Solution for pseudogene issue in GFF3 for Artemis

pseudogene_issue.py

import sys, os, string
if len(sys.argv) != 2:
	print 'You seem to have forgotten to provide the input GFF3 file.'
	exit()

if __name__ == "__main__":
	found = False
	with open(sys.argv[1],  'r') as file:
	  outfile = open(os.path.basename(sys.argv[1]).replace(".gff",  "_corrected.gff"),  'w')
	  for line in file:
	    if found and ('exon' in line):
	      found = False
	      continue
	    if 'pseudogene' in line:
	      found = True
	      continue
	    if 'gap' in line:
	      continue
	    outfile.write(line)

	  outfile.close()

Try to avoid reading entire file in memory. So instead of this ...

lines = files.readlines()

try this

file = open('file.txt','r')
for line in file:
  blah blah.....

Even better

with open('file', 'r') as file:
   for line in file:
     blah blah .....

Consult the python standard documentation for the advantage of using it.