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#                                #
# Last modified 04/17/2015       # 
#                                #
# Georgi Marinov                 #
#                                # 
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import sys
import string
from sets import Set

def run():

    if len(sys.argv) < 2:
        print 'usage: python %s gtf outfile' % sys.argv[0]
        print '	Note: the script print out all CDS features annotated as exons' % sys.argv[0]
        sys.exit(1)

    gtf = sys.argv[1]
    outfile = open(sys.argv[2],'w')

    listoflines = open(gtf)
    for line in listoflines:
        if line.startswith('#'):
            continue
        fields = line.strip().split('\t')
        if fields[2] != 'CDS':
            continue
        outfile.write(line)
        outline = fields[0] + '\t' + fields[1] + '\t' + 'exon' + '\t' + fields[3] + '\t' + fields[4] + '\t' + fields[5] + '\t' + fields[6] + '\t' + fields[7] + '\t' + fields[8]
        outfile.write(outline + '\n')

    outfile.close()

run()