parser = argparse.ArgumentParser(
description=
'takes bed as input, get the middle point and extend it to both sides')
parser.add_argument('-i', required=True, help='input')
parser.add_argument('-o', required=True, help='output')
parser.add_argument('-g', required=True, help='genomeFile')
parser.add_argument('-w', required=True, help='windowSize')
args = parser.parse_args()
bedFile = args.i
output = args.o
genome = args.g
windowSize = int(args.w)
chrDict = {}
for line in open(genome, 'r'):
ll = line.split('\t')
chrDict[ll[0]] = int(ll[1])
def line2newLine(line):
bedLine = bed.bedline(line)
chromosome = bedLine.chromosome()
start = bedLine.start()
newEnd = min(start + windowSize, chrDict[chromosome])
return bedLine.newline(start, newEnd)
generalUtils.lineBasedFileOperation(bedFile, output, line2newLine, [])
parser = argparse.ArgumentParser(description='fix fragment length if possible')
parser.add_argument('-i', required=True, help='<Required> input')
parser.add_argument('-c1',
required=True,
help='<Required> start position tab for first file')
parser.add_argument('-c2',
required=True,
help='<Required> start position tab for second file')
parser.add_argument('-o', required=True, help='<Required> output')
args = parser.parse_args()
input = args.i
output = args.o
s1tab = int(args.c1) - 1
s2tab = int(args.c2) - 1
def bedClosest2distance(line, s1tab, s2tab):
ll = line.split('\t')
start1 = int(ll[s1tab])
end1 = int(ll[s1tab + 1])
start2 = int(ll[s2tab])
end2 = int(ll[s2tab + 1])
pos1 = generalUtils.mean([start1, end1])
pos2 = generalUtils.mean([start2, end2])
distance = pos2 - pos1
return str(distance)
generalUtils.lineBasedFileOperation(input, output, bedClosest2distance,
[s1tab, s2tab])
parser.add_argument('-o', required= True, help='output')
parser.add_argument('-w', required= True, help='windowSize')
parser.add_argument('-g', required= False, default=False, help='genomeFile')
parser.add_argument('--randomMid', required= False, action='store_true', help='for cases of .5 middle point, randomly select between positions 0 or 1')
args = parser.parse_args()
bedFile = args.i
output = args.o
windowSize = int(args.w)
if args.g:
chromosomeSizes = {}
for line in open(args.g, 'r'):
ll = line.split('\t')
chromosomeSizes[ll[0]] = int(ll[1])
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)
generalUtils.lineBasedFileOperation(bedFile, output, getInterval, [])
#!/usr/bin/env python
import generalUtils
import argparse
import gff
parser = argparse.ArgumentParser(
description='prints a meta field from gff by order')
parser.add_argument('-i', required=True, help='<Required> input')
parser.add_argument('-o', required=True, help='<Required> output')
parser.add_argument('-f', required=True, help='<Required> field of interest')
args = parser.parse_args()
generalUtils.lineBasedFileOperation(args.i, args.o,
gff.getGeneInformationFromGFFline,
[args.f])
import sys
import argparse
import generalUtils
import fasta
from sequence import DNA
parser = argparse.ArgumentParser(
description='convert cufflinks output to bed file with counts')
parser.add_argument('-i', required=True, help='<Required> input')
parser.add_argument('-s', required=True, help='<Required> strand')
parser.add_argument('-o', required=True, help='<Required> output')
args = parser.parse_args()
def cuffLinksLine2bedLine(line, strand):
ll = line.split('\t')
locus = ll[6]
locusL = locus.split(':')
chromosome = locusL[0]
interval = locusL[1]
intervalL = interval.split('-')
start = intervalL[0]
end = intervalL[1]
FPKM = ll[9]
LL = [chromosome, start, end, strand, FPKM]
return '\t'.join(LL)
generalUtils.lineBasedFileOperation(args.i, args.o, cuffLinksLine2bedLine,
[args.s])