def findSamAlignments(samfile,start,end): ret = [0 for x in range(end-start+1)] def lineCheck(line): if line[0] == "@": return #header line pieces = line.split() seqname = pieces[0] pos = int(pieces[3]) testnumber = int(pieces[1]) if testnumber&0x4 == 0x4: pass else: ret[pos-start]+=1 efficientFileRead(samfile,lineCheck) return ret
def findBamAlignments(bamfile,chrom,start,end):
samtoolsViewRegion(bamfile,chrom,start,end,"temp")
alignRange = [start,end]
def rangeCheck(line):
if line[0] == "@":
return #header line
pieces = line.split()
seqname = pieces[0]
ch = pieces[2]
pos = int(pieces[3])
testnumber = int(pieces[1])
if testnumber&0x4 == 0x4:
pass
else:
if pos < alignRange[0]:
alignRange[0] = pos
if pos > alignRange[1]:
alignRange[1] = pos
efficientFileRead("temp",rangeCheck)
def lineCheck(line):
if line[0] == "@":
return #header line
pieces = line.split()
seqname = pieces[0]
ch = pieces[2]
pos = int(pieces[3])
testnumber = int(pieces[1])
if testnumber&0x4 == 0x4:
pass
elif ch == chrom:
ret[pos-start]+=1
ret = [0 for x in range(alignRange[1]-alignRange[0]+1)]
efficientFileRead("temp",lineCheck)
runCommand("rm temp")
return ret
sys.exit()
filename = args[0]
try:
length = int(args[1])
except ValueError:
print "expandBed.py filename length"
print "expecting int value for length"
sys.exit()
def lineParse(line):
split = line.split("\t")
sc = 1
try:
int(split[3])
sc = split[3]
line = bedtools.BEDLine(split[0],split[1],split[2],score = sc)
except:
sc = split[4]
line = bedtools.BEDLine(split[0],split[1],split[2],split[3],score = sc)
print line.chrom + "\t" + str(line.start) + "\t" + str(line.end+length) + "\t" + line.name + "\t" + str(line.score) + "\t" + line.strand
efficientFileRead(filename,lineParse)
#lines = bedtools.BEDFile(filename).lines
#for line in lines:
# for i in range(line.start,line.end+1):
# print line.chrom + "\t" + str(i) + "\t" + str(i+length) + "\t" + line.name + "\t" + line.score + "\t" + line.strand