<html><head><base href="x-msg://113/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi David<div><br></div><div>Sorry about this, but it looks like we had the wrong version of DBEntryAdaptor checked in to branch 62. </div><div>I have checked in the correct version, please checkout the DBEntryAdaptor module again.</div><div><br></div><div>Thanks</div><div>Monika</div><div><br><div><div>On 13 Jun 2011, at 14:44, BURT David 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-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" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div class="WordSection1" style="page: WordSection1; "><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Hi Monika<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">I still get the wrong version<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">With same error about add_linkage_type<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">When you look at<span class="Apple-converted-space"> </span></span>DBEntryAdaptor.pm what do you find at line 1262 and 1263?<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">I am sorry I can’t understand how CVS picks up the wrong version?<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Dave<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Professor David W. Burt<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Chair of Comparative Genomics<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Dept. Genomics and Genetics<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">The Roslin Institute and Royal (Dick) School of Veterinary Studies<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">The Roslin Institute Building<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">University of Edinburgh<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Easter Bush Campus<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Midlothian EH25 9RG<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Phone: +44 (0)131 651 9216<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Lab: +44 (0)131 651 9380<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Fax: +44 (0)131 651 9105<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Email:<span class="Apple-converted-space"> </span><a href="mailto:Dave.Burt@roslin.ed.ac.uk" style="color: blue; text-decoration: underline; ">Dave.Burt@roslin.ed.ac.uk</a><o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">WWW site:<span class="Apple-converted-space"> </span><a href="http://www.roslin.ed.ac.uk/dave-burt/" style="color: blue; text-decoration: underline; ">http://www.roslin.ed.ac.uk/dave-burt/</a><o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">The 6th International chick meeting - Edinburgh:<span class="Apple-converted-space"> </span><a href="http://www.roslin.ed.ac.uk/chick6/" style="color: blue; text-decoration: underline; ">http://www.roslin.ed.ac.uk/chick6/</a><o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Roslin Institute is a company limited by guarantee, registered in Scotland (registered number SC157100) and a Scottish Charity (registered number SC023592). Our registered office is at Roslin, Midlothian, EH25 9PS. VAT registration number 847380013.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">The information contained in this e-mail (including any attachments) is confidential and is intended for the use of the addressee only. The opinions expressed within this e-mail (including any attachments) are the opinions of the sender and do not necessarily constitute those of Roslin Institute (Edinburgh) ("the Institute") unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute<o:p></o:p></span></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, 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-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; ">From:</span></b><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; "><span class="Apple-converted-space"> </span>Monika Komorowska [mailto:monika@ebi.ac.uk]<span class="Apple-converted-space"> </span><br><b>Sent:</b><span class="Apple-converted-space"> </span>13 June 2011 14:18<br><b>To:</b><span class="Apple-converted-space"> </span>BURT David<br><b>Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:dev@ensembl.org" style="color: blue; text-decoration: underline; ">dev@ensembl.org</a><br><b>Subject:</b><span class="Apple-converted-space"> </span>Re: [ensembl-dev] FW: ensembl api query<o:p></o:p></span></div></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Hi David<o:p></o:p></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Would you mind creating a new sub-directory say ensembl_v62 in your home directory, cd into it and checkout version 62 again, using this command:<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span class="apple-style-span"><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">$ cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl checkout -r branch-ensembl-62 ensembl-api</span></span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Add the new path to the PERL5LIB variable in your .cshrc file:<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">setenv PERL5LIB ${PERL5LIB}:${HOME}/ensembl_v62/ensembl/modules<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">and delete any other paths to ensembl/modules<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">You'll need to source the .cshrc file <o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Hopefully this time your script will pick up the correct version of the API<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Thanks<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Monika<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">On 13 Jun 2011, at 14:02, BURT David wrote:<o:p></o:p></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><br><br><o:p></o:p></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Hi Monika,</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Many thanks – I think we are getting close.</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">1_Attached is my copy of<span class="apple-converted-space"> </span></span>DBEntryAdaptor found in D:\Bioinformatics\Ensembl\src\ensembl\modules\Bio\EnsEMBL\DBSQL<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">As you can see “add_linkage_type” is at line 1263 in DBEntryAdaptor in this version 62<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "> <o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Here’s an extract [since file too big for dev list]<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> if ( defined($linkage_type)</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> && $linkage_type ne ""</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> && !