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sv_genotype_inv.py
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#!/usr/bin/env python
import argparse, sys
import pysam
from collections import Counter
from argparse import RawTextHelpFormatter
__author__ = "Author ([email protected])"
__version__ = "$Revision: 0.0.1 $"
__date__ = "$Date: 2014-03-19 14:31 $"
# --------------------------------------
# define functions
def get_args():
parser = argparse.ArgumentParser(formatter_class=RawTextHelpFormatter, description="\
sv_genotype.py\n\
author: " + __author__ + "\n\
version: " + __version__ + "\n\
description: Basic python script template")
parser.add_argument('-a', '--regionA', required=True, help='breakpoint region A (chrom:start-end)')
parser.add_argument('-b', '--regionB', required=True, help='breakpoint region B (chrom:start-end)')
parser.add_argument('-c', '--strandA', required=True, help='strand of region A (+ or -)')
parser.add_argument('-d', '--strandB', required=True, help='strand of region B (+ or -)')
parser.add_argument('-i', '--id', required=False, default=1, help='id for the SV')
#parser.add_argument('-c', '--landing', required=False, default=None, help='landing area (chrom:start-end)')
parser.add_argument('-f', '--splflank', type=int, required=False, default=20, help='min number of split read query bases flanking breakpoint on either side [20]')
parser.add_argument('-F', '--discflank', type=int, required=False, default=20, help='min number of discordant read query bases flanking breakpoint on either side [20]')
parser.add_argument('-l', '--readlength', type=int, required=False, default=101, help='max read length in bam file')
parser.add_argument('-z', '--z', type=float, required=False, default=3, help='z-score of inner-span to be considered discordant (default: 3)')
parser.add_argument('-B', '--bam', type=pysam.Samfile, required=True, default=None, help='full bam file for sample')
parser.add_argument('-S', '--splitters', type=pysam.Samfile, required=False, default=None, help='split-read bam file for sample')
parser.add_argument('-D', '--discordants', type=pysam.Samfile, required=False, default=None, help='discordant-read bam file for sample')
parser.add_argument('-v', '--verbose', required=False, action='store_true', help='verbose')
# parse the arguments
args = parser.parse_args()
# send back the user input
return args
# primary function
def sv_genotype(sv_id, regionA, regionB, strandA, strandB, splflank, discflank, readlength, z, bam, splitters, discordants, verbose):
(chromA, pos_stringA) = regionA.split(':')
(startA, endA) = map(int, pos_stringA.split('-'))
(chromB, pos_stringB) = regionB.split(':')
(startB, endB) = map(int, pos_stringB.split('-'))
split_counter = Counter() # counts the number of splitters over each breakpoint
for split_read in splitters.fetch(chromA, startA - 1, endA):
if verbose:
print split_read
#i = split_read.pos + split_read.inferred_length
#print split_read.pos, i, split_read.cigar
if strandA == '+' and split_read.cigar[0][0] == 0: # and split_read.pnext > startB - readlength:
split_counter[split_read.pos + split_read.cigar[0][1]] += 1
elif strandA == '-' and split_read.cigar[-1][0] == 0:
split_counter[split_read.aend - split_read.cigar[-1][1] + 1] += 1
#print split_counter[2911653]
for posA in range(startA, endA + 1):
ref_counter = 0
# make sure these are actually ref
for ref_read in bam.fetch(chromA, posA - 1, posA):
if verbose:
print ref_read
#print ref_read.pos, ref_read.pos + ref_read.inferred_length, ref_read.aend
if not ref_read.is_duplicate and posA - ref_read.pos >= splflank and ref_read.aend - posA >= splflank:
ref_counter += 1
print '\t'.join(map(str, (chromA, posA, ref_counter, split_counter[posA], 'spl_A', sv_id)))
# now do the same over regionB
split_counter = Counter() # counts the number of splitters over each breakpoint
for split_read in splitters.fetch(chromB, startB - 1, endB):
if verbose:
print split_read
#print split_read.positions[-1]
if strandB == '+' and split_read.cigar[0][0] == 0:
split_counter[split_read.pos + split_read.cigar[0][1]] += 1
elif strandB == '-' and split_read.cigar[-1][0] == 0: # and split_read.pnext > startB - readlength:
