<html><head><base href="x-msg://14/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Alan,</div><div>The EPO_LOW_COVERAGE alignments can be downloaded from the following ftp site:</div><div><br></div><a href="ftp://ftp.ensembl.org/pub/release-67/emf/ensembl-compara/epo_35_eutherian/">ftp://ftp.ensembl.org/pub/release-67/emf/ensembl-compara/epo_35_eutherian/</a><br><div><div><br></div><div>Cheers</div><div>Kathryn</div><div><br></div><br class="Apple-interchange-newline"><blockquote type="cite"><div ocsi="x"><div style="margin-top: 0px; margin-bottom: 0px; ">Hi Stephen,<br><br>Thanks a lot. The basic_ma.pl<a></a><a></a><span class="Apple-converted-space"> </span>you attached worked great for downloading small regions. I need to download genome-wide EPO_LOW_COVERAGE<a></a><a></a><span class="Apple-converted-space"> </span>alignments for some analyses we are trying to do on the gibbon genome. I was hoping to be able to use the script to download alignments for each chromosome, but when I tried that with chr22<a></a><a></a><span class="Apple-converted-space"> </span>I got a "DBD<a></a><a></a>::mysql<a></a><a></a>::st<a></a><a></a>execute failed: Lost connection to MySQL<a></a><a></a><span class="Apple-converted-space"> </span>server during query" error. It looks like whole chromosomes cannot easily be download via the API. Is there somewhere that I can download the EPO_LOW_COVERAGE<a></a><a></a><span class="Apple-converted-space"> </span>alignments as text files? I googled<a></a><a></a><span class="Apple-converted-space"> </span>around and I have not been able to find a place to download them.</div><p style="margin-top: 0px; margin-bottom: 0px; "> </p><div style="margin-top: 0px; margin-bottom: 0px; "><font face="times new roman">Thanks,</font></div><p style="margin-top: 0px; margin-bottom: 0px; "> </p><div style="margin-top: 0px; margin-bottom: 0px; "><font face="times new roman">Alan</font> <br>________________________________________<br>From:<span class="Apple-converted-space"> </span><a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a><a></a><a></a><span class="Apple-converted-space"> </span>[<a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a><a></a><a></a>] On Behalf Of Stephen Fitzgerald [<a href="mailto:stephenf@ebi.ac.uk">stephenf@ebi.ac.uk</a><a></a><a></a>]<br>Sent: Thursday, June 14, 2012 9:36 AM<br>To: Ensembl<a></a><a></a><span class="Apple-converted-space"> </span>developers list<br>Subject: Re: [ensembl<a></a><a></a>-dev] Problem with DumpAlignedGenes.pl<a></a><a></a><span class="Apple-converted-space"> </span>script<br><br>Hi Alan, I've commited<a></a><a></a><span class="Apple-converted-space"> </span>some changes to the DumpAlignedGenes.pl<a></a><a></a><span class="Apple-converted-space"> </span>in cvs<a></a><a></a><br>(head) which should make it easier to use for retrieving multiple<br>alignments. The --set_of_species<a></a><a></a><span class="Apple-converted-space"> </span>flag is used to find alignments<br>consisting of that particular set of species (this is why you see the<br>exception below as the EPO_LOW_COVERAGE<a></a><a></a><span class="Apple-converted-space"> </span>alignments consists of 35 species<br>and not just human:rat:mouse<a></a><a></a>).<br>I've added a new flag "--species_set_name<a></a><a></a>" which will make it easier to<br>get alignments from the EPO_LOW_COVERAGE<a></a><a></a><span class="Apple-converted-space"> </span>set.<br><br>eg<a></a><a></a>.