[ensembl-dev] GenomicAlignBlock and MethodLinkSpeciesSet

[Stephen Fitzgerald]

Hi Diego,
once you have the genomic_align_blocks, restrict these using the reference 
coord positions and get a listref of genomic_align objects. Once you have 
the genomic_align objects you can filter these using the species name, 
aligned sequence string, etc..

################
foreach my $genomic_align_block( @{ $all_genomic_align_blocks }) {
  my $restricted_gab = $genomic_align_block->restrict_between_reference_positions($ref_start, $ref_end);
  foreach my $genomic_align(@{ $restricted_gab->get_all_GenomicAligns() }){
   print $genomic_align->dnafrag->genome_db->name, "\n";
   my $seq = $genomic_align->aligned_sequence;
   if($seq =~ /[ACGT]/){
    print $seq, "\n";
   }
  }
}
################

Cheers,
Stephen.



On Fri, 15 Feb 2013, Diego Dominguez Munilla wrote:

> 
> Hello!
> 
> I'm stock trying to get a specific GenomeAlignBlock
> 
> I've got a MethodLinkSpeciesSet from this parammeters:
> method_link_type="PECAN" : species_set_name="amniotes"
> But what i'm looking for is a species_set with birds (chicken, turkey, zebrafinch) and lizard,
> but PECAN aligned, to extract 4 homologuos sequences.
> Every way I've tried always resulted retrieving the homologous region for all amniotes
> I'm sure that there is a right way to get it but after reading all the
> "Compara Help" it's been impossible.
> 
> Thanks
> 
> Best  Regards.
> 
> Diego Dominguez
> 
> 
>