#!/usr/bin/env python
import os
import sys
import argparse
import generalUtils
import bed

if not '--test' in sys.argv:
	parser = argparse.ArgumentParser(description='seperate intervals into bins')
	parser.add_argument('-i', required= True, help='input')
	parser.add_argument('-o', required= True, help='output')
	parser.add_argument('-c', required=  True, help='column of interval identifier')
	args = parser.parse_args()

	bedFile = args.i
	outBedFile = args.o
	intervalIdColumn = int(args.c)
else:
	bedFile = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'utils', 'testFiles', 'binnedBedExample_count.bed')
	outBedFile = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'utils', 'testFiles', 'binnedBedExample_count_clustered.bed')
	intervalIdColumn = 7

filein = open(bedFile, 'r')
out = open(outBedFile, 'w')

intervalNumber = 0
previousIntervalId = None
newLL = []
for line in filein:
	ll = line.strip().split('\t')
	intervalId = ll[intervalIdColumn - 1]
	if intervalId != previousIntervalId:
		previousIntervalId = intervalId
		if newLL:
			out.write('\t'.join(newLL) + '\n')
		newLL = ll[:intervalIdColumn]
		newLL += [ll[intervalIdColumn]]
	else:
		newLL += [ll[intervalIdColumn]]
else:
	out.write('\t'.join(newLL) + '\n')
out.close()
8b567048c924a04a356edd315d8db49afe256364
<mask token>

<mask token>
if not '--test' in sys.argv:
    parser = argparse.ArgumentParser(description='seperate intervals into bins'
        )
    parser.add_argument('-i', required=True, help='input')
    parser.add_argument('-o', required=True, help='output')
    parser.add_argument('-c', required=True, help=
        'column of interval identifier')
    args = parser.parse_args()
    bedFile = args.i
    outBedFile = args.o
    intervalIdColumn = int(args.c)
else:
    bedFile = os.path.join(os.path.dirname(os.path.realpath(__file__)),
        'utils', 'testFiles', 'binnedBedExample_count.bed')
    outBedFile = os.path.join(os.path.dirname(os.path.realpath(__file__)),
        'utils', 'testFiles', 'binnedBedExample_count_clustered.bed')
    intervalIdColumn = 7
<mask token>
for line in filein:
    ll = line.strip().split('\t')
    intervalId = ll[intervalIdColumn - 1]
    if intervalId != previousIntervalId:
        previousIntervalId = intervalId
        if newLL:
            out.write('\t'.join(newLL) + '\n')
        newLL = ll[:intervalIdColumn]
        newLL += [ll[intervalIdColumn]]
    else:
        newLL += [ll[intervalIdColumn]]
else:
    out.write('\t'.join(newLL) + '\n')
out.close()

<mask token>
if not '--test' in sys.argv:
    parser = argparse.ArgumentParser(description='seperate intervals into bins'
        )
    parser.add_argument('-i', required=True, help='input')
    parser.add_argument('-o', required=True, help='output')
    parser.add_argument('-c', required=True, help=
        'column of interval identifier')
    args = parser.parse_args()
    bedFile = args.i
    outBedFile = args.o
    intervalIdColumn = int(args.c)
else:
    bedFile = os.path.join(os.path.dirname(os.path.realpath(__file__)),
        'utils', 'testFiles', 'binnedBedExample_count.bed')
    outBedFile = os.path.join(os.path.dirname(os.path.realpath(__file__)),
        'utils', 'testFiles', 'binnedBedExample_count_clustered.bed')
    intervalIdColumn = 7
filein = open(bedFile, 'r')
out = open(outBedFile, 'w')
intervalNumber = 0
previousIntervalId = None
newLL = []
for line in filein:
    ll = line.strip().split('\t')
    intervalId = ll[intervalIdColumn - 1]
    if intervalId != previousIntervalId:
        previousIntervalId = intervalId
        if newLL:
            out.write('\t'.join(newLL) + '\n')
        newLL = ll[:intervalIdColumn]
        newLL += [ll[intervalIdColumn]]
    else:
        newLL += [ll[intervalIdColumn]]
else:
    out.write('\t'.join(newLL) + '\n')
out.close()

import os
import sys
import argparse
import generalUtils
import bed
if not '--test' in sys.argv:
    parser = argparse.ArgumentParser(description='seperate intervals into bins'
        )
    parser.add_argument('-i', required=True, help='input')
    parser.add_argument('-o', required=True, help='output')
    parser.add_argument('-c', required=True, help=
        'column of interval identifier')
    args = parser.parse_args()
    bedFile = args.i
    outBedFile = args.o
    intervalIdColumn = int(args.c)
else:
    bedFile = os.path.join(os.path.dirname(os.path.realpath(__file__)),
        'utils', 'testFiles', 'binnedBedExample_count.bed')
    outBedFile = os.path.join(os.path.dirname(os.path.realpath(__file__)),
        'utils', 'testFiles', 'binnedBedExample_count_clustered.bed')
    intervalIdColumn = 7
filein = open(bedFile, 'r')
out = open(outBedFile, 'w')
intervalNumber = 0
previousIntervalId = None
newLL = []
for line in filein:
    ll = line.strip().split('\t')
    intervalId = ll[intervalIdColumn - 1]
    if intervalId != previousIntervalId:
        previousIntervalId = intervalId
        if newLL:
            out.write('\t'.join(newLL) + '\n')
        newLL = ll[:intervalIdColumn]
        newLL += [ll[intervalIdColumn]]
    else:
        newLL += [ll[intervalIdColumn]]
else:
    out.write('\t'.join(newLL) + '\n')
out.close()

#!/usr/bin/env python
import os
import sys
import argparse
import generalUtils
import bed

if not '--test' in sys.argv:
	parser = argparse.ArgumentParser(description='seperate intervals into bins')
	parser.add_argument('-i', required= True, help='input')
	parser.add_argument('-o', required= True, help='output')
	parser.add_argument('-c', required=  True, help='column of interval identifier')
	args = parser.parse_args()

	bedFile = args.i
	outBedFile = args.o
	intervalIdColumn = int(args.c)
else:
	bedFile = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'utils', 'testFiles', 'binnedBedExample_count.bed')
	outBedFile = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'utils', 'testFiles', 'binnedBedExample_count_clustered.bed')
	intervalIdColumn = 7

filein = open(bedFile, 'r')
out = open(outBedFile, 'w')

intervalNumber = 0
previousIntervalId = None
newLL = []
for line in filein:
	ll = line.strip().split('\t')
	intervalId = ll[intervalIdColumn - 1]
	if intervalId != previousIntervalId:
		previousIntervalId = intervalId
		if newLL:
			out.write('\t'.join(newLL) + '\n')
		newLL = ll[:intervalIdColumn]
		newLL += [ll[intervalIdColumn]]
	else:
		newLL += [ll[intervalIdColumn]]
else:
	out.write('\t'.join(newLL) + '\n')
out.close()