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

[Eduardo Andrés León]

umm, but I lost the coordinates (which I really need them)


On 28 Jan 2013, at 14:35, "Kathryn Beal" <kbeal at ebi.ac.uk> wrote:

> 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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===================================================
Eduardo Andrés León
Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 5054/3063)
e-mail: eandres at cnio.es        Fax: (+34) 91 224 69 76
Unidad de Bioinformática       Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas
C.P.: 28029                Zip Code: 28029
C/. Melchor Fernández Almagro, 3    Madrid (Spain)
http://bioinfo.cnio.es	http://bioinfo.cnio.es/people/eandres
===================================================

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