[ensembl-dev] Compara: project from Human to Mouse

[Kathryn Beal]

Hi Ben,
I'm not sure if this is quite what you want, but you can restrict the blocks you get from fetch_all_by_MethodLinkSpeciesSet_Slice to just the slice by adding a boolean as the 5th parameter e.g

my $gabs = $gab_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice($hsap_mmus_blastz_mlss, $hsap_slice,undef,undef,1);

Cheers
Kathryn

On 4 Dec 2012, at 14:04, Benoît Ballester wrote:

> I may have found the solution myself. 
> 
> I used align_slices to get coordinates of my human slice on the Genomic Align Block /Genomic Align.
> Then I used those coordinates to restrict the human and mouse genomic_aligns
> 
> 
> Ben
> 
> 
> On 3 Dec 2012, at 19:00, Benoît Ballester wrote:
> 
>> Dear Compara, 
>> 
>> I have a few slices (~100bp) I'd like to project from human to mouse using the BLASTZ alignment (I am on v65). 
>> Looking at the example scripts, and digging into my memories, I got to the point where I have the genomic_align objects. 
>> 
>> However I'd like to have the Mouse coordinates (the exact projection from human, ~100bp) and not the entire genomic_align. 
>> I remember that there is another step to get the exact mouse coordinates. 
>> 
>> Would you please remind me what this next step is ? 
>> 
>> Thanks, 
>> 
>> #--8< ----Example script 
>> 
>>   my $gabs = $gab_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice($hsap_mmus_blastz_mlss, $hsap_slice);
>> 
>>   foreach my $gab (@$gabs) {
>> 
>> 	my $genomic_aligns = $gab->get_all_GenomicAligns();
>> 
>> 	foreach my $genomic_align (@$genomic_aligns) {
>> 	    print
>> 		$genomic_align->dnafrag->genome_db->name, " ",
>> 		$genomic_align->dnafrag->coord_system_name, " ",
>> 		$genomic_align->dnafrag->name, " [",
>> 		$genomic_align->dnafrag_start, " - ",
>> 		$genomic_align->dnafrag_end, "] ",
>> 		$genomic_align->dnafrag_strand, #")\n",
>> 		$genomic_align->dnafrag_end - $genomic_align->dnafrag_start, "\n",
>> 		"\n"
>> 	}
>> 	print "\n";
>>   }
>> 
>> 
>> #-- Example output
>> Line: chr1      5482670 5482784 5482727
>> homo_sapiens chromosome 1 [5482702 - 5484342] 11640
>> mus_musculus chromosome 4 [152209531 - 152211053] -11522
>> 
>> 
>> 
>> Ben 
>> wxw
>> 
>> 
>> --
>> Benoît Ballester, PhD
>> Inserm U1090, TAGC
>> Marseille - France
>> +33 4 91 82 87 39
>> 
>> 
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
> 
> --
> Benoît Ballester, PhD
> Inserm U1090, TAGC
> Marseille - France
> +33 4 91 82 87 39
> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/