[ensembl-dev] API compara

[MARIA T. MARTÍN CAMPOS]

Hello,

I have something like this:

*my $all_genomic_align_blocks =
$genomic_align_block_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice(
        $mlss, $region, undef, undef, "restrict");
*
  *  foreach my $genomic_align_block ( @{ $all_genomic_align_blocks } )
{
   your code here??
}
*

Thanks!!!


2013/2/15 Hardip Patel <hardip.patel at anu.edu.au>

> 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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