[ensembl-dev] Missing IDS in ENSEMBL database

[Duarte Molha]

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
NM_001167607.1
NM_001199987.1
NM_001204090.1
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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20120525/bca98f82/attachment.html>