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

[Benoît Ballester]

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