[ensembl-dev] Another API question about Alignments between mouse / human

Kathryn Beal kbeal at ebi.ac.uk
Mon Jan 28 13:35:22 GMT 2013


Hi,
You can use the AlignSlice to get the alignment, i.e. add the following lines:

my $align_slice_adaptor =
      Bio::EnsEMBL::Registry->get_adaptor("Multi", "compara", "AlignSlice");

my $align_slice = $align_slice_adaptor->fetch_by_Slice_MethodLinkSpeciesSet($source_org_slice, $methodLinkSpeciesSet, 'expanded', 'restrict');

print $alignIO $align_slice->get_SimpleAlign;

I also used the "clustalw" as the format for AlignIO.

I hope that helps,
Cheers
Kathryn

Kathryn Beal, PhD
European Bioinformatics Institute  (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, UK 
Tel. +44 (0)1223 494458
www.ensembl.org

On 28 Jan 2013, at 10:27, Eduardo Andrés León wrote:

> Dear all,
> 	I'm trying to match the mouse sequence(2-28403186:28403879)  into the human genome using ensembl 67.
> 
> Using the web, I've got the following :
> 
> http://may2012.archive.ensembl.org/Mus_musculus/Location/Compara_Alignments?align=410&db=core&r=2%3A28403186-28403879
> 
> mus_musculus:2 > 	chromosome:NCBIM37:2:28403186:28403879:1
> homo_sapiens:9 > 	chromosome:GRCh37:9:100149814:100149843:-1
> supercontig:GRCh37:GL000220.1:11378:11383:-1
> chromosome:GRCh37:9:135978315:135979072:-1
> 
> 
> 
> But when I use the API, I obtain more than 55 fragments (attached as a zip file) :
> 
> <alignment.3012.17691580863.txt.zip>
> 
> The code for extracting the data is the following :
> 
> getAlignMent(2,28403186,28403879);
> 
> 	sub getAlignMent{
> 		my ($source_org_chr,$source_org_start,$source_org_end)=@_;
> 
> 		#Auto-configure the registry
> 		Bio::EnsEMBL::Registry->load_registry_from_db(
> 			-host=>"ensembldb.cnio.es",
> 			-user=>"ensembl");
> 
> 
> 		# Get the Compara Adaptor for MethodLinkSpeciesSets
> 		my $method_link_species_set_adaptor =
> 		    Bio::EnsEMBL::Registry->get_adaptor(
> 		      "Multi", "compara", "MethodLinkSpeciesSet");
> 
> 		# Get the MethodLinkSpecieSet for source_org-mouse lastz-net alignments
> 		my $methodLinkSpeciesSet = $method_link_species_set_adaptor->
> 			fetch_by_method_link_type_registry_aliases("BLASTZ_NET", ["mouse", "human"]);
> 
> 		# Define the start and end positions for the alignment
> 		# Get the source_org *core* Adaptor for Slices
> 		my $source_org_slice_adaptor =
> 		    Bio::EnsEMBL::Registry->get_adaptor(
> 		      "mouse", "core", "Slice");
> 
> 		# Get the slice corresponding to the region of interest
> 		my $source_org_slice = $source_org_slice_adaptor->fetch_by_region(
> 		    "chromosome", $source_org_chr, $source_org_start, $source_org_end);
> 
> 		# Get the Compara Adaptor for GenomicAlignBlocks
> 		my $genomic_align_block_adaptor =
> 		    Bio::EnsEMBL::Registry->get_adaptor(
> 		      "Multi", "compara", "GenomicAlignBlock");
> 
> 		# The fetch_all_by_MethodLinkSpeciesSet_Slice() returns a ref.
> 		# to an array of GenomicAlingBlock objects (source_org is the reference species) 
> 		my $all_genomic_align_blocks = $genomic_align_block_adaptor->
> 		    fetch_all_by_MethodLinkSpeciesSet_Slice(
> 		        $methodLinkSpeciesSet, $source_org_slice, undef, undef, "restrict");
> 
> 		# set up an AlignIO to format SimpleAlign output
> 		my $outputAl="alignment." . rand(10000) . ".txt";
> 		open(OUT,">$outputAl") || die "3 $!\n";
> 		my $alignIO = Bio::AlignIO->newFh(-interleaved => 0,
> 		                                  -fh => \*OUT,
> 		                                  -format => 'pfam',
> 		                                  -idlength => 20);
> 
> 		# print the restricted alignments
> 		if (scalar(@{$all_genomic_align_blocks})==0){
> 			open(NMR,">>chr$source_org_chr\_No_mapping_regions.txt") || die "$!\n";
> 			print NMR "$source_org_chr\t$source_org_start\t$source_org_end\n";
> 			close NMR;
> 			return();
> 		}
> 		else{
> 			foreach my $genomic_align_block ( @{ $all_genomic_align_blocks } ) {
> 				print $alignIO $genomic_align_block->get_SimpleAlign;
> 			}
> 			close OUT;
> 		}
> 	}
> 
> This same happens with other segments, but not all of them.
> 
> So, can anybody tell me how to extract the same records the web shows ?
> 
> Regards and thanks in advance !
> 
> 
> 
> 
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