Solution for pseudogene issue in GFF3 for Artemis

pseudogene_issue.py

import sys, os

if len(sys.argv) != 2:
	print 'You seem to have forgotten to provide the input GGF3 file.'
	exit()

if __name__ == "__main__":
	found = False
	END = outofbound = issues = 0
	outfile = open(os.path.basename(sys.argv[1]).replace(".gff", "_corrected.gff"), 'w')
	with open (sys.argv[1], 'r') as file:
		for line in file:
			if line.startswith('##sequence-region') is True:
				END = (line.split(' '))[2].rstrip()
			try:
				row = line.split('\t')
				if found and row[2] == 'exon':
					issues += 1
					continue
				if row[2] == 'pseudogene':
					found = True
				if row[2] == 'gap' and row[3] > END:
					outofbound += 1
					continue
				outfile.write(line)
			except IndexError:
				outfile.write(line)
		outfile.close()
	#print "# of issues  =  %d" % issues
	#print "# Out of bound gaps = %d" % outofbound