[Bioperl-l] bp_genbank2gff problems

[Lincoln Stein]

The bp_genbank2gff problem is now fixed.  I am now looking into the 
loaders to see whether it is true that they don't handle the combined 
annotation/fasta format.

Lincoln

On Monday 15 December 2003 02:56 pm, Neil Saunders wrote:
> > This is a bug and it shall be fixed.
>
> Good to know!  Thanks.
>
> I switched back to bioperl 1.2.3 on the woody box.  The
> bp_genbank2gff script with that version seems to behave differently
> and works quite well, although it throws exceptions on some gb
> files leading to incomplete GFF output.
>
> Another query - Currently I'm using csplit to split my GFF3 files
> into a 'GFF' portion and a 'fasta' portion, then passing them as
> arguments to bp_load_gff.pl.  Is this strictly necessary?  I guess
> the ideal situation would be a working bp_genbank2gff and a
> bp_load_gff that could process the fasta portion too.
>
> Look forward to the latest (I know you guys work fast),
>
> Neil