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<div>Hi Kathryn and Stephen,</div>
<div><font face="tahoma"></font> </div>
<div><font face="tahoma">Thanks for helping me out with DumpAlignedGenes.pl<a></a>. The scripts that both of you sent me now work, but there is another problem. According to the help, you can get alignments from multiple species using this:</font></div>
<div><font face="tahoma"></font> </div>
<div>[--set_of_species<a></a> species1:species2:species3<a></a>:...]</div>
<div><font face="tahoma"></font> </div>
<div><font face="tahoma">I ran both of your scripts with this command line</font></div>
<div><font face="tahoma"></font> </div>
<div><font face="tahoma"><a></a><font face="tahoma">perl</font> DumpAlignedGenes.pl<a></a> --set_of_species<a></a> "human:rat:mouse<a></a>"</font></div>
<div><font face="tahoma"></font> </div>
<div><font face="tahoma">but I get this error (line numbers based on the script Kathryn sent):</font></div>
<div><font face="tahoma"></font> </div>
<div>-------------------- WARNING ----------------------<br>
MSG: No Bio::EnsEMBL<a></a>::Compara<a></a>::MethodLinkSpeciesSet<a></a> found for<br>
<EPO_LOW_COVERAGE<a></a>> and homo_sapiens<a></a>(GRCh37<a></a>), rattus_norvegicus<a></a>(RGSC3.4<a></a>), mus_musculus<a></a>(NCBIM37<a></a>)<br>
FILE: Compara<a></a>/DBSQL<a></a>/MethodLinkSpeciesSetAdaptor.pm<a></a> LINE: 508<br>
CALLED BY: DumpAlignedGenes.kathryn.pl<a></a> LINE: 385<br>
Ensembl<a></a> API version = 67<br>
---------------------------------------------------</div>
<div>-------------------- EXCEPTION --------------------<br>
MSG: The database do not contain any EPO_LOW_COVERAGE<a></a> data for human:rat:mouse<a></a>!<br>
STACK toplevel<a></a> DumpAlignedGenes.kathryn.pl:389<a></a><br>
Ensembl<a></a> API version = 67<br>
---------------------------------------------------</div>
<div><font face="tahoma"></font> </div>
<div><font face="tahoma">This is after setting the alignment_type<a></a> to "EPO_LOW_COVERAGE<a></a>" which is what I want to use, but I get a similar error if I use the default alignment_type<a></a> of BLASTZ_NET<a></a>.</font></div>
<div><font face="tahoma"></font> </div>
<div><font face="tahoma">What I ultimately want to do is pull out multiple alignments for all species in the 35 eutherian<a></a> mammals EPO_LOW_COVERAGE<a></a> for a set of genes that I am interested in analyzing. Can I do that with this script?</font></div>
<div><font face="tahoma"></font> </div>
<div dir="ltr"><font color="#000000" size="2" face="Tahoma">Thanks,</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">Alan</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div style="DIRECTION: ltr" id="divRpF407163">
<hr tabindex="-1">
<font color="#000000" size="2" face="Tahoma"><b>From:</b> dev-bounces@ensembl.org [dev-bounces@ensembl.org<a></a>] On Behalf Of Kathryn Beal [kbeal@ebi.ac.uk<a></a>]<br>
<b>Sent:</b> Thursday, May 31, 2012 5:24 AM<br>
<b>To:</b> Ensembl<a></a> developers list<br>
<b>Subject:</b> Re: [ensembl<a></a>-dev] Problem with DumpAlignedGenes.pl<a></a> script<br>
</font><br>
</div>
<div></div>
<div>Hi Alan,
<div>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 to the cvs<a></a> ensembl-compara<a></a> HEAD code. I'll send a separate email with this attached for you.</div>
<div><br>
</div>
<div>Cheers</div>
<div>Kathryn<br>
<div><br class="Apple-interchange-newline">
<blockquote type="cite"><span class="Apple-style-span">
<div>
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<div><font color="#000000" size="2" face="Tahoma">Hi,</font></div>
<div>
<div style="FONT-FAMILY: Tahoma; DIRECTION: ltr; COLOR: rgb(0,0,0); FONT-SIZE: x-small">
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">I am trying to use the DumpAlignedGenes.pl<a></a><a></a><a></a><span class="Apple-converted-space"> </span>in version 67 of the ensembl-compara<a></a><a></a><a></a><span class="Apple-converted-space"> </span>API. I have made
the following necessary changes to the script (attached script has these changes):</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">1. When running the script without arguments as a test I get this error:</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr">------------------ DEPRECATED ---------------------<br>
Deprecated method call in file DumpAlignedGenes.pl<a></a><a></a><a></a><span class="Apple-converted-space"> </span>line 365.<br>
Method Bio::EnsEMBL<a></a><a></a><a></a>::DBSQL<a></a><a></a><a></a>::MetaContainer<a></a><a></a><a></a>::get_Species<a></a><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><a></a>() / $self->get_classification<a></a><a></a><a></a>() / $self->get_scientific_name<a></a><a></a><a></a>() instead<br>
Ensembl<a></a><a></a><a></a> API version = 67<br>
---------------------------------------------------</div>
<div dir="ltr">-------------------- EXCEPTION --------------------<br>
MSG: No matches found for name 'Homininae<a></a><a></a><a></a><span class="Apple-converted-space"> </span>Homo sapiens' and assembly '--undef<a></a><a></a><a></a>--'<br>
STACK Bio::EnsEMBL<a></a><a></a><a></a>::Compara<a></a><a></a><a></a>::DBSQL<a></a><a></a><a></a>::GenomeDBAdaptor<a></a><a></a><a></a>::fetch_by_name_assembly<a></a><a></a><a></a><span class="Apple-converted-space"> </span>/home/rharris1<a></a><a></a><a></a>/work/ensembl<a></a><a></a><a></a>/api<a></a><a></a><a></a>/ensembl-compara<a></a><a></a><a></a>/modules/Bio/EnsEMBL<a></a><a></a><a></a>/Compara<a></a><a></a><a></a>/DBSQL<a></a><a></a><a></a>/GenomeDBAdaptor.pm:131<a></a><a></a><a></a><br>
