[Bioperl-l] Bio::DB::GFF still a nightmare...

Lincoln Stein lstein at cshl.edu
Thu Mar 30 15:11:01 EST 2006


Hi Marco,

There is no Bio::DB::GFF3 module, and there is no attachment! Send out the 
data file and the script you are using and I'll comment on it.

Lincoln

On Wednesday 29 March 2006 21:19, Marco Blanchette wrote:
> Dear all--
>
> There¹s definitely something I don¹t get with the Bio::DB::GFF3 module...
> When I run the following script, I get the drawing I want but contaminated
> with pieces of overlapping genes (see attached CG17800.png_v1). My
> understanding is that the aggregate pre-mRNAs contain the attribute
> ŒGene->CG_ID¹ (see the output). So when I uncomment line 25 '-attributes =>
> {Gene => $gene},' in order to get only the transcript from the queried gene

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Lincoln D. Stein
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