split_counter[split_read.aend - split_read.cigar[-1][1] + 1] += 1
# maybe use AlignedRead.positions to get the overlap.
# or AlignedRead.overlap
for posB in range(startB, endB + 1):
ref_counter = 0
# make sure these are actually ref
for ref_read in bam.fetch(chromB, posB - 1, posB):
if not ref_read.is_duplicate and posB - ref_read.pos >= splflank and ref_read.aend - posB >= splflank:
ref_counter += 1
print '\t'.join(map(str, (chromB, posB, ref_counter, split_counter[posB], 'spl_B', sv_id)))
#for split_read in splitters.fetch(break_chrom, break_pos - 1, break_pos):
# print split_read.pos + split_read.inferred_length
# now do the spanning coverage over region A
mean_ospan = 320
sd_ospan = 80
mean_ispan = mean_ospan - (2 * discflank)
sd_ispan = 80
ref_span_counter = Counter()
disc_span_counter = Counter()
for read in bam.fetch(chromA, startA - 1 - (mean_ospan + sd_ospan * z), endA + (mean_ospan + sd_ospan * z)):
if not read.is_secondary and not read.is_unmapped and not read.mate_is_unmapped:
if read.tid == read.rnext and strandA == '+' and strandB == '-' and not read.is_reverse and read.mate_is_reverse:
if verbose:
print read
#print read.pos, read.qstart, read.qlen, read.pos - read.qstart
#print read.pos, read.positions[0], read.positions[-1], read.aend
mate = bam.mate(read)
#print mate
#print "MATE", mate.pos, mate.pos - mate.qstart
ispan_left = read.pos + discflank
ispan_right = mate.aend - discflank - 1
ispan = ispan_right - ispan_left
#print ispan_left, ispan_right, ispan
if ispan > 0 and ispan < mean_ispan + sd_ispan * z and read.qlen >= discflank and mate.qlen >= discflank:
#print read
# print ispan
# CHECK FOR 1-OFF PROBLEMS HERE
for posA in range(ispan_left + 1, ispan_right + 1):
ref_span_counter[posA] += 1
# also, maybe don't limit the right side to < endB, but allow it to go some number of stdevs to the right.
elif ispan > 0 and ispan_right + 1 > startB and ispan_right + 1 < endB + (mean_ispan + sd_ispan * z) and read.qlen >= discflank and mate.qlen >= discflank:
if verbose:
print read
#print ispan_left, ispan_right, ispan
#print read.cigar[-1][0]
#print read.alen, read.qlen, read.rlen
for posA in range(ispan_left + 1, ispan_right + 1):
disc_span_counter[posA] += 1
for posA in range(startA, endA + 1):
print '\t'.join(map(str, (chromA, posA, ref_span_counter[posA], disc_span_counter[posA], 'disc_A', sv_id)))
# do the same over region B
ref_span_counter = Counter()
disc_span_counter = Counter()
for read in bam.fetch(chromB, startB - 1 - (mean_ospan + sd_ospan * z), endB + (mean_ospan + sd_ospan * z)):
if read.tid == read.rnext and ((strandA == '+' and not read.mate_is_reverse) or (strandA == '-' and read.mate_is_reverse)) and (strandB == '-' and read.is_reverse and not read.mate_is_reverse:
if verbose:
print read
#print read.pos, read.pos - read.qstart
mate = bam.mate(read)
#print mate
#print "MATE", mate.pos, mate.pos - mate.qstart
ispan_left = mate.pos + discflank
ispan_right = read.aend - discflank - 1
ispan = ispan_right - ispan_left
#print ispan_left, ispan_right, ispan, mate.tlen
if ispan > 0 and ispan < mean_ispan + sd_ispan * z and read.qlen >= discflank and mate.qlen >= discflank:
# print read
# print ispan
# CHECK FOR 1-OFF PROBLEMS HERE
for posB in range(ispan_left + 1, ispan_right + 1):
ref_span_counter[posB] += 1
# also, maybe don't limit the right side to < endB, but allow it to go some number of stdevs to the right.
elif ispan > 0 and ispan_left + 1 > startA - (mean_ispan + sd_ispan *z) and ispan_left + 1 < endA and read.qlen >= discflank and mate.qlen >= discflank:
if verbose:
print read
#print ispan_left, ispan_right, ispan
#print read.cigar[-1][0]
#print read.alen, read.qlen, read.rlen
for posB in range(ispan_left + 1, ispan_right + 1):
disc_span_counter[posB] += 1
for posB in range(startB, endB + 1):
print '\t'.join(map(str, (chromB, posB, ref_span_counter[posB], disc_span_counter[posB], 'disc_B', sv_id)))
def ispan(read, mate,
def ispan(read, readlength):
if not read.is_reverse:
# these are (a,b] intervals
left = read.positions[-1] + 1
right = read.pnext
else:
left = read.pnext + readlength
right = read.positions[0]
return right - left
# --------------------------------------
# main function
def main():
# parse the command line args
args = get_args()
# call primary function
sv_genotype(args.id, args.regionA, args.regionB, args.strandA, args.strandB, args.splflank, args.discflank, args.readlength, args.z, args.bam, args.splitters, args.discordants, args.verbose)
# close the bam files
args.bam.close()
if args.splitters:
args.splitters.close()
if args.discordants:
args.discordants.close()
# initialize the script
if __name__ == '__main__':
sys.exit(main())