<div dir="ltr">Dear Mathieu,<div><br></div><div>Thanks a lot for your help, it ended up working with $genomic_align->genomic_align_block_id</div><div><br></div><div>Sophie.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 3 July 2015 at 13:12, Matthieu Muffato <span dir="ltr"><<a href="mailto:muffato@ebi.ac.uk" target="_blank">muffato@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Sophie,<br>
<br>
Sorry for the delayed reply. I think $genomic_align->dbID() and $genomic_align_block->dbID() are what you need.<br>
<br>
$genomic_align->genomic_align_block_id() returns the dbID of the $genomic_align_block it is drawn from<br>
<br>
Matthieu<div><div class="h5"><br>
<br>
On 01/07/15 16:54, Sophie Marion de Procé wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
Dear all,<br>
<br>
I'm trying to obtain genomic_align objects using EPO mammals alignments<br>
from Compara, with the API 67.<br>
My aim is to look at the genomic_align_blocks and see if they are<br>
contiguous for a specific set of species. To group the genomic_align<br>
objects within a genomic_align_block, I've tried to use the<br>
$genomic_align_block->dbID() and<br>
$genomic_align_block->reference_genomic_align_id() functions, as well as<br>
the $genomic_align->genomic_align_block_id function.<br>
These seem to give the sort of id I need, however, regardless of the<br>
method I use, I do no get an id for the first and last genomic_align of<br>
each genomic_align_block!<br>
The error message is always something like "Use of uninitialized value<br>
$dbID in concatenation (.) or string"<br>
<br>
Could you please tell me what I'm doing wrong? Or suggest another way to<br>
achieve this?<br>
<br>
Below is a snippet of my code.<br>
<br>
Many thanks,<br>
Sophie.<br>
<br>
<br>
my $genomic_align_blocks =<br>
$genomic_align_block_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice($method_link_species_set,<br>
$query_slice,undef,undef,1);<br>
my @species = ("human","dog","mouse");<br>
foreach my $givenSp (@species) {<br>
foreach my $genomic_align_block (@$genomic_align_blocks) {<br>
my $dbID = $genomic_align_block->dbID();<br>
my $refID = $genomic_align_block->reference_genomic_align_id();<br>
my $genomic_aligns = $genomic_align_block->get_all_GenomicAligns();<br>
BLOCK: foreach my $genomic_align (@$genomic_aligns) {<br>
my $dnafrag = $genomic_align->dnafrag;<br>
my $genomic_align_dbID = $genomic_align->dbID;<br>
my $genome_db = $genomic_align->genome_db;<br>
my $gabID = $genomic_align->genomic_align_block_id;<br>
my $species = $genome_db->name;<br>
next BLOCK if ($species ne $givenSp);<br>
$countSpBlocks{$species} = $nbBlocks;<br>
my $chr = $dnafrag->name;<br>
my $start = $genomic_align->dnafrag_start;<br>
my $end = $genomic_align->dnafrag_end;<br>
my $strand = $genomic_align->dnafrag_strand;<br>
my $name = $dnafrag->name();<br>
my $sizeBlock = $end - $start + 1;<br>
print ("$species\t$start\t$end\t$strand\t$name\t$sizeBlock\t$gabID\t");<br>
}<br>
}<br>
}<br>
<br>
<br>
<br></div></div>
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<br>
</blockquote>
<br>
-- <br>
Matthieu Muffato, Ph.D.<br>
Ensembl Compara and TreeFam Project Leader<br>
European Bioinformatics Institute (EMBL-EBI)<br>
European Molecular Biology Laboratory<br>
Wellcome Trust Genome Campus, Hinxton<br>
Cambridge, CB10 1SD, United Kingdom<br>
Room  A3-145<br>
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</blockquote></div><br></div>