[ensembl-dev] Question regarding refseq transcript selector

Duarte Molha duartemolha at gmail.com
Wed Jul 12 10:02:55 BST 2017


I understand your point about the CCDS. But for my purposes I am not trying
to reannotate genes.. I just want to ignore some of the transcripts you
have selected for that particular gene (XM_ transcripts) and then select
the canonical transcript based on the remaining ones.

Many thanks

Duarte



[image: --]
Duarte Molha
[image: https://]about.me/duarte
<https://about.me/duarte?promo=email_sig>

On 11 July 2017 at 10:14, Kieron Taylor <ktaylor at ebi.ac.uk> wrote:

> Hi Duarte,
>
> CCDS data is a big part of how Ensembl currently chooses its canonical
> transcripts, in that we want our decisions to reflect the consensus of
> several resources. It is not essential to the process and you will still
> get reasonable decisions without it, but they might differ from what
> Ensembl publishes.
>
> You can reduce the amount of warnings by only instantiating
> TranscriptSelector once, as opposed to for every feature or set of
> features. Then you get one warning at setup. If you really demand quiet
> output, then you always delete line 81 from TranscriptSelector. There
> should be no consequences for you doing this.
>
> You can learn more about CCDS here: http://www.ensembl.org/info/
> genome/genebuild/ccds.html
> We use CCDS data to populate a core-like database and then create a
> DBAdaptor which used by the TranscriptSelector.
>
> I hope that covers the salient points.
>
> Kieron
>
>
>
> Kieron Taylor PhD.
> Ensembl Developer
>
> EMBL, European Bioinformatics Institute
>
>
>
>
>
>
> > On 10 Jul 2017, at 09:29, Duarte Molha <duartemolha at gmail.com> wrote:
> >
> > Dear Devs.
> >
> > In a discussion some time ago here in the forum (
> http://lists.ensembl.org/pipermail/dev/2016-July/012031.html ) regarding
> how I could make use of Ensembl logical canonical programming to modify a
> refseq gene to remove XM_ transcripts and for the selection of canonical
> transcripts of only NM_ transcripts,  Andy suggested that I could use
> something like this:
> >
> > my $selector = Bio::EnsEMBL::Utils::TranscriptSelector->new();
> > # get a gene from somewhere and modify to remove the XMs
> > my $canonical_transcript = $selector->select_canonical_
> transcript_for_Gene($gene);
> >
> > I followed his advise and integrated it into my code as follows:
> > my $mod_gene = $gene;
> > my $selector = Bio::EnsEMBL::Utils::TranscriptSelector->new();
> > foreach my $transcript (@{$mod_gene->get_all_Transcripts()}){
> >       if ($options->{query} =~ /refseq/ && $transcript->stable_id() !~
> /^NM_/){
> >               $mod_gene->remove_Transcript($transcript);
> >       }
> > }
> > my $canonical_transcript = $selector->select_canonical_
> transcript_for_Gene($mod_gene);
> > $mod_gene->canonical_transcript($canonical_transcript);
> >
> > $gene=$mod_gene;
> >
> >
> > This seems to do the job, however my script keeps issuing warnings
> >
> > -------------------- WARNING ----------------------
> > MSG: Running without CCDS DB
> > FILE: EnsEMBL/Utils/TranscriptSelector.pm LINE: 80
> > CALLED BY: getFeatures.pl  LINE: 985
> > Date (localtime)    = Fri Jul  7 17:32:54 2017
> > Ensembl API version = 83
> >
> > ---------------------------------------------------
> >
> > I believe the problem is that I am not providing a CCDS DB on the line
> > my $selector = Bio::EnsEMBL::Utils::TranscriptSelector->new();
> > I read the documentation and that seems to be an optional parameter.
> >
> > Can you tell me if this is a problem and if it is how I can set the CCDS
> DB and if not how I can stop these warnings being issued?
> >
> > Many thanks
> >
> > Duarte
> > _______________________________________________
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