$linkage_types{$refID}->{$linkage_key} )</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> {</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> $source_xref = ( defined($source_xref_id)</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> ? $self->fetch_by_dbID($source_xref_id)</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> : undef );</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> $seen{$refID}</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> ->add_linkage_type( $linkage_type, $source_xref || () );</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> $linkage_types{$refID}->{$linkage_key} = 1;</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> }</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> } ## end while ( my $arrRef = shift...</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> } ## end while ( my $rowcache = $sth...</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">2_This was downloaded using instructions from Ensembl (see below) using CVS</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">$ cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl login</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Logging in to :pserver:cvsuser@cvs.sanger.ac.uk:2401/cvsroot/ensembl</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">CVS password: CVSUSER</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">NB: You can install as many Ensembl APIs as you need in this way. To install all the APIs in one go, use the command:</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">$ cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl checkout -r branch-ensembl-62 ensembl-api</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">3_However, I found an old install – based on version 56 – this worked up to version 59, but software failed after that.</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Any more thoughts? Looks like my version 62 is wrong?</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Dave</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span><o:p></o:p></div></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Professor David W. Burt</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Chair of Comparative Genomics</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Dept. Genomics and Genetics</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">The Roslin Institute and Royal (Dick) School of Veterinary Studies</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">The Roslin Institute Building</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">University of Edinburgh</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Easter Bush Campus</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Midlothian EH25 9RG</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); "> </span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Phone: +44 (0)131 651 9216</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Lab: +44 (0)131 651 9380</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Fax: +44 (0)131 651 9105</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Email:<span class="apple-converted-space"> </span><a href="mailto:Dave.Burt@roslin.ed.ac.uk" style="color: blue; text-decoration: underline; ">Dave.Burt@roslin.ed.ac.uk</a></span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">WWW site:<span class="apple-converted-space"> </span><a href="http://www.roslin.ed.ac.uk/dave-burt/" style="color: blue; text-decoration: underline; ">http://www.roslin.ed.ac.uk/dave-burt/</a></span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">The 6th International chick meeting - Edinburgh:<span class="apple-converted-space"> </span><a href="http://www.roslin.ed.ac.uk/chick6/" style="color: blue; text-decoration: underline; ">http://www.roslin.ed.ac.uk/chick6/</a></span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); "> </span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">Roslin Institute is a company limited by guarantee, registered in Scotland (registered number SC157100) and a Scottish Charity (registered number SC023592). Our registered office is at Roslin, Midlothian, EH25 9PS. VAT registration number 847380013.</span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); "> </span><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10.5pt; font-family: Consolas; color: rgb(31, 73, 125); ">The information contained in this e-mail (including any attachments) is confidential and is intended for the use of the addressee only. The opinions expressed within this e-mail (including any attachments) are the opinions of the sender and do not necessarily constitute those of Roslin Institute (Edinburgh) ("the Institute") unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute</span><o:p></o:p></div></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span><o:p></o:p></div></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; padding-top: 3pt; padding-right: 0cm; padding-bottom: 0cm; padding-left: 0cm; border-width: initial; border-color: initial; "><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; ">From:</span></b><span class="apple-converted-space"><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; "> </span></span><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; ">Monika Komorowska [mailto:monika@ebi.ac.uk]<span class="apple-converted-space"> </span><br><b>Sent:</b><span class="apple-converted-space"> </span>13 June 2011 11:01<br><b>To:</b><span class="apple-converted-space"> </span>BURT David<br><b>Cc:</b><span class="apple-converted-space"> </span><a href="mailto:dev@ensembl.org" style="color: blue; text-decoration: underline; ">dev@ensembl.org</a><br><b>Subject:</b><span class="apple-converted-space"> </span>Re: [ensembl-dev] FW: ensembl api query</span><o:p></o:p></div></div></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "> <o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Hi David<o:p></o:p></div></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "> <o:p></o:p></div></div></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Are you sure you're using version 62, I just tried your script on 62 and didn't get the error.<o:p></o:p></div></div></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">I can't see a call to add_linkage_type at line 1262 in DBEntryAdaptor in version 62 either.<o:p></o:p></div></div></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "> <o:p></o:p></div></div></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Can you add these two lines to your code, to get the API version you're running:<o:p></o:p></div></div></div><div><div><div style="border-top-style: dotted; border-right-style: dotted; border-bottom-style: dotted; border-left-style: dotted; 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; "><pre id="podParagraph" style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 12pt; margin-left: 0cm; font-size: 10pt; font-family: 'Courier New'; z-index: auto; "><span style="font-family: Courier; ">use Bio::EnsEMBL::ApiVersion;</span><o:p></o:p></pre><pre style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 10pt; font-family: 'Courier New'; "><span style="font-family: Courier; "> printf( "The API version used is %s\n", software_version() );</span><o:p></o:p></pre></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "> <o:p></o:p></div></div></div></div></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "> <o:p></o:p></div></div></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Regards<o:p></o:p></div></div></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Monika<o:p></o:p></div></div></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "> <o:p></o:p></div></div><div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">On 12 Jun 2011, at 18:46, BURT David wrote:<o:p></o:p></div></div></div><p class="MsoNormal" style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 12pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "> <o:p></o:p></p><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">any more ideas on problem below?