[ensembl-dev] "Member adaptor" deprecated warning in Ensembl Compara perl API

Miguel Pignatelli mp at ebi.ac.uk
Mon Jun 3 14:47:54 BST 2013


Hi Samiul,

You may also find useful the different options that get_SimpleAlign 
offers. For example...

my $simple_align = $this_homology->get_SimpleAlign(-append_sp_short_name 
=> 1 );

... will return the alignment appending the species short name to the ids.

These options are explained in the documentation of the method:

http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1AlignedMemberSet.html#a7b941b5394c882b95db0ab106b7ac2f5

Hope this helps,

M;

On 03/06/13 12:57, Samiul Hasan wrote:
> Hi Miguel,
>
> I just worked through the documentation and managed to answer my own question. Solution below. Many thanks for your help with this - much appreciated.
>
> Best wishes, Samiul
>
>
> foreach my $this_homology (@$all_homologies) {
>
>          my $genomes = $this_homology->get_all_GenomeDBs_by_member_source_name("ENSEMBLPEP");
>
>           #first get aligned genome information
>            #this will print the human and the species details
>          foreach my $g (@{$genomes}) {
>
>                  print "GENOME: ", "\t", $g->taxon_id, "\t", $g->get_short_name, "\t",
>                  $g->name, "\n";
>
>          }
>
>          #get the alignment
>          my $simple_align = $this_homology->get_SimpleAlign();    #protein alignment
>
>          #rename identifiers etc...
>
> }
>
>
>
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-- 

Miguel Pignatelli, PhD

Ensembl Developer - Comparative Genomics
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK
Room A3-33
Phone + 44 (0) 1223 494 598
Fax   + 44 (0) 1223 494 468




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