[ensembl-dev] API compara

[Hardip Patel]

Hi

You can use something like following to remove the unwanted species.

foreach my $current_alignment_slice (@{$align_slice->get_all_Slices}) {
        my $name = $current_alignment_slice->genome_db->name;
        if ($name eq "gallus_gallus" || $name eq "meleagris_gallopavo"){
         my $seq = $current_alignment_slice->seq;
          if ($seq =~ /[ACGT]/){
            print $gene->stable_id."\t".$current_alignment_slice->genome_db->taxon_id."\t".$current_alignment_slice->seq."\n";
          }
        }
}


Cheers


On 15/02/2013, at 9:57 AM, MARIA T. MARTÍN CAMPOS <alnitak817 at gmail.com> wrote:

> 
> 
> ---------- Forwarded message ----------
> From: MARIA T. MARTÍN CAMPOS <alnitak817 at gmail.com>
> Date: 2013/2/14
> Subject: API compara
> To: dev at ensembl.org
> 
> 
> Good night,
> 
> my name is Trinidad Martín and I am working in a project where we have to study some sequences : anolis carolinensi, gallus gallus, meleagris_gallopavo and taeniopygia_guttata. I used a method called $mlss = $mlssa->fetch_by_method_link_type_species_set_name("PECAN","amniotes"); and i want to align their sequencies, but just for these 4 species and $mlss contains all amniota vertebrate. I would like to know if I can find a method that returns me a $mlss just with these 4 species, searching by name maybe... or can I filter from the genomic align block??
> 
> Thank you very much!!
> 
> Trinidad Martín
> 
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