[ensembl-dev] Members, GeneMembers and SeqMembers in Ensembl 76

[Ed Gray]

Hi All,

 

I am writing some code right now that uses Members, GeneMembers and SeqMembers.  Is it true that the Member is being deprecated in the upcoming Ensembl 76 release?  

 

If so, 

 

1) Almost all of the relevant examples use what may soon be deprecated code.  FOr instance http://useast.ensembl.org/info/docs/api/compara/compara_tutorial.html has the stanza of code below just after a stanza example that has GeneMember objects.  

my $homology = $homologies->[0]; # take one of the homologies and look into it
foreach my $member (@{$homology->get_all_Members}) {
  # each AlignedMember contains both the information on the SeqMember and in
  # relation to the homology
  print (join " ", map { $member->$_ } qw(stable_id taxon_id))."\n";
  print (join " ", map { $member->$_ } qw(perc_id perc_pos perc_cov))."\n";
}

 

2) Will get_all_Members still be available after r75?

 

3) Is there any plan on adjusting the tutorials etc. for GeneMembers and SeqMembers?

 

4) How different will the Compara API be in r76?  Again, I am currently writing code to try to take advantage of what I understand to be more Compara data in r76 but I am concerned the API will be different and I will have to re-write.

 

So many questions, I know, but is there some guidance you could give on the topic of Compara API changes and deprecations coming in ensembl 76?

 

Many, many thanks,

Ed

 




 		 	   		  
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