Hi Enrico<br><br>That warning still indicates you are not on the correct version. This can sometimes happens when you have downloaded the api using a command line. Trying something more like<br><br>wget "http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&only_with_tag=branch-ensembl-68&view=tar"<br><br>The & is interpreted as a request to fork the download command.<br><br>Should you need other versions you can replace the version in the above location with the required one. For instance to get 67 you can use<br><br>wget "http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&only_with_tag=branch-ensembl-67&view=tar"<br><br><br>As for gencode7 data I believe it is available with release 62; hopefully someone will be happy to correct me should I be wrong. I strongly recommend always using the api equal to the release<br><br> Andy<br><br>enrico1970@yahoo.com wrote:<br><br><div style="color:#000; background-color:#fff; font-family:Courier New, courier, monaco, monospace, sans-serif;font-size:14pt"><div><span>Dear Kieron,<br></span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><span>thank you very much for the answer.</span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><span>I downloaded the ensemble core code from the page </span><span>http://www.ensembl.org/info/docs/api/api_installation.html, in the section "Download the API packages you need: ensembl" at the link:</span><span> </span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style:
normal;"><br><span></span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><span>http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&only_with_tag=branch-ensembl-68&view=tar</span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><br><span></span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><span>I inserted db_version => 68 in the code and it retrieves the list of databases,</span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style:
normal;"><span>but when I run the code to retrieve CDS, cDNA, 5' and 3' (that you'll find at the end of this e-mail) it reports the error:</span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><br><span></span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><span>"For homo_sapiens_core_68_37 there is a difference in the software release (69) and the database release (68). You should update one of these to ensure that your script does not crash."</span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><span>I would really appreciate if you could reply to the following
questions:</span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><br>
<span></span></div>
<div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><span>-How may understand which version of the code I downloaded (the link contained "</span><span>branch-ensembl-68</span><span>" but it is not recognised as version 68) <br></span></div>
<div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><span></span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><span>-How can I retrieve the release 68 of the software? <br></span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;">-<span>How can I retrieve the older relases of the software (I will need to compare the results with with</span> Gencode v7<span> that it could use a different annotation version) ? <br>
</span>
</div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><br>
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<div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;">Thanks,</div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;">Enrico<br>
<span></span></div>
<div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><span></span></div><br><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;">You can find the <span>code to retrieve CDS, cDNA, 5' and 3' below</span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><br><span></span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><span><br> </span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color:
transparent; font-style: normal;">use Bio::EnsEMBL::Registry;<br><br>my $registry = 'Bio::EnsEMBL::Registry';<br>$registry->load_registry_from_db(<br> -host => 'ensembldb.ensembl.org', # alternatively 'useastdb.ensembl.org'<br> -user => 'anonymous',<br> -verbose => 1,<br> db_version => 68<br>);<br><br>my $slice_adaptor = $registry->get_adaptor( "Human", 'Core', 'Slice' );<br>my $slice = $slice_adaptor->fetch_by_region( 'chromosome', 'X', 1e6, 10e6 );<br><br>my $genes = $slice->get_all_Genes();<br><br>my $transcripts = $gene->get_all_Transcripts();<br># The spliced_seq() method returns the concatenation of the exon<br># sequences. This is the cDNA of the transcript<br>print "cDNA: ", $transcript->spliced_seq(), "\n";<br><br># The translateable_seq() method returns only the CDS of the transcript<br>print "CDS: ", $transcript->translateable_seq(),
"\n";<br><br># UTR sequences are obtained via the five_prime_utr() and<br># three_prime_utr() methods<br>my $fiv_utr = $transcript->five_prime_utr();<br>my $thr_utr = $transcript->three_prime_utr();<br><br>print "5' UTR: ", ( defined $fiv_utr ? $fiv_utr->seq() : "None" ), "\n";<br>print "3' UTR: ", ( defined $thr_utr ? $thr_utr->seq() : "None" ), "\n";<br><br># The protein sequence is obtained from the translate() method. If the<br># transcript is non-coding, undef is returned.<br>my $protein = $transcript->translate();<br><br>print "Translation: ", ( defined $protein ? $protein->seq() : "None" ), "\n";<br></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent;
font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0);
font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><br></div> <div style="font-family: Courier New, courier, monaco, monospace, sans-serif; font-size: 14pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span
style="font-weight:bold;">From:</span></b> Kieron Taylor <ktaylor@ebi.ac.uk><br> <b><span style="font-weight: bold;">To:</span></b> enrico1970@yahoo.com; Ensembl developers list <dev@ensembl.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Monday, 8 October 2012, 20:03<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [ensembl-dev] Ensemble api tutorial<br> </font> </div> <br>Dear Enrico,<br><br>This error is consistent with using the wrong version of the API for a given database.<br><br>Under these circumstances you can use the -verbose => 1 flag in load_registry_from_db() to highlight the problem.<br><br>If you have checked head code out of CVS, your code will be too new for our public servers. You can correct this with either a release 68 code download, or (less recommended) add the db_version => 68 argument to the load_registry command.<br><br>Regards,<br><br>On 8 Oct 2012, at 18:29, <a
ymailto="mailto:enrico1970@yahoo.com" href="mailto:enrico1970@yahoo.com">enrico1970@yahoo.com</a> wrote:<br><br>> Dear Support,<br>> I am executing the code to "get a list of all Ensemble databases installed on a given database host" from <a href="http://www.ensembl.org/info/docs/api/core/core_tutorial.html" target="_blank">http://www.ensembl.org/info/docs/api/core/core_tutorial.html</a><br>> but when I run the code it does not return any database or any error.<br>> <br>> Please find the code below.<br>> <br>> Thanks,<br>> <br>> Enrico<br>> <br>> use Bio::EnsEMBL::Registry;<br>> <br>> my $registry = 'Bio::EnsEMBL::Registry';<br>> <br>> $registry->load_registry_from_db(<br>> -host => 'ensembldb.ensembl.org', # alternatively 'useastdb.ensembl.org'<br>> -user => 'anonymous'<br>> );<br>> <br>> my @db_adaptors = @{ $registry->get_all_DBAdaptors() };<br>>
<br>> foreach my $db_adaptor (@db_adaptors) {<br>> my $db_connection = $db_adaptor->dbc();<br>> <br>> printf(<br>> "species/group\t%s/%s\ndatabase\t%s\nhost:port\t%s:%s\n\n",<br>> $db_adaptor->species(), $db_adaptor->group(),<br>> $db_connection->dbname(), $db_connection->host(),<br>> $db_connection->port()<br>> );<br>> }<br>> _______________________________________________<br>> Dev mailing list <a ymailto="mailto:Dev@ensembl.org" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>> Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>> Ensembl Blog: <a href="http://www.ensembl.info/"
target="_blank">http://www.ensembl.info/</a><br><br>Kieron Taylor PhD.<br>Ensembl Core software developer<br><br>EMBL - European Bioinformatics Institute<br><br><br><br><br><br> </div> </div> </div>