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

[Benoît Ballester]

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
> 
> 
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--
Benoît Ballester, PhD
Inserm U1090, TAGC
Marseille - France
+33 4 91 82 87 39