<html><head><base href="x-msg://3275/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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 ensembl-compara 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" style="border-collapse: separate; 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 ocsi="x"><div style="font-family: Tahoma; direction: ltr; color: rgb(0, 0, 0); font-size: x-small; "><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><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 (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><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> API version = 67<br>---------------------------------------------------</div><div dir="ltr">-------------------- 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>STACK Bio::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>/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> 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><span class="Apple-converted-space"> </span>= $this_meta_container_adaptor<a></a><a></a>->get_Species<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><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/_/;</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><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> 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> Rattus<a></a><a></a><span class="Apple-converted-space"> </span>norvegicus<a></a><a></a>' and assembly '--undef<a></a><a></a>--'<br>STACK Bio::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>/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> 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><span class="Apple-converted-space"> </span>= $meta_container_adaptor<a></a><a></a>->get_scientific_name<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><span class="Apple-converted-space"> </span>= $meta_container_adaptor<a></a>->get_scientific_name<a></a>;<br>$source_binomial_id<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>" on unblessed reference at DumpAlignedGenes.pl<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><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>(</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">Epigenomics</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><span><DumpAlignedGenes.pl></span>_______________________________________________<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></span></blockquote></div><br></div></body></html>