<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Nicolas,<div class="">In the current release there are 248,916 transcript in the human database so the API fetched all of them before processing them. Then the gene knows which transcript is canonical but a transcript doesn’t knows if it’s canonical which means more queries from the API.</div><div class=""><br class=""></div><div class="">Because of the way the API works it is usually faster to use a slice object to get your gene/transcripts or any other object.</div><div class="">Unless you are really restricted by memory, I would use a foreach loop instead of the while loop with shift.</div><div class=""><br class=""></div><div class="">my $slice_adaptor = $reg->get_adaptor(‘human’, ‘core’, ’slice’);</div><div class="">foreach my $slice (@{$slice_adaptor->fetch_all(’toplevel’)}) {</div><div class=""> foreach my $gene (@{$slice->get_all_Genes}) {</div><div class=""> my $transcript = $gene->canonical_transcript;</div><div class=""> print $transcript->stable_id, “\n”;</div><div class=""> }</div><div class="">}<br class=""><div><br class=""></div><div>We are close to a new release so the servers can also be a bit overloaded.</div><div><br class=""></div><div>Thanks</div><div>Thibaut</div><div><br class=""><blockquote type="cite" class=""><div class="">On 17 Sep 2019, at 16:15, Olson, Andrew <<a href="mailto:olson@cshl.edu" class="">olson@cshl.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Hi Nicolas,</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">For bulk operations that are pretty easy, I like to just query the database directly.</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">echo "select t.* from transcript t, gene g where t.transcript_id = g.canonical_transcript_id and g.is_current = 1” | mysql … > canonicalTranscripts.txt</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Andrew</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">On Sep 17, 2019, at 10:49 AM, Nicolas Thierry-Mieg <<a href="mailto:Nicolas.Thierry-Mieg@univ-grenoble-alpes.fr" class="">Nicolas.Thierry-Mieg@univ-grenoble-alpes.fr</a>> wrote:<br class=""><br class="">Hi list,<br class=""><br class="">I want to obtain the list of Ensembl Human "canonical" transcripts.<br class="">As far as I can see this is not available in the GTF or GFF files that can be downloaded from <a href="http://ftp.ensembl.org" class="">ftp.ensembl.org</a> .<br class=""><br class="">So, I wrote the following small script that uses the perl API to connect to ensembl. My script works, but it's very slow: it took more than 16 hours, just to obtain 66832 ENST identifiers... I'ld expect it to take seconds or minutes, not hours. I must be doing something very wrong but I can't see it.<br class="">Please help, what is wrong with the code below?<br class="">Or if the issue is permanently saturated ensembl servers, is there some other way I could obtain the ensembl canonical transcripts? I tried using the UCSC Table Browser, but there are discrepancies between their "knownCanonical" table and the ensembl canonical transcripts. I also tried biomart but couldn't find "canonical" anywhere.<br class=""><br class=""><br class="">use Bio::EnsEMBL::Registry;<br class="">my $reg = "Bio::EnsEMBL::Registry";<br class="">$reg->load_registry_from_db(<br class=""> -host => '<a href="http://ensembldb.ensembl.org" class="">ensembldb.ensembl.org</a>',<br class=""> -user => 'anonymous',<br class=""> -species => 'homo sapiens'<br class=""> );<br class="">my $transcripts_adaptor = $reg->get_adaptor('human', 'core', 'transcript');<br class="">my $transcripts = $transcripts_adaptor->fetch_all;<br class=""><br class="">while(my $transcript = shift @{$transcripts}) {<br class=""> ($transcript->is_canonical) || next;<br class=""> print $transcript->stable_id."\n" ;<br class="">}<br class=""><br class=""><br class="">Thanks!<br class="">Regards,<br class="">Nicolas<br class=""><br class=""><br class="">_______________________________________________<br class="">Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">Posting guidelines and subscribe/unsubscribe info:<span class="Apple-converted-space"> </span><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.ensembl.org_mailman_listinfo_dev-5Fensembl.org&d=DwICAg&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=ic-pQ08gnhTpvpqfp3_6Uw&m=thfiDlexwfeY-yTcNwP7qpwgWqIZRFegrqeZWtXHPJQ&s=eCdySxAcksmzOro4PpPFfIMSbYapkfEH2bxIcfiOtWA&e=" class="">https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.ensembl.org_mailman_listinfo_dev-5Fensembl.org&d=DwICAg&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=ic-pQ08gnhTpvpqfp3_6Uw&m=thfiDlexwfeY-yTcNwP7qpwgWqIZRFegrqeZWtXHPJQ&s=eCdySxAcksmzOro4PpPFfIMSbYapkfEH2bxIcfiOtWA&e=</a><span class="Apple-converted-space"> </span>Ensembl Blog:<span class="Apple-converted-space"> </span><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ensembl.info_&d=DwICAg&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=ic-pQ08gnhTpvpqfp3_6Uw&m=thfiDlexwfeY-yTcNwP7qpwgWqIZRFegrqeZWtXHPJQ&s=76ALP_8cUWCIkw5wr56dajimDo-tNzjXSQtp4DQ7gME&e=" class="">https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ensembl.info_&d=DwICAg&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=ic-pQ08gnhTpvpqfp3_6Uw&m=thfiDlexwfeY-yTcNwP7qpwgWqIZRFegrqeZWtXHPJQ&s=76ALP_8cUWCIkw5wr56dajimDo-tNzjXSQtp4DQ7gME&e=</a><span class="Apple-converted-space"> </span><br class=""></blockquote><br style="caret-color: rgb(0, 0, 0); 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