<html><head><base href="x-msg://15/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Duarte,<div>I went through the four first of your IDs:</div><div><br><div><div>On 25 May 2012, at 10:14, Duarte Molha wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div lang="EN-GB" link="blue" vlink="purple"><div class="WordSection1" style="page: WordSection1; "><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Dear Developers<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">I created a simple script to output the exons of specific transcripts with NM ids.<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">It works fine for all but a small list of IDS. The large majority of the failed IDS have been suppressed from NCBI<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Because they were found to be a “ <i>nonsense-mediated mRNA decay (NMD) candidate</i>” so I do not mind eliminating those records from my query.<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><em><span style="font-size: 10pt; font-family: Arial, sans-serif; color: black; border-top-style: none; border-right-style: none; border-bottom-style: none; border-left-style: none; border-top-color: windowtext; border-right-color: windowtext; border-bottom-color: windowtext; border-left-color: windowtext; border-top-width: 1pt; border-right-width: 1pt; border-bottom-width: 1pt; border-left-width: 1pt; padding-top: 0cm; padding-right: 0cm; padding-bottom: 0cm; padding-left: 0cm; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: white; font-style: normal; background-position: initial initial; background-repeat: initial initial; "><o:p> </o:p></span></em></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><em><span style="font-size: 10pt; font-family: Arial, sans-serif; color: black; border-top-style: none; border-right-style: none; border-bottom-style: none; border-left-style: none; border-top-color: windowtext; border-right-color: windowtext; border-bottom-color: windowtext; border-left-color: windowtext; border-top-width: 1pt; border-right-width: 1pt; border-bottom-width: 1pt; border-left-width: 1pt; padding-top: 0cm; padding-right: 0cm; padding-bottom: 0cm; padding-left: 0cm; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: white; font-style: normal; background-position: initial initial; background-repeat: initial initial; ">However some of the ones that fail are in NCBI database and for some reason ENSEMBL is not able to query them:<o:p></o:p></span></em></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><em><span style="font-size: 10pt; font-family: Arial, sans-serif; color: black; border-top-style: none; border-right-style: none; border-bottom-style: none; border-left-style: none; border-top-color: windowtext; border-right-color: windowtext; border-bottom-color: windowtext; border-left-color: windowtext; border-top-width: 1pt; border-right-width: 1pt; border-bottom-width: 1pt; border-left-width: 1pt; padding-top: 0cm; padding-right: 0cm; padding-bottom: 0cm; padding-left: 0cm; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: white; font-style: normal; background-position: initial initial; background-repeat: initial initial; ">NM</span></em>_001040409.1</div></div></div></span></blockquote>It is an NMD transcript.<br><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div lang="EN-GB" link="blue" vlink="purple"><div class="WordSection1" style="page: WordSection1; "><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">NM_001167607.1</div></div></div></span></blockquote>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</div><div><a href="http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000196743;r=5:150591711-150650001;t=ENST00000523466">http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000196743;r=5:150591711-150650001;t=ENST00000523466</a><br><blockquote type="cite"><div lang="EN-GB" link="blue" vlink="purple"><div class="WordSection1" style="page: WordSection1; "><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">NM_001199987.1</div></div></div></blockquote>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.</div><div><a href="http://www.ncbi.nlm.nih.gov/gene/?term=NM_001199987.1">http://www.ncbi.nlm.nih.gov/gene/?term=NM_001199987.1</a></div><div><a href="http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000165264;r=9:32552997-32573160;t=ENST00000379847">http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000165264;r=9:32552997-32573160;t=ENST00000379847</a><br><blockquote type="cite"><div lang="EN-GB" link="blue" vlink="purple"><div class="WordSection1" style="page: WordSection1; "><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; line-height: 12pt; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: white; vertical-align: baseline; position: static; z-index: auto; ">NM_001204090.1<o:p></o:p></div></div></div></blockquote>Same problem as above, we did not use this sequence.</div><div><br></div><div>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</div><div><br></div><div>Regards</div><div>Thibaut</div><div><br><blockquote type="cite"><div lang="EN-GB" link="blue" vlink="purple"><div class="WordSection1" style="page: WordSection1; "><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">NM_001242881.1<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">NM_014249.2<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">NM_015584.3<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">NM_024728.2<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Can you tell me how to retrieve these from the database?<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Here is the portion of my script I use to retrieve the data:<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">foreach my $query_transcript (@transcripts_of_interest) {<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "> chomp $query_transcript;<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "> my $transcript = "";<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "> if ($query_transcript =~ /ENST/i){<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "> $transcript = $transcript_adaptor->fetch_by_stable_id("$query_transcript");<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "> }<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "> else{<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "> ($transcript) = @{ $transcript_adaptor->fetch_all_by_external_name("$query_transcript”);<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "> }<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "> unless ($transcript){<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "> $progress->message("Query: $query_transcript failed");<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "> next;<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "> }<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "> foreach my $exon ( @{ $transcript->get_all_Exons() } ) {<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "> my $estring = feature2string($exon);<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "> print "$query_transcript:\t$estring\n";<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "> }<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "> $next_update = $progress->update() if (++$j > $next_update);<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">}<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Best regards<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="PT" style="font-size: 10pt; font-family: Arial, sans-serif; ">Duarte Molha<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div></div>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org" style="color: blue; text-decoration: underline; ">Dev@ensembl.org</a><br>List admin (including subscribe/unsubscribe):<span class="Apple-converted-space"> </span><a href="http://lists.ensembl.org/mailman/listinfo/dev" style="color: blue; text-decoration: underline; ">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog:<span class="Apple-converted-space"> </span><a href="http://www.ensembl.info/" style="color: blue; text-decoration: underline; ">http://www.ensembl.info/</a><br></div></blockquote></div><br></div></body></html>