<br><br>made a few changes - still not working on my system (tried two PCs)<br><br>interesting - I can get $dbe->display_id() but nothing from $dbe->dbname()<br>also able to get versions, release and other parameters but no dbname (this is w=oine of the things I wanted)<br>so looks like the external database name is not being assigned<br><br>however Bert and Daniel get the simple script to work<br><br>I have re-sinatlled v62 - still odd behaviour<br><br>"Can't locate object method "add_linkage_type" via package "Bio::EnsEMBL::IdentityXref"<br>at /cygdrive/c/Bioinformatics/Ensembl/src/ensembl/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm line 1262."<br><br>where there is no add_linkage_type metrhod in Bio::EnsEMBL::IdentityXref<br><br>so I think must be earlier problem related to dbname not being assigned<br><br>must be something with my setup?<br><br><br><br>Recently ran a "simple" test of my Ensembl perl api install using an example from the core tutorial - to list external database entries.<br><br>Perl program and output is attached and below.<br><br>PERL SCRIPT<br>==========<br><br>#!/bin/perl.exe -w<br><br>use strict;<br><br>use Bio::EnsEMBL::Registry;<br>my $registry = 'Bio::EnsEMBL::Registry';<br>$registry->load_registry_from_db(-host => 'ensembldb.ensembl.org', -user => 'anonymous');<br><br>print $gene_adaptor->dbc->dbname."\n";<br>print $gene_adaptor->dbc->port."\n\n";<br><br># Define a helper subroutine to print DBEntries<br>sub print_DBEntries<br>{<br> my $db_entries = shift;<br><br> foreach my $dbe ( @{$db_entries} ) {<br> printf "\tXREF %s (%s)\n", $dbe->display_id(), $dbe->dbname();<br> }<br>}<br><br>my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );<br><br># Get the 'COG6' gene from human<br>my $gene = $gene_adaptor->fetch_by_display_label('COG6');<br><br>print "GENE ", $gene->stable_id(), "\n";<br>print_DBEntries( $gene->get_all_DBEntries() );<br><br>foreach my $transcript ( @{ $gene->get_all_Transcripts() } ) {<br> print "TRANSCRIPT ", $transcript->stable_id(), "\n";<br> print_DBEntries( $transcript->get_all_DBEntries() );<br><br> # Watch out: pseudogenes have no translation<br> if ( defined $transcript->translation() ) {<br> my $translation = $transcript->translation();<br><br> print "TRANSLATION ", $translation->stable_id(), "\n";<br> print_DBEntries( $translation->get_all_DBEntries() );<br> }<br>}<br><br><br>OUTPUT<br>======<br><br>homo_sapiens_core_62_37g<br>5306<br><br>GENE ENSG00000133103<br>Use of uninitialized value in printf at<span class="apple-converted-space"> </span><a href="http://test.pl" style="color: blue; text-decoration: underline; ">test.pl</a><span class="apple-converted-space"> </span>line 39.<br> XREF OTTHUMG00000016768 ()<br>Use of uninitialized value in printf at<span class="apple-converted-space"> </span><a href="http://test.pl" style="color: blue; text-decoration: underline; ">test.pl</a><span class="apple-converted-space"> </span>line 39.<br> XREF COG6 ()<br>TRANSCRIPT ENST00000416691<br><br>Can't locate object method "add_linkage_type" via package "Bio::EnsEMBL::IdentityXref"<br>at /cygdrive/c/Bioinformatics/Ensembl/src/ensembl/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm line 1262.<br><br><br><br>--<span class="apple-converted-space"> </span><br>The University of Edinburgh is a charitable body, registered in<br>Scotland, with registration number SC005336.<br><br><dbentry_errors.txt><dbentry_test.pl>_______________________________________________<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>_______________________________________________<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><o:p></o:p></div></div></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "> <o:p></o:p></div></div><div><div><div><div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 13.5pt; font-family: Helvetica, sans-serif; color: black; ">Monika Komorowska</span><o:p></o:p></div></div></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 13.5pt; font-family: Helvetica, sans-serif; color: black; ">EnsEMBL Software Developer</span><o:p></o:p></div></div></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 13.5pt; font-family: Helvetica, sans-serif; color: black; "> </span><o:p></o:p></div></div></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 13.5pt; font-family: Helvetica, sans-serif; color: black; ">European Bioinformatics Institute (EMBL-EBI)</span><o:p></o:p></div></div></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 13.5pt; font-family: Helvetica, sans-serif; color: black; ">tel: +44(0) 1233 494 409</span><o:p></o:p></div></div></div></div></div></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "> <o:p></o:p></div></div></div></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div><div><div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 13.5pt; font-family: Helvetica, sans-serif; color: black; ">Monika Komorowska<o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 13.5pt; font-family: Helvetica, sans-serif; color: black; ">EnsEMBL Software Developer<o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 13.5pt; font-family: Helvetica, sans-serif; color: black; "><o:p> </o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 13.5pt; font-family: Helvetica, sans-serif; color: black; ">European Bioinformatics Institute (EMBL-EBI)<o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 13.5pt; font-family: Helvetica, sans-serif; color: black; ">tel: +44(0) 1233 494 409<o:p></o:p></span></div></div></div></div></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div></div></div></span></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: 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; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; 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 style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; 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 style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; 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 style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Monika Komorowska</div><div>EnsEMBL Software Developer</div><div><br></div><div>European Bioinformatics Institute (EMBL-EBI)<br></div><div>tel: +44(0) 1233 494 409</div></div></span></div></span></div></span></span>
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