<br>perl<a></a><a></a> DumpAlignedGenes.pl<a></a><a></a> --alignment_type<a></a><a></a><span class="Apple-converted-space"> </span>EPO_LOW_COVERAGE<a></a><a></a><br>--species_set_name<a></a><a></a><span class="Apple-converted-space"> </span>mammals --seq_region<a></a><a></a><span class="Apple-converted-space"> </span>8 --seq_region_start<a></a><a></a><span class="Apple-converted-space"> </span>21180813<br>--seq_region_end<a></a><a></a><span class="Apple-converted-space"> </span>21188452 --species rat --genes_from<a></a><a></a><span class="Apple-converted-space"> </span>chimp<br><br>I've also attahed<a></a><a></a><span class="Apple-converted-space"> </span>a basic script which will allow you to get all the<br>alignments from the EPO_LOW_COVERAGE<a></a><a></a><span class="Apple-converted-space"> </span>when you define a reference species<br>and coordinates (I've hard-coded "sus_scrofa<a></a><a></a>" as the reference).<br><br>You may also find some parts of this script of use:<br><a href="http://www.ebi.ac.uk/~stephenf/Workshops/Cambridge_march2012/Exercises/Solutions/align_slice.txt">http://www.ebi.ac.uk/~stephenf/Workshops/Cambridge_march2012/Exercises/Solutions/align_slice.txt</a><br><br>(It prints the nucleotide bases and assembly positions for both the pig<br>myostatin<a></a><a></a> (MSTN<a></a><a></a>) gene and it's bovine ortholog<a></a><a></a><span class="Apple-converted-space"> </span>where the aligned sequences<br>differ)<br><br>and the output from it is here:<br><a href="http://www.ebi.ac.uk/~stephenf/Workshops/Cambridge_march2012/Exercises/Solutions/align_slice.out.txt">http://www.ebi.ac.uk/~stephenf/Workshops/Cambridge_march2012/Exercises/Solutions/align_slice.out.txt</a><br><br>If you have any more questions, get back in touch.<br><br>All the best,<br>Stephen.<br><br><br><br><br>On Wed, 13 Jun 2012, Harris, Ronald Alan wrote:<br><br>> Hi Kathryn and Stephen,<br>><br>> Thanks for helping me out with DumpAlignedGenes.pl<a></a><a></a>. The scripts that both of you sent me now work, but there is another problem. According to the help,<br>> you can get alignments from multiple species using this:<br>><br>> [--set_of_species<a></a><a></a><span class="Apple-converted-space"> </span>species1:species2:species3<a></a><a></a>:...]<br>><br>> I ran both of your scripts with this command line<br>><br>> perl<a></a><a></a> DumpAlignedGenes.pl<a></a><a></a><span class="Apple-converted-space"> </span>--set_of_species<a></a><a></a><span class="Apple-converted-space"> </span>"human:rat:mouse<a></a><a></a>"<br>><br>> but I get this error (line numbers based on the script Kathryn sent):<br>><br>> -------------------- WARNING ----------------------<br>> MSG: No Bio::EnsEMBL<a></a><a></a>::Compara<a></a><a></a>::MethodLinkSpeciesSet<a></a><a></a><span class="Apple-converted-space"> </span>found for<br>> <EPO_LOW_COVERAGE<a></a><a></a>> and homo_sapiens<a></a><a></a>(GRCh37<a></a><a></a>), rattus_norvegicus<a></a><a></a>(RGSC3.4<a></a><a></a>), mus_musculus<a></a><a></a>(NCBIM37<a></a><a></a>)<br>> FILE: Compara<a></a><a></a>/DBSQL<a></a><a></a>/MethodLinkSpeciesSetAdaptor.pm<a></a><a></a><span class="Apple-converted-space"> </span>LINE: 508<br>> CALLED BY: DumpAlignedGenes.kathryn.pl<a></a><a></a> LINE: 385<br>> Ensembl<a></a><a></a><span class="Apple-converted-space"> </span>API version = 67<br>> ---------------------------------------------------<br>> -------------------- EXCEPTION --------------------<br>> MSG: The database do not contain any EPO_LOW_COVERAGE<a></a><a></a><span class="Apple-converted-space"> </span>data for human:rat:mouse<a></a><a></a>!<br>> STACK toplevel<a></a><a></a><span class="Apple-converted-space"> </span>DumpAlignedGenes.kathryn.pl:389<a></a><a></a><br>> Ensembl<a></a><a></a><span class="Apple-converted-space"> </span>API version = 67<br>> ---------------------------------------------------<br>><br>> This is after setting the alignment_type<a></a><a></a><span class="Apple-converted-space"> </span>to "EPO_LOW_COVERAGE<a></a><a></a>" which is what I want to use, but I get a similar error if I use the default alignment_type<a></a><a></a><br>> of BLASTZ_NET<a></a><a></a>.