def line2position(line, reverseFlag):
def reversePosition(position):
return -1 * (position + 1)
chr1 = 0
s1 = 1
e1 = 2
ll = line.strip().split('\t')
chr1name = ll[0].strip()
chr2name = False
for i in range(1, len(ll) - 2):
if ll[i].strip() == chr1name:
chr2 = i
break
s2 = chr2 + 1
e2 = chr2 + 2
chromosomeA = ll[chr1]
startA = int(ll[s1])
endA = int(ll[e1])
midA = (startA + endA) / 2
startB = int(ll[s2])
endB = int(ll[e2])
midB = (startB + endB) / 2
damagePosition = midB - midA
if reverseFlag:
bedLine = bedline(line)
strand = bedLine.strand()
if strand == "-":
damagePosition = reversePosition(damagePosition)
else:
if strand != "+" and strand != ".":
raise ValueError("strand is an unexpected character:" + strand)
return damagePosition
def getInterval(line, randomness=False):
bedLine = bed.bedline(line)
middlePoint = bedLine.midpoint()
start = middlePoint - windowSize
end = middlePoint + windowSize
if args.g:
chromosome = bedLine.chromosome()
chrEnd = chromosomeSizes[chromosome]
if start > 0 and end < chrEnd:
return bedLine.newline(start, end)
return False
return bedLine.newline(start, end)
def seqObject2bedLine(seq, regexMotif):
lines = []
indexList = regexMotif.getIndexList(seq.getSequence())
startList = indexList[0]
endList = indexList[1]
for i in range(len(startList)):
bedLine = bed.bedline(fastaHeader2bedLine(seq.getHeader()))
lines.append(bedLine.chromosome() + "\t" +
str(bedLine.start() + startList[i]) + "\t" +
str(bedLine.start() + endList[i]) + "\t" + "+" + "\n")
if DNAreverseComplementFlag:
reverseComplementMotif = regexMotif.DNA_complement().reverse()
indexList = reverseComplementMotif.getIndexList(seq.getSequence())
startList = indexList[0]
endList = indexList[1]
for i in range(len(startList)):
bedLine = bed.bedline(fastaHeader2bedLine(seq.getHeader()))
lines.append(bedLine.chromosome() + "\t" +
str(bedLine.start() + startList[i]) + "\t" +
str(bedLine.start() + endList[i]) + "\t" + "-" + "\n")
return lines
#!/usr/bin/env python
import os
import sys
import argparse
import fileinput
from collections import Counter
from bed import bedline
parser = argparse.ArgumentParser()
parser = argparse.ArgumentParser(description='converts bed to one side bed (start or end)')
parser.add_argument('-i', nargs='?', type=argparse.FileType('r'), default=sys.stdin, help='input')
parser.add_argument('-o', nargs='?', type=argparse.FileType('w'), default=sys.stdout, help='output')
parser.add_argument('-s', default='start', choices=['start', 'end'], help='side (start or end)')
parser.add_argument('-l', type=int, default=1000, help='length of each side')
args = parser.parse_args()
bedFile = args.i
out = args.o
sideLength = int(args.l)
side = args.s
for line in bedFile:
bedLine = bedline(line)
if side == 'start':
referencePoint = bedLine.start()
else:
referencePoint = bedLine.end()
start = referencePoint - sideLength
end = referencePoint + sideLength
if start > 0:
out.write(bedLine.newline(start, end) + '\n')
os.system("cp " + args.b + " " + args.o)
sys.exit()
afile = open(args.a, 'r')
bfile = open(args.b, 'r')
out = open(args.o, 'w')
for lineB, lineA in izip(bfile, afile):
llA = lineA.strip().split('\t')
stringA = '_'.join([llA[0], llA[1], llA[2], llA[5]])
llB = lineB.strip().split('\t')
stringB = '_'.join([llB[0], llB[1], llB[2], llB[5]])
while stringB != stringA:
BL_A = bedline(lineA)
BL_B = bedline(lineB)
llA = lineA.strip().split('\t')
print(llA)
stringA = '_'.join([llA[0], llA[1], llA[2], llA[5]])
llB = lineB.strip().split('\t')
stringB = '_'.join([llB[0], llB[1], llB[2], llB[5]])
walkA = False
walkB = False
if BL_A.chromosome() > BL_B.chromosome():
walkB = True
walkA = False
elif BL_A.chromosome() < BL_B.chromosome():
def line2newLine(line):
bedLine = bed.bedline(line)
chromosome = bedLine.chromosome()
start = bedLine.start()
newEnd = min(start + windowSize, chrDict[chromosome])
return bedLine.newline(start, newEnd)
import bed
import sys
import argparse
from pybedtools import BedTool
from bed import bedline
parser = argparse.ArgumentParser(description='retrieves certain fragment lengths')
parser.add_argument('-b', reqiured=True, help='input')
parser.add_argument('-o', reqiured=True, nargs='?', type=argparse.FileType('w'), default=sys.stdout, help='output')
parser.add_argument('-a', reqiured=True, help='interval file')
parser.add_argument('-fasta', required=False, default=False, help='fasta file')
args = parser.parse_args()
inputFile = args.b
out = args.o
bedFile = args.a
a = BedTool(inputFile)
b = BedTool(bedFile)
a_and_b = a.intersect(b, c=True)
for line in a_and_b:
bedLine = bedline(str(line))
TTcount = bedLine.getFasta().count('TT')
out.write(bedLine.addField([str(TTcount)]))
# out.write(str(a_and_b))
