Mercurial > repos > vipints > fml_gff3togtf
diff gtf_to_gff.py @ 5:6e589f267c14
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author | devteam |
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date | Tue, 04 Nov 2014 12:15:19 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gtf_to_gff.py Tue Nov 04 12:15:19 2014 -0500 @@ -0,0 +1,85 @@ +#!/usr/bin/env python +""" +Convert Gene Transfer Format [GTF] to Generic Feature Format Version 3 [GFF3]. + +Usage: python gtf_to_gff.py in.gtf > out.gff3 + +Requirement: + GFFParser.py: https://github.com/vipints/GFFtools-GX/blob/master/GFFParser.py + helper.py : https://github.com/vipints/GFFtools-GX/blob/master/helper.py + +Copyright (C) + 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany. + 2012-2014 Memorial Sloan Kettering Cancer Center New York City, USA. +""" + +import re +import sys +import GFFParser +import helper + +def GFFWriter(gtf_content): + """ + write the feature information to GFF format + + @args gtf_content: Parsed object from gtf file + @type gtf_content: numpy array + """ + + print '##gff-version 3' + + for ent1 in gtf_content: + + chr_name = ent1['chr'] + strand = ent1['strand'] + start = ent1['start'] + stop = ent1['stop'] + source = ent1['source'] + ID = ent1['name'] + Name = ent1['gene_info']['Name'] + + Name = ID if not Name else Name + + print '%s\t%s\tgene\t%d\t%d\t.\t%s\t.\tID=%s;Name=%s' % (chr_name, source, start, stop, strand, ID, Name) + + for idx, tid in enumerate(ent1['transcripts']): + print idx + print tid + + t_start = ent1['exons'][idx][0][0] + t_stop = ent1['exons'][idx][-1][-1] + t_type = ent1['transcript_type'][idx] + + utr5_exons, utr3_exons = [], [] + if ent1['exons'][idx].any() and ent1['cds_exons'][idx].any(): + utr5_exons, utr3_exons = helper.buildUTR(ent1['cds_exons'][idx], ent1['exons'][idx], strand) + + print '%s\t%s\t%s\t%d\t%d\t.\t%s\t.\tID=%s;Parent=%s' % (chr_name, source, t_type, t_start, t_stop, strand, tid[0], ID) + + for ex_cod in utr5_exons: + print '%s\t%s\tfive_prime_UTR\t%d\t%d\t.\t%s\t.\tParent=%s' % (chr_name, source, ex_cod[0], ex_cod[1], strand, tid[0]) + + for ex_cod in ent1['cds_exons'][idx]: + print '%s\t%s\tCDS\t%d\t%d\t.\t%s\t%d\tParent=%s' % (chr_name, source, ex_cod[0], ex_cod[1], strand, ex_cod[2], tid[0]) + + for ex_cod in utr3_exons: + print '%s\t%s\tthree_prime_UTR\t%d\t%d\t.\t%s\t.\tParent=%s' % (chr_name, source, ex_cod[0], ex_cod[1], strand, tid[0]) + + for ex_cod in ent1['exons'][idx]: + print '%s\t%s\texon\t%d\t%d\t.\t%s\t.\tParent=%s' % (chr_name, source, ex_cod[0], ex_cod[1], strand, tid[0]) + + +def __main__(): + + try: + gtf_fname = sys.argv[1] + except: + print __doc__ + sys.exit(-1) + + gtf_file_content = GFFParser.Parse(gtf_fname) + + GFFWriter(gtf_file_content) + +if __name__ == "__main__": + __main__()