<br>><br>> What I ultimately want to do is pull out multiple alignments for all species in the 35 eutherian<a></a><a></a><span class="Apple-converted-space"> </span>mammals EPO_LOW_COVERAGE<a></a><a></a><span class="Apple-converted-space"> </span>for a set of genes that I am<br>> interested in analyzing. Can I do that with this script?<br>><br>> Thanks,<br>><br>> Alan<br>><br>><br>><br>> _________________________________________________________________________________________________________________________________________________________<br>> From:<span class="Apple-converted-space"> </span><a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a><a></a><a></a><span class="Apple-converted-space"> </span>[<a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a><a></a><a></a>] On Behalf Of Kathryn Beal [<a href="mailto:kbeal@ebi.ac.uk">kbeal@ebi.ac.uk</a><a></a><a></a>]<br>> Sent: Thursday, May 31, 2012 5:24 AM<br>> To: Ensembl<a></a><a></a><span class="Apple-converted-space"> </span>developers list<br>> Subject: Re: [ensembl<a></a><a></a>-dev] Problem with DumpAlignedGenes.pl<a></a><a></a><span class="Apple-converted-space"> </span>script<br>><br>> Hi Alan, As you may have noticed, this script has not been updated for some time. I've made various updates and the script now works. I've committed this<br>> to the cvs<a></a><a></a> ensembl-compara<a></a><a></a><span class="Apple-converted-space"> </span>HEAD code. I'll send a separate email with this attached for you.<br>><br>> Cheers<br>> Kathryn<br>><br>> Hi,<br>><br>> I am trying to use the DumpAlignedGenes.pl<a></a><a></a><span class="Apple-converted-space"> </span>in version 67 of the ensembl-compara<a></a><a></a><span class="Apple-converted-space"> </span>API. I have made the following necessary changes to the script<br>> (attached script has these changes):<br>><br>> 1. When running the script without arguments as a test I get this error:<br>><br>> ------------------ DEPRECATED ---------------------<br>> Deprecated method call in file DumpAlignedGenes.pl<a></a><a></a><span class="Apple-converted-space"> </span>line 365.<br>> Method Bio::EnsEMBL<a></a><a></a>::DBSQL<a></a><a></a>::MetaContainer<a></a><a></a>::get_Species<a></a><a></a><span class="Apple-converted-space"> </span>is deprecated.<br>> Call is deprecated. Use $self->get_common_name<a></a><a></a>() / $self->get_classification<a></a><a></a>() / $self->get_scientific_name<a></a><a></a>() instead<br>> Ensembl<a></a><a></a><span class="Apple-converted-space"> </span>API version = 67<br>> ---------------------------------------------------<br>> -------------------- EXCEPTION --------------------<br>> MSG: No matches found for name 'Homininae<a></a><a></a><span class="Apple-converted-space"> </span>Homo sapiens' and assembly '--undef<a></a><a></a>--'<br>> STACKBio<a></a><a></a>::EnsEMBL<a></a><a></a>::Compara<a></a><a></a>::DBSQL<a></a><a></a>::GenomeDBAdaptor<a></a><a></a>::fetch_by_name_assembly<a></a><a></a><span class="Apple-converted-space"> </span>/home/rharris1<a></a><a></a>/work/ensembl<a></a><a></a>/api<a></a><a></a>/ensembl-compara<a></a><a></a>/modules/Bio/EnsEMBL<a></a><a></a>/Compara<a></a><a></a>/DBSQL<a></a><a></a>/<br>> GenomeDBAdaptor.pm:131<a></a><a></a><br>> STACK toplevel<a></a><a></a><span class="Apple-converted-space"> </span>DumpAlignedGenes.pl:369<a></a><a></a><br>> Ensembl<a></a><a></a><span class="Apple-converted-space"> </span>API version = 67<br>><br>> I changed line 365 from<br>><br>> my $this_binomial_id<a></a><a></a><span class="Apple-converted-space"> </span>= $this_meta_container_adaptor<a></a><a></a>->get_Species<a></a><a></a>->binomial;<br>><br>> to<br>><br>> my $this_binomial_id<a></a><a></a><span class="Apple-converted-space"> </span>= $this_meta_container_adaptor<a></a><a></a>->get_scientific_name<a></a><a></a>;<br>> $this_binomial_id<a></a><a></a><span class="Apple-converted-space"> </span>=~ s/\s/_/;<br>><br>> which fixes this error.