pos_to_bedgraph.py

import sys

class Line(object):
	def __init__(self, line):
		self.fields = line.split('\t')
		self.chrom = self.fields[0]
		self.start = int(self.fields[1])
		self.end = int(self.fields[2])
		self.depth = int(self.fields[3])


"""
C8628693	0	1	0
C8628693	1	2	0
C8628693	2	3	0
C8628693	3	4	1
C8628693	4	5	1
C8628693	5	6	2
C8628693	6	7	2
C8628693	7	8	2
C8628693	8	9	2
"""

prev = None
min_start = None
max_end = None
for line in sys.stdin:
	curr = Line(line)

	if prev is None:
		min_start = curr.start
		prev = curr
		continue

	# depth change. report BEDGRAPH
	if curr.chrom == prev.chrom and \
	curr.depth != prev.depth:
		print prev.chrom, min_start, max_end, prev.depth
		min_start = curr.start
		max_end = curr.end
	# same chrom and depth. update max_end
	elif curr.chrom == prev.chrom and \
	curr.depth == prev.depth:
		max_end = curr.end
	# chromosome change. report then reset
	elif curr.chrom != prev.chrom:
		print prev.chrom, min_start, max_end, prev.depth
		min_start = curr.start
		max_end = curr.end		

	prev = curr

# handle the final block in the file.
print prev.chrom, min_start, max_end, prev.depth

run.sh

cat test.txt | python pos_to_bedgraph.py
C8628693 0 3 0
C8628693 3 5 1
C8628693 5 9 2
D8628693 0 3 0
D8628693 3 5 1
D8628693 5 9 2

test.txt

C8628693	0	1	0
C8628693	1	2	0
C8628693	2	3	0
C8628693	3	4	1
C8628693	4	5	1
C8628693	5	6	2
C8628693	6	7	2
C8628693	7	8	2
C8628693	8	9	2
D8628693	0	1	0
D8628693	1	2	0
D8628693	2	3	0
D8628693	3	4	1
D8628693	4	5	1
D8628693	5	6	2
D8628693	6	7	2
D8628693	7	8	2
D8628693	8	9	2