GBROWSEOLD2GFF3(1)

NAME
gbrowseold2gff3.pl format convert a GFF file

SYNOPSIS
gbrowseold2gff3.pl < in.gbrowse > out.gff3

    This is a simple conversion, almost line by line, from a GBrowse 1.6 compatible to a GBrowse 2.0 compatible format for genes.

OPTIONS
    hints       convert gff format for intron hints to gff3
    source      fill this into the second column

DESCRIPTION
    example input:

   chromosome_1    AUGUSTUS      gene    12656   14013   0.05    +       .       Gene g1
   chromosome_1    AUGUSTUS      mRNA    12656   14013   0.05    +       .       mRNA g1.t1 ; Gene g1
   chromosome_1    AUGUSTUS      tss     12656   12656   .       +       .       mRNA g1.t1
   chromosome_1    AUGUSTUS      5'-UTR  12656   12867   0.21    +       .       mRNA g1.t1
   chromosome_1    AUGUSTUS      start_codon     12868   12870   .       +       0       mRNA g1.t1
   chromosome_1    AUGUSTUS      initial 12868   12993   0.85    +       0       mRNA g1.t1
   chromosome_1    AUGUSTUS      terminal        13249   13479   0.99    +       0       mRNA g1.t1
   chromosome_1    AUGUSTUS      intron  12994   13248   0.99    +       .       mRNA g1.t1
   chromosome_1    AUGUSTUS      CDS     12868   12993   0.85    +       0       mRNA g1.t1
   chromosome_1    AUGUSTUS      CDS     13249   13479   0.99    +       0       mRNA g1.t1
   chromosome_1    AUGUSTUS      stop_codon      13477   13479   .       +       0       mRNA g1.t1
   chromosome_1    AUGUSTUS      3'-UTR  13480   14013   0.22    +       .       mRNA g1.t1
   chromosome_1    AUGUSTUS      tts     14013   14013   .       +       .       mRNA g1.t1

    example output:

   chromosome_1    AUGUSTUS      gene    12656   14013   0.05    +       .       ID=g1
   chromosome_1    AUGUSTUS      mRNA    12656   14013   0.05    +       .       ID=g1.t1;Parent=g1
   chromosome_1    AUGUSTUS      five_prime_utr  12656   12867   0.21    +       .       Parent=g1.t1
   chromosome_1    AUGUSTUS      start_codon     12868   12870   .       +       0       Parent=g1.t1
   chromosome_1    AUGUSTUS      intron  12994   13248   0.99    +       .       Parent=g1.t1
   chromosome_1    AUGUSTUS      CDS     12868   12993   0.85    +       0       Parent=g1.t1
   chromosome_1    AUGUSTUS      CDS     13249   13479   0.99    +       0       Parent=g1.t1
   chromosome_1    AUGUSTUS      stop_codon      13477   13479   .       +       0       Parent=g1.t1
   chromosome_1    AUGUSTUS      three_prime_utr 13480   14013   0.22    +       .       Parent=g1.t1