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<div><font color="#000000" size="2" face="Tahoma">Hi,</font></div>
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<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> in version 67 of the ensembl-compara<a></a><a></a> 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> 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> 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> 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> /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> 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> = $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> = $this_meta_container_adaptor<a></a><a></a>->get_scientific_name<a></a><a></a>;<br>
$this_binomial_id<a></a><a></a> =~ 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> 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> 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> 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> /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> 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> = $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> = $meta_container_adaptor<a></a>->get_scientific_name<a></a>;<br>
$source_binomial_id<a></a> =~ 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> 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> = $align_slice<a></a><a></a>->{'slices'}->{$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>
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