This tiny script takes bedtools (or similar) output and prints the first and last 10 rows for a contig

getFirstLast10Rows.py

import Queue
import sys
# prints first 10 and last 10 rows for each contig
# does NOT guarantee that the first and 10 don't overlap (use uniq)
fh = open(sys.argv[1])
header = fh.readline()
q = Queue.Queue(10) # for the last elements

current_contig = ""
for line in fh:
    ll = line.split()
    contig = ll[0]

    if contig != current_contig:
        # print last queue
        while not q.empty():
            print q.get(),
        # now make new one
        current_contig = contig
        seen_counter = 1
        print line,
        continue

    seen_counter += 1
    if seen_counter <= 10:
        print line,
    try:
        q.put(line, block=False)
    except Queue.Full:
        # throw away one
        q.get()
        q.put(line, block=False)

# print last queue
while not q.empty():
    print q.get(),