def sniffBed(path):
scoreNames = set()
bedRegions = []
tempfile = open(path, 'r')
for line in tempfile:
line = bedLine(line.split())
if not hasattr(line,'name') or not hasattr(line,'score'):
continue
bedRegions.append(line)
scoreNames.add(line.name)
tempfile.close()
return (scoreNames,bedRegions)
def __init__(self, line):
temp = bedLine(line)
self.chromosome = temp.chromosome
self.start = temp.start
def run(args):
infile = open(args.infile, "r")
outfile = open(args.outfile, "w")
failfile = None
if args.failfile != "":
failfile = open(args.failfile, "w")
errfile = None
if args.errfile != "":
errfile = open(args.errfile, "w")
if args.expression != "":
tempfile = open(args.expression, "r")
expression = tempfile.readline()
tempfile.close()
else:
expression = "True"
columns = []
if args.columns != "":
tempfile = open(args.columns, "r")
for line in tempfile:
line = line.strip()
columns.append(line)
tempfile.close()
bedRegions = None
if args.bed != "":
bedRegions = []
tempfile = open(args.bed, "r")
for line in tempfile:
bedRegions.append(bedLine(line.split()))
tempfile.close()
for line in infile:
if len(line) <= 1:
continue
elif line.startswith("#"):
outfile.write(line)
if failfile != None:
failfile.write(line)
if errfile != None:
errfile.write(line)
continue
else:
line = vcfLine(line.strip().split("\t"))
expArgs = []
for c in columns:
if c == "CHROM":
line.extractChrAndPos()
expArgs.append(line.chromosome)
elif c == "POS":
line.extractChrAndPos()
expArgs.append(line.position)
elif c == "ID":
line.extractChrAndPos()
expArgs.append(line.name)
elif c == "QUAL":
line.extractQual()
expArgs.append(line.qual)
elif c == "FILTER":
line.extractFilters()
expArgs.append(line.filters)
else:
line.extractInfo()
expArgs.append(line.info.get(c, "."))
# first see if it fails the .bed regions
if bedRegions != None:
passedBed = False
line.extractChrAndPos()
for bed in bedRegions:
if bed.contains(line.chromosome, line.position):
passedBed = True
break
if not passedBed:
if failfile != None:
failfile.write(str(line))
continue
exp = expression % tuple(expArgs)
try:
result = eval(exp)
if result == True:
outfile.write(str(line))
elif result == False:
if failfile != None:
failfile.write(str(line))
else:
if errfile != None:
errfile.write(str(line))
except:
if errfile != None:
errfile.write(str(line))
infile.close()
outfile.close()
if errfile != None:
errfile.close()
def __init__(self, line):
temp = bedLine(line)
self.chromosome = temp.chromosome
self.start = temp.start
