<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi David<div><br></div><div>Are you sure you're using version 62, I just tried your script on 62 and didn't get the error.</div><div>I can't see a call to add_linkage_type at line 1262 in DBEntryAdaptor in version 62 either.</div><div><br></div><div>Can you add these two lines to your code, to get the API version you're running:</div><div><span class="Apple-style-span" style="font-family: Times; "></span><div><span class="Apple-style-span" style="font-family: Times; "><pre id="podParagraph" style="border-top-style: dotted; border-right-style: dotted; border-bottom-style: dotted; border-left-style: dotted; border-top-width: 1px; border-right-width: 1px; border-bottom-width: 1px; border-left-width: 1px; font-family: courier; white-space: pre; position: static; z-index: auto; ">use Bio::EnsEMBL::ApiVersion;<br>
printf( "The API version used is %s\n", software_version() );</pre></span><div><br></div></div></div><div><br></div><div>Regards</div><div>Monika</div><div><br><div><div>On 12 Jun 2011, at 18:46, BURT David wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>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 <a href="http://test.pl">test.pl</a> line 39.<br> XREF OTTHUMG00000016768 ()<br>Use of uninitialized value in printf at <a href="http://test.pl">test.pl</a> 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>-- <br>The University of Edinburgh is a charitable body, registered in<br>Scotland, with registration number SC005336.<br><br><span><dbentry_errors.txt></span><span><dbentry_test.pl></span>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>List admin (including subscribe/unsubscribe): <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>List admin (including subscribe/unsubscribe): <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></div></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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