<div dir="ltr">Dear all,<div><br><div>I'm trying to obtain genomic_align objects using EPO mammals alignments from Compara, with the API 67.</div><div>My aim is to look at the genomic_align_blocks and see if they are contiguous for a specific set of species. To group the genomic_align objects within a genomic_align_block, I've tried to use the $genomic_align_block->dbID() and $genomic_align_block->reference_genomic_align_id() functions, as well as the $genomic_align->genomic_align_block_id function.</div><div>These seem to give the sort of id I need, however, regardless of the method I use, I do no get an id for the first and last genomic_align of each genomic_align_block!</div><div>The error message is always something like "Use of uninitialized value $dbID in concatenation (.) or string"</div><div><br></div><div>Could you please tell me what I'm doing wrong? Or suggest another way to achieve this?</div><div><br></div><div>Below is a snippet of my code.</div><div><br></div><div>Many thanks,</div><div>Sophie.</div><div><br></div><div><br></div><div><div>my $genomic_align_blocks = $genomic_align_block_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice($method_link_species_set, $query_slice,undef,undef,1);</div><div>my @species = ("human","dog","mouse");<br></div><div>foreach my $givenSp (@species) {</div><div><span class="" style="white-space:pre">   </span>foreach my $genomic_align_block (@$genomic_align_blocks) {<br></div><div><span class="" style="white-space:pre">               </span>my $dbID = $genomic_align_block->dbID();<br></div><div><span class="" style="white-space:pre">              </span>my $refID = $genomic_align_block->reference_genomic_align_id();</div><div><span class="" style="white-space:pre">         </span>my $genomic_aligns = $genomic_align_block->get_all_GenomicAligns();</div><div><span class="" style="white-space:pre">             </span>BLOCK: foreach my $genomic_align (@$genomic_aligns) {</div><div><span class="" style="white-space:pre">                      </span>my $dnafrag = $genomic_align->dnafrag;</div><div><span class="" style="white-space:pre">                  </span>my $genomic_align_dbID = $genomic_align->dbID;</div><div><span class="" style="white-space:pre">                  </span>my $genome_db = $genomic_align->genome_db;</div><div><span class="" style="white-space:pre">                      </span>my $gabID = $genomic_align->genomic_align_block_id;</div><div><span class="" style="white-space:pre">                     </span>my $species = $genome_db->name;</div><div><span class="" style="white-space:pre">                 </span>next BLOCK if ($species ne $givenSp);</div><div><span class="" style="white-space:pre">                      </span>$countSpBlocks{$species} = $nbBlocks;<br></div><div><span class="" style="white-space:pre">                    </span>my $chr = $dnafrag->name;</div><div><span class="" style="white-space:pre">                       </span>my $start = $genomic_align->dnafrag_start;</div><div><span class="" style="white-space:pre">                      </span>my $end = $genomic_align->dnafrag_end;</div><div><span class="" style="white-space:pre">                  </span>my $strand = $genomic_align->dnafrag_strand;</div><div><span class="" style="white-space:pre">                    </span>my $name = $dnafrag->name();</div><div><span class="" style="white-space:pre">                    </span>my $sizeBlock = $end - $start + 1;</div><div><span class="" style="white-space:pre">                 </span>print ("$species\t$start\t$end\t$strand\t$name\t$sizeBlock\t$gabID\t");</div><div><span class="" style="white-space:pre">          </span>}</div><div><span class="" style="white-space:pre">  </span>}</div><div>}</div></div><div><br></div></div></div>