[ensembl-dev] genomic_align id on Compara API 67

[Sophie Marion de Procé]

Dear Mathieu,

Thanks a lot for your help, it ended up working
with $genomic_align->genomic_align_block_id

Sophie.

On 3 July 2015 at 13:12, Matthieu Muffato <muffato at ebi.ac.uk> wrote:

> Dear Sophie,
>
> Sorry for the delayed reply. I think $genomic_align->dbID() and
> $genomic_align_block->dbID() are what you need.
>
> $genomic_align->genomic_align_block_id() returns the dbID of the
> $genomic_align_block it is drawn from
>
> Matthieu
>
>
> On 01/07/15 16:54, Sophie Marion de Procé wrote:
>
>> Dear all,
>>
>> I'm trying to obtain genomic_align objects using EPO mammals alignments
>> from Compara, with the API 67.
>> 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.
>> 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!
>> The error message is always something like "Use of uninitialized value
>> $dbID in concatenation (.) or string"
>>
>> Could you please tell me what I'm doing wrong? Or suggest another way to
>> achieve this?
>>
>> Below is a snippet of my code.
>>
>> Many thanks,
>> Sophie.
>>
>>
>> my $genomic_align_blocks =
>>
>> $genomic_align_block_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice($method_link_species_set,
>> $query_slice,undef,undef,1);
>> my @species = ("human","dog","mouse");
>> foreach my $givenSp (@species) {
>> foreach my $genomic_align_block (@$genomic_align_blocks) {
>> my $dbID = $genomic_align_block->dbID();
>> my $refID = $genomic_align_block->reference_genomic_align_id();
>> my $genomic_aligns = $genomic_align_block->get_all_GenomicAligns();
>> BLOCK: foreach my $genomic_align (@$genomic_aligns) {
>> my $dnafrag = $genomic_align->dnafrag;
>> my $genomic_align_dbID = $genomic_align->dbID;
>> my $genome_db = $genomic_align->genome_db;
>> my $gabID = $genomic_align->genomic_align_block_id;
>> my $species = $genome_db->name;
>> next BLOCK if ($species ne $givenSp);
>> $countSpBlocks{$species} = $nbBlocks;
>> my $chr = $dnafrag->name;
>> my $start = $genomic_align->dnafrag_start;
>> my $end = $genomic_align->dnafrag_end;
>> my $strand = $genomic_align->dnafrag_strand;
>> my $name = $dnafrag->name();
>> my $sizeBlock = $end - $start + 1;
>> print ("$species\t$start\t$end\t$strand\t$name\t$sizeBlock\t$gabID\t");
>> }
>> }
>> }
>>
>>
>>
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>>
> --
> Matthieu Muffato, Ph.D.
> Ensembl Compara and TreeFam Project Leader
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus, Hinxton
> Cambridge, CB10 1SD, United Kingdom
> Room  A3-145
> Phone + 44 (0) 1223 49 4631
> Fax   + 44 (0) 1223 49 4468
>
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