STACK toplevel<a></a><a></a><a></a><span class="Apple-converted-space"> </span>DumpAlignedGenes.pl:369<a></a><a></a><a></a><br>
Ensembl<a></a><a></a><a></a> API version = 67</div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">I changed line 365 from</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">my $this_binomial_id<a></a><a></a><a></a><span class="Apple-converted-space"> </span>= $this_meta_container_adaptor<a></a><a></a><a></a>->get_Species<a></a><a></a><a></a>->binomial;</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">to</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr">my $this_binomial_id<a></a><a></a><a></a><span class="Apple-converted-space"> </span>= $this_meta_container_adaptor<a></a><a></a><a></a>->get_scientific_name<a></a><a></a><a></a>;<br>
$this_binomial_id<a></a><a></a><a></a><span class="Apple-converted-space"> </span>=~ s/\s/_/;</div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">which fixes this error.</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">2. I also get this similar error:</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">------------------ DEPRECATED ---------------------<br>
Deprecated method call in file DumpAlignedGenes.pl<a></a><a></a><a></a><span class="Apple-converted-space"> </span>line 436.<br>
Method Bio::EnsEMBL<a></a><a></a><a></a>::DBSQL<a></a><a></a><a></a>::MetaContainer<a></a><a></a><a></a>::get_Species<a></a><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><a></a>() / $self->get_classification<a></a><a></a><a></a>() / $self->get_scientific_name<a></a><a></a><a></a>() instead<br>
Ensembl<a></a><a></a><a></a> API version = 67<br>
---------------------------------------------------</font></div>
<div dir="ltr"><font face="tahoma">-------------------- EXCEPTION --------------------<br>
MSG: No matches found for name 'Murinae<a></a><a></a><a></a> Rattus<a></a><a></a><a></a><span class="Apple-converted-space"> </span>norvegicus<a></a><a></a><a></a>' and assembly '--undef<a></a><a></a><a></a>--'<br>
STACK Bio::EnsEMBL<a></a><a></a><a></a>::Compara<a></a><a></a><a></a>::DBSQL<a></a><a></a><a></a>::GenomeDBAdaptor<a></a><a></a><a></a>::fetch_by_name_assembly<a></a><a></a><a></a><span class="Apple-converted-space"> </span>/home/rharris1<a></a><a></a><a></a>/work/ensembl<a></a><a></a><a></a>/api<a></a><a></a><a></a>/ensembl-compara<a></a><a></a><a></a>/modules/Bio/EnsEMBL<a></a><a></a><a></a>/Compara<a></a><a></a><a></a>/DBSQL<a></a><a></a><a></a>/GenomeDBAdaptor.pm:131<a></a><a></a><a></a><br>
STACK toplevel<a></a><a></a><a></a><span class="Apple-converted-space"> </span>DumpAlignedGenes.pl:440<a></a><a></a><a></a><br>
Ensembl<a></a><a></a><a></a> API version = 67<br>
---------------------------------------------------</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">
<div dir="ltr"><font face="tahoma">I changed line 436 from</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma"></font></div>
<div dir="ltr"><font face="tahoma">my $source_binomial_id<a></a><a></a><a></a><span class="Apple-converted-space"> </span>= $meta_container_adaptor<a></a><a></a><a></a>->get_scientific_name<a></a><a></a><a></a>;</font></div>
<div dir="ltr"><font face="tahoma"></font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">to</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma"></font></div>
<div dir="ltr">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/_/;</div>
<div dir="ltr"><font face="tahoma"></font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">which fixes this error.</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">---------------------------------------------------------------------</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">Now I am getting this error:</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">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.</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">Here is line 463:</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr">my $mapped_genes<a></a><a></a><a></a><span class="Apple-converted-space"> </span>= $align_slice<a></a><a></a><a></a>->{'slices'}->{$source_genome_db<a></a><a></a><a></a>->name}->get_all_Genes<a></a><a></a><a></a>(</div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">>>>How do I fix this error?<<<</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">Thank you for your time.</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">Alan</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma"></font> </div>
</font></div>
<div><font size="2" face="Tahoma">R. Alan Harris, Ph.D.</font></div>
<div><font size="2" face="tahoma">Assistant Professor</font></div>
<div><font size="2" face="tahoma">Bioinformatics Research Laboratory</font></div>
<div><font size="2" face="tahoma"><a></a><font size="2" face="tahoma"><a></a></font><font size="2" face="tahoma"><font size="2" face="tahoma"><a></a></font></font><font size="2" face="tahoma"><font size="2" face="tahoma"><font size="2" face="tahoma">Epigenomics</font></font></font> Data
Analysis and Coordination Center</font></div>
<div><font size="2" face="tahoma">Department of Molecular and Human Genetics</font></div>
<div><font size="2" face="tahoma">Baylor College of Medicine</font></div>
<div><font size="2" face="tahoma">Houston, TX 77030</font></div>
<div><font size="2" face="tahoma">713-798-7695</font></div>
</div>
</div>
</div>
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