sort_gff.py

import sys

infile = sys.argv[1]
outfile = sys.argv[2]

gff_list = []
fh = open(infile)
for x in fh:
    if x[0] == '#': continue
    y = x.strip().split('\t')
    gff_list.append(y)

gff_list.sort(key=lambda a:int(a[3]))
gff_list.sort(key=lambda a:a[0])

fh = open(outfile,'w')
for x in gff_list:
    fh.write("\t".join(x) + "\n")