<html><head><base href="x-msg://229/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi David<div><br></div><div>You are right in that you need to handle probe and probesets independently, this has always been the case.</div><div><br></div><div>You could potentially have a single point of access if you use the DBEntryAdaptor directly:</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>DBEntryAdaptor::fetch_all_by_name($transcript->stable_id);</div><div><br></div><div>However, this would get all the DBEntry objects for that transcript, and you would have to filter out the Probe/ProbeSet entries and then fetch them via their respective adaptors. I think this is a much less efficient way of accessing the data, but does make information about the xref available via DBEntry->linkage_annotation.</div><div><br></div><div>If you haven't already seen the examples script, you can find it here:</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> ensembl-functgenomics/scripts/examples</span>/microarray_annotation_example.pl</div><div><br></div><div>I hope this helps.</div><div><br></div><div>Thanks</div><div><br></div><div>Nath</div><div><br></div><div><br></div><div><div><div>On 27 Apr 2012, at 12:54, David Bauer 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="DE" 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; "><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(31, 73, 125); ">Answer to myself:<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; "><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(31, 73, 125); "><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; "><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(31, 73, 125); ">These are probes and not probesets. So one must use the probe adapter.<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; "><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(31, 73, 125); ">This was different in earlier versions of the funcgen api.<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; "><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(31, 73, 125); ">The current implementation is cleaner but also more confusing ;-)<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; "><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(31, 73, 125); "><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; "><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(31, 73, 125); ">Kind regards,<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; "><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(31, 73, 125); ">David.<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; "><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div><div style="border-right-style: none; border-bottom-style: none; border-left-style: none; border-width: initial; border-color: initial; border-top-style: solid; border-top-color: rgb(181, 196, 223); border-top-width: 1pt; padding-top: 3pt; padding-right: 0cm; padding-bottom: 0cm; padding-left: 0cm; "><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; ">Von:</span></b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; "><span class="Apple-converted-space"> </span><a href="mailto:dev-bounces@ensembl.org" style="color: blue; text-decoration: underline; ">dev-bounces@ensembl.org</a><span class="Apple-converted-space"> </span>[mailto:dev-bounces@ensembl.org]<br><b>Gesendet:</b><span class="Apple-converted-space"> </span>Freitag, 27. April 2012 12:44<br><b>An:</b><span class="Apple-converted-space"> </span>Ensembl developers list (<a href="mailto:dev@ensembl.org" style="color: blue; text-decoration: underline; ">dev@ensembl.org</a>)<br><b>Betreff:</b><span class="Apple-converted-space"> </span>[ensembl-dev] get Illumina probesets via api<o:p></o:p></span></div></div></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="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">Hi,<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; "><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; "><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; "><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">I’m trying to get Illumina probesets mapped to a transcript via<span style="color: rgb(31, 73, 125); "><o:p></o:p></span></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; "><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(31, 73, 125); "><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; "><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">my @probesets = @{$pba->fetch_all_by_linked_Transcript($transcript)}<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; "><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(31, 73, 125); "><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; "><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">This gives me all probesets from the various Affy chips but the Illumina, Codelink and Phalanx (displayed on the web page) are missing.<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; "><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">Is there some different api call I must use to get those mappings ? (using version 66)<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; "><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; "><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; "><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">Kind regards,<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; "><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">David.</span><span style="font-size: 8pt; font-family: Arial, sans-serif; "><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></span></blockquote></div><br><div>
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