '\t'.join(map(str, [chrom1, breakStart1, breakEnd1, chrom2, breakStart2, breakEnd2, ID, score, strand1, strand2, queryStart1, queryEnd1, queryStart2, queryEnd2, minNonOverlap, queryLength, qualScores, variant]))
    
def main():
    usage = "%prog -b <bedpe> -c <contigFile.bedpe> [options]\nVersion: 0.1\nAuthor: Mitchell L. Leibowitz\nEdited: 25 Aug, 2010\n\n\
Note: Add slop at your own risk.\n\nPrints modified bedpe so bedpe entry 1 is always less than bedpe entry 2"
    parser = OptionParser(usage)
    parser.add_option("-i", dest="contigFile", metavar="FILE", help="BEDPE file containing the split contigs; requires 10 column bedpe plus 11-14 as query coordinates")
    parser.add_option("-s", dest="splitReadSlop", metavar="INT", type="int", default=1, help="Bidirectional slop around the breakpoint [default = 1]")
    parser.add_option("-r", dest="localRange", default=1000000, type="int", metavar="INT", help="the range of coordinates considered local (for breakpoint classification) [default = 1000000]; Calculated by subtracting field 6 from field 2.")
    
    (opts, args) = parser.parse_args()

    if opts.contigFile is None:
        parser.print_help()
        print
    else:
        splitterToBreakpoint(opts.contigFile, opts.splitReadSlop, opts.localRange)
   
if __name__ == "__main__":
        sys.exit(main())