[ensembl-dev] Missing IDS in ENSEMBL database

Carlos Garcia Giron cgg at sanger.ac.uk
Fri May 25 12:35:57 BST 2012


Dear Duarte,

The method is called "fetch_all_by_external_name" and it can be found for:

Bio::EnsEMBL::DBSQL::GeneAdaptor::fetch_all_by_external_name() 
Bio::EnsEMBL::DBSQL::TranscriptAdaptor::fetch_all_by_external_name() 
Bio::EnsEMBL::DBSQL::TranslationAdaptor::fetch_all_by_external_name()

I hope it helps.

Kind regards,
Carlos

Duarte Molha wrote:
>
> Dear Thibaut Hourlier
>
> I was searching the doxygen documentation for that method call you 
> indicated but do not seem to be able to find it.
>
> It is a method call for a transcript adaptor?
>
> Best regards
>
> Duarte
>
> *From:* dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] *On 
> Behalf Of *Duarte Molha
> *Sent:* 25 May 2012 12:02
> *To:* Ensembl developers list
> *Subject:* Re: [ensembl-dev] Missing IDS in ENSEMBL database
>
> Thanks Thibaut Hourlier
>
> I just get very confused with all these IDS with the same format 
> meaning different things!
>
> Best regards
>
> Duarte
>
> *From:* dev-bounces at ensembl.org <mailto:dev-bounces at ensembl.org> 
> [mailto:dev-bounces at ensembl.org] *On Behalf Of *Thibaut Hourlier
> *Sent:* 25 May 2012 11:20
> *To:* Ensembl developers list
> *Subject:* Re: [ensembl-dev] Missing IDS in ENSEMBL database
>
> Dear Duarte,
>
> I went through the four first of your IDs:
>
> On 25 May 2012, at 10:14, Duarte Molha wrote:
>
> Dear Developers
>
> I created a simple script to output the exons of specific transcripts 
> with NM ids.
>
> It works fine for all but a small list of IDS. The large majority of 
> the failed IDS have been suppressed from NCBI
>
> Because they were found to be a “ /nonsense-mediated mRNA decay (NMD) 
> candidate/” so I do not mind eliminating those records from my query.
>
> / /
>
> /However some of the ones that fail are in NCBI database and for some 
> reason ENSEMBL is not able to query them:/
>
> /NM/_001040409.1
>
> It is an NMD transcript.
>
> NM_001167607.1
>
> It is an exon supporting feature and not a transcript supporting 
> feature, i think this is the reason you don't get it with your script
>
> http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000196743;r=5:150591711-150650001;t=ENST00000523466
>
> NM_001199987.1
>
> If you look in the Gene database at NCBI you will see that there is 2 
> other sequences for NDUFB6, which are the transcript supporting 
> feature for the 2 transcripts in Ensembl for the gene.
>
> http://www.ncbi.nlm.nih.gov/gene/?term=NM_001199987.1
>
> http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000165264;r=9:32552997-32573160;t=ENST00000379847
>
> NM_001204090.1
>
> Same problem as above, we did not use this sequence.
>
> What you can do is to use the HGNC identifier of these failing IDs in 
> the fetch_all_by_external_id method, i.e. NM_001199987.1 -> NDUFB6
>
> Regards
>
> Thibaut
>
> NM_001242881.1
>
> NM_014249.2
>
> NM_015584.3
>
> NM_024728.2
>
> Can you tell me how to retrieve these from the database?
>
> Here is the portion of my script I use to retrieve the data:
>
> foreach my $query_transcript (@transcripts_of_interest) {
>
> chomp $query_transcript;
>
> my $transcript = "";
>
> if ($query_transcript =~ /ENST/i){
>
> $transcript = 
> $transcript_adaptor->fetch_by_stable_id("$query_transcript");
>
> }
>
> else{
>
> ($transcript) = @{ 
> $transcript_adaptor->fetch_all_by_external_name("$query_transcript”);
>
> }
>
> unless ($transcript){
>
> $progress->message("Query: $query_transcript failed");
>
> next;
>
> }
>
> foreach my $exon ( @{ $transcript->get_all_Exons() } ) {
>
> my $estring = feature2string($exon);
>
> print "$query_transcript:\t$estring\n";
>
> }
>
> $next_update = $progress->update() if (++$j > $next_update);
>
> }
>
> Best regards
>
> Duarte Molha
>
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