[Bioperl-l] about Bio::DB::GFF

[Tuan A. Tran]

Hi,

I read instructions about how to use Bio::DB::GFF.  I quoted the last
part of it.
At the end of it, there is a comment
"This limitation will be corrected in the next version of Bio::DB::GFF"

I just wonder if there is a new version in which this limitation is corrected.

Tuan

----------------------------------------------------------------------------------
This module will accept GFF3 files, as described at
http://song.sourceforge.net/gff3.shtml. However, the implementation
has some limitations.


    1. GFF version string is required
    The GFF file b<must> contain the version comment:

     ##gff-version 3

    Unless this version string is present at the top of the GFF file, the
loader will attempt to parse the file in GFF2 format, with
less-than-desirable results.

    2. Only one level of nesting allowed
    A major restriction is that Bio::DB::GFF only allows one level of
nesting of features.  For nesting, the Target tag will be used
preferentially followed by the ID tag, followed by the Parent tag.
This means that if genes are represented like this:

      XXXX XXXX gene XXXX XXXX XXXX ID=myGene
  XXXX XXXX mRNA XXXX XXXX XXXX ID=myTranscript;Parent=myGene
  XXXX XXXX exon XXXX XXXX XXXX Parent=myTranscript
  XXXX XXXX exon XXXX XXXX XXXX Parent=myTranscript

    Then there will be one group called myGene containing the "gene"
feature and one group called myTranscript containing the mRNA, and two
exons.

    You can work around this restriction to some extent by using the Alias
attribute literally:

      XXXX XXXX gene XXXX XXXX XXXX ID=myGene
  XXXX XXXX mRNA XXXX XXXX XXXX ID=myTranscript;Parent=myGene;Alias=myGene
  XXXX XXXX exon XXXX XXXX XXXX Parent=myTranscript;Alias=myGene
  XXXX XXXX exon XXXX XXXX XXXX Parent=myTranscript;Alias=myGene

    This limitation will be corrected in the next version of Bio::DB::GFF.