<br>><br>> 2. I also get this similar error:<br>><br>> ------------------ DEPRECATED ---------------------<br>> Deprecated method call in file DumpAlignedGenes.pl<a></a><a></a><span class="Apple-converted-space"> </span>line 436.<br>> Method Bio::EnsEMBL<a></a><a></a>::DBSQL<a></a><a></a>::MetaContainer<a></a><a></a>::get_Species<a></a><a></a><span class="Apple-converted-space"> </span>is deprecated.<br>> Call is deprecated. Use $self->get_common_name<a></a><a></a>() / $self->get_classification<a></a><a></a>() / $self->get_scientific_name<a></a><a></a>() instead<br>> Ensembl<a></a><a></a><span class="Apple-converted-space"> </span>API version = 67<br>> ---------------------------------------------------<br>> -------------------- EXCEPTION --------------------<br>> MSG: No matches found for name 'Murinae<a></a><a></a> Rattus<a></a><a></a><span class="Apple-converted-space"> </span>norvegicus<a></a><a></a>' and assembly '--undef<a></a><a></a>--'<br>> STACKBio<a></a><a></a>::EnsEMBL<a></a><a></a>::Compara<a></a><a></a>::DBSQL<a></a><a></a>::GenomeDBAdaptor<a></a><a></a>::fetch_by_name_assembly<a></a><a></a><span class="Apple-converted-space"> </span>/home/rharris1<a></a><a></a>/work/ensembl<a></a><a></a>/api<a></a><a></a>/ensembl-compara<a></a><a></a>/modules/Bio/EnsEMBL<a></a><a></a>/Compara<a></a><a></a>/DBSQL<a></a><a></a>/<br>> GenomeDBAdaptor.pm:131<a></a><a></a><br>> STACK toplevel<a></a><a></a><span class="Apple-converted-space"> </span>DumpAlignedGenes.pl:440<a></a><a></a><br>> Ensembl<a></a><a></a><span class="Apple-converted-space"> </span>API version = 67<br>> ---------------------------------------------------<br>><br>> I changed line 436 from<br>><br>> my $source_binomial_id<a></a><a></a><span class="Apple-converted-space"> </span>= $meta_container_adaptor<a></a><a></a>->get_scientific_name<a></a><a></a>;<br>><br>> to<br>><br>> my $source_binomial_id<a></a><a></a><span class="Apple-converted-space"> </span>= $meta_container_adaptor<a></a><a></a>->get_scientific_name<a></a><a></a>;<br>> $source_binomial_id<a></a><a></a><span class="Apple-converted-space"> </span>=~ s/\s/_/;<br>><br>> which fixes this error.<br>><br>> ---------------------------------------------------------------------<br>><br>> Now I am getting this error:<br>><br>> Can't call method "get_all_Genes<a></a><a></a>" on unblessed reference at DumpAlignedGenes.pl<a></a><a></a><span class="Apple-converted-space"> </span>line 463.<br>><br>> Here is line 463:<br>><br>> my $mapped_genes<a></a><a></a><span class="Apple-converted-space"> </span>= $align_slice<a></a><a></a>->{'slices'}->{$source_genome_db<a></a><a></a>->name}->get_all_Genes<a></a><a></a>(<br>><br>> >>>How do I fix this error?<<<<br>><br>><br>> Thank you for your time.<br>><br>> Alan<br>><br>><br>> R. Alan Harris, Ph.D.<br>> Assistant Professor<br>> Bioinformatics Research Laboratory<br>> Epigenomics<a></a><a></a><span class="Apple-converted-space"> </span>Data Analysis and Coordination Center<br>> Department of Molecular and Human Genetics<br>> Baylor College of Medicine<br>> Houston, TX 77030<br>> 713-798-7695<br>> <DumpAlignedGenes.pl<a></a><a></a>>_______________________________________________<br>> Dev mailing list <span class="Apple-converted-space"> </span><a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><a></a><a></a><br>> List admin (including subscribe/unsubscribe):<span class="Apple-converted-space"> </span><a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>> Ensembl<a></a><a></a><span class="Apple-converted-space"> </span>Blog:<span class="Apple-converted-space"> </span><a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br>><br>><br>><br>></div>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">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">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog:<span class="Apple-converted-space"> </span><a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></div></blockquote></div><br></body></html>