<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Wanbo,<div>It is currently not possible to dump a subset of species using this method. The set_of_species parameter is used to select which EPO alignment to choose (e.g. this can either be the complete set of the13 species used for this alignment or a short cut "mammals"). You also need to define where to find the species databases (the --db parameter) and the species used for this seq_region (the --species parameter). Also, currently it is only possible to get the ancestral sequences in maf or emf format (the --format parameter).</div><div><br></div><div>eg</div><div> perl ~/src/ensembl_main/ensembl-compara/scripts/dumps/DumpMultiAlign.pl --db <a href="mysql://anonymous@ensembldb:5306/71">mysql://anonymous@ensembldb:5306/71</a> --compara_url <a href="mysql://anonymous@ensembldb:5306/ensembl_compara_71">mysql://anonymous@ensembldb:5306/ensembl_compara_71</a> --seq_region 3 --seq_region_start 10000000 --seq_region_end 10004000 --alignment_type EPO --set_of_species mammals --species cow --restrict --output_file test.epo --output_format maf</div><div><br></div><div>We also have dumps of the EPO 13 way eutherian alignments in emf format on the public ftp site </div><div><a href="ftp://ftp.ensembl.org/pub/release-71/emf/ensembl-compara/epo_13_eutherian/">ftp://ftp.ensembl.org/pub/release-71/emf/ensembl-compara/epo_13_eutherian/</a></div><div><br></div><div>I hope that helps,</div><div>Cheers</div><div>Kathryn</div><div><br><div apple-content-edited="true">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><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-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 style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Kathryn Beal, PhD<br>European Bioinformatics Institute (EMBL-EBI)<br>Wellcome Trust Genome Campus, Hinxton<br>Cambridge CB10 1SD, UK <br>Tel. +44 (0)1223 494458<br><a href="http://www.ensembl.org/">www.ensembl.org</a><br></div></span></div></div>
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<br><div><div>On 17 Jun 2013, at 12:40, Wanbo Li wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear all,<br><br>I am trying to figure out how to extract ancestral sequence for cow based on EPO alignments.<br><br>Firstly, I tried the following command to download the EPO alignments for four species "horse:dog:pig:cow". I got errors listed below, I will be very glad if someone let me know what I am doing wrong here.<br><br>perl ./ensembl-compara/scripts/dumps/DumpMultiAlign.pl --compara_url <a href="mysql://anonymous@ensembldb:5306/ensembl_compara_71">mysql://anonymous@ensembldb:5306/ensembl_compara_71</a> --seq_region 3 --seq_region_start 2000 --seq_region_end 6000 --alignment_type EPO --set_of_species horse:dog:pig:cow --restrict --output_file test.epo<br><br>Could not connect to database ensembl_compara_71 as user anonymous using [DBI:mysql:database=ensembl_compara_71;host=ensembldb;port=5306] as a locator:<br>Unknown MySQL server host 'ensembldb' (1) at /home/wanbo/src/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm line 312.<br><br>-------------------- EXCEPTION --------------------<br>MSG: No matches found for name 'equus_caballus' and assembly '--undef--'<br>STACK Bio::EnsEMBL::Compara::DBSQL::GenomeDBAdaptor::fetch_by_name_assembly /home/wanbo/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/GenomeDBAdaptor.pm:136<br>STACK Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::__ANON__ /home/wanbo/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm:583<br>STACK Bio::EnsEMBL::Utils::Exception::try /home/wanbo/src/ensembl/modules/Bio/EnsEMBL/Utils/Exception.pm:528<br>STACK Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_by_method_link_type_registry_aliases /home/wanbo/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm:584<br>STACK toplevel ./ensembl-compara/scripts/dumps/DumpMultiAlign.pl:425<br>Date (localtime) = Mon Jun 17 13:21:20 2013<br>Ensembl API version = 71<br>---------------------------------------------------<br><br><br>Then another question, if I could dump the EPO alignments later on, how should I extract ancestral sequence for cow?<br><br><br>Sincerely,<br><br>Wanbo<br>_______________________________________________<br>Dev mailing list <a 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">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></body></html>