def parseBreaksLineNew(line, breakends):
items = line.strip().split()
if float(items[8]) < 0:
return
coords = items[0].split(':')
chr = coords[0]
if chr[:3] != "chr":
chr = "chr" + chr
pos = map(int, coords[1].split('-'))
breakend = Breakend(chr, min(pos), items[2] == '-', "BND" + str(len(breakends)) + ":" + items[0] + ":" + items[1], finish=max(pos))
breakend.mates = [None]
coords2 = items[1].split(':')
chr2 = coords2[0]
if chr2[:3] != "chr":
chr2 = "chr" + chr2
pos2 = map(int, coords2[1].split('-'))
breakend.remoteChr = [chr2]
breakend.remoteStart = [min(pos2)]
breakend.remoteFinish = [max(pos2)]
breakend.remoteOrientation = [items[3] == '-']
breakend.adjacency_cov = [-1, float(items[5])]
breakend.germline = (items[4] == 'germline')
breakends.append(breakend)
def parseBreaksLineTabbed(line, breakends): items = line.strip().split() if float(items[8]) < 0: assert False return chr = items[0] if chr[:3] != "chr": chr = "chr" + chr leftCoords = chr + ":" + items[4] + "-" + items[5] chr2 = items[6] if chr2[:3] != "chr": chr2 = "chr" + chr2 rightCoords = chr2 + ":" + items[7] + "-" + items[8] breakend = Breakend(chr, int(items[4]), items[9] == '-', "BND" + str(len(breakends)) + ":" + leftCoords + ":" + rightCoords, finish=int(items[5])) breakend.mates = [None] breakend.remoteChr = [chr2] breakend.remoteStart = [int(items[7])] breakend.remoteFinish = [int(items[8])] breakend.remoteOrientation = [items[10] == '-'] breakend.adjacency_cov = [-1, float(items[11])] breakend.germline = False breakends.append(breakend)
def parseBreaksLineNew(line, breakends):
items = line.strip().split()
if float(items[8]) < 0:
return
coords = items[0].split(':')
chr = coords[0]
if chr[:3] != "chr":
chr = "chr" + chr
pos = map(int, coords[1].split('-'))
breakend = Breakend(chr,
min(pos),
items[2] == '-',
"BND" + str(len(breakends)) + ":" + items[0] + ":" +
items[1],
finish=max(pos))
breakend.mates = [None]
coords2 = items[1].split(':')
chr2 = coords2[0]
if chr2[:3] != "chr":
chr2 = "chr" + chr2
pos2 = map(int, coords2[1].split('-'))
breakend.remoteChr = [chr2]
breakend.remoteStart = [min(pos2)]
breakend.remoteFinish = [max(pos2)]
breakend.remoteOrientation = [items[3] == '-']
breakend.adjacency_cov = [-1, float(items[5])]
breakend.germline = (items[4] == 'germline')
breakends.append(breakend)
def parseBreaksLine(line, breakends):
items = line.strip().split()
if float(items[11]) < 0:
return
if items[0][:3] != "chr":
items[0] = "chr" + items[0]
breakend = Breakend(items[0],
items[1],
items[3] == '-',
"BND" + str(len(breakends)) + ":" + items[0] + ":" +
items[1] + items[3] + ">>" + items[4] + ":" +
items[5] + items[7],
finish=int(items[2]))
breakend.mates = [None]
if items[4][:3] != "chr":
items[4] = "chr" + items[4]
breakend.remoteChr = [items[4]]
breakend.remoteStart = [int(items[5])]
breakend.remoteFinish = [int(items[6])]
breakend.remoteOrientation = [items[7] == '-']
breakend.germline = (items[8] == 'GERMLINE')
breakend.adjacency_cov = [-1, float(items[9])]
breakends.append(breakend)
def parseBreaksLineTabbed(line, breakends):
items = line.strip().split()
if float(items[8]) < 0:
assert False
return
chr = items[0]
if chr[:3] != "chr":
chr = "chr" + chr
leftCoords = chr + ":" + items[4] + "-" + items[5]
chr2 = items[6]
if chr2[:3] != "chr":
chr2 = "chr" + chr2
rightCoords = chr2 + ":" + items[7] + "-" + items[8]
breakend = Breakend(chr,
int(items[4]),
items[9] == '-',
"BND" + str(len(breakends)) + ":" + leftCoords + ":" +
rightCoords,
finish=int(items[5]))
breakend.mates = [None]
breakend.remoteChr = [chr2]
breakend.remoteStart = [int(items[7])]
breakend.remoteFinish = [int(items[8])]
breakend.remoteOrientation = [items[10] == '-']
breakend.adjacency_cov = [-1, float(items[11])]
breakend.germline = False
breakends.append(breakend)
def parseBreaksLine(line, breakends): items = line.strip().split() if float(items[11]) < 0: return if items[0][:3] != "chr": items[0] = "chr" + items[0] breakend = Breakend(items[0], items[1], items[3] == '-', "BND" + str(len(breakends)) + ":" + items[0] + ":" + items[1] + items[3] + ">>" + items[4] + ":" + items[5] + items[7], finish=int(items[2])) breakend.mates = [None] if items[4][:3] != "chr": items[4] = "chr" + items[4] breakend.remoteChr = [items[4]] breakend.remoteStart = [int(items[5])] breakend.remoteFinish = [int(items[6])] breakend.remoteOrientation = [items[7] == '-'] breakend.germline = (items[8] == 'GERMLINE') breakend.adjacency_cov = [-1, float(items[9])] breakends.append(breakend)
