[Bioperl-l] Re: [apollo] Guidance for a newbie

[Lincoln Stein]

On Saturday 04 October 2003 03:28 pm, Andrew Nunberg wrote:
> I am trying to convert genbank records into a format that is readable
> by Appollo.
> I can achieve this with gff format but I would like to do some
> curation/annotation so I am now trying to create game xml.
>

Hi,

This is the same problem that I have.  The approach that I am taking is to 
rewrite the GAME SequenceIO module in Bioperl so that it creates the correct 
version of GAME (the version it currently creates is incompatible with 
Bioperl).  Then what you want to do will be as easy as:

	$in = Bio::SeqIO->new(-file=>'genbank_file',-format=>'genbank');
	$out = Bio::SeqIO->new(-file=>'genbank_file.game',-format=>'GAME');
	while (my $seq = $in->next_seq) {
		$out->write_seq($seq);
	}

Because of many other obligations, this is moving very slowly and don't expect 
much progress until things lighten up for me in November.  If you or anyone 
else on these lists want to work on this, I will gladly share my notes and 
what I've got so far.

Lincoln

On Saturday 04 October 2003 03:28 pm, Andrew Nunberg wrote:
> I am trying to convert genbank records into a format that is readable
> by Appollo.
> I can achieve this with gff format but I would like to do some
> curation/annotation so I am now trying to create game xml.
>
> I see two basic strategies, creating annotation or
> computational_analysis tracks
> In either case, i am lacking data to make the xml
>
> For annotation there is a requirement for one more sequences to go with
> the 'gene'.
> for computational_analysis i am require to give output
> this is according to the dtd i have.
>
> Has anyone tried to do this and what approach did you take?
> Is it possible to fake the sequence requirement for annotations?
> so far the only xml that has worked is one with just the root sequence
> and nothing else..
>
> Thanks
> Andy
> ---------------------------------------------------
> Andrew Nunberg Ph.D
> Bioinfomagician
> Orion Genomics
> 4041 Forest Park
> St Louis, MO
> 314-615-6989
> anunberg at oriongenomics.com
> www.oriongenomics.com
>
> _______________________________________________
> apollo mailing list
> apollo at mail.fruitfly.org
> http://mail.fruitfly.org/mailman/listinfo/apollo

-- 
Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)