[ensembl-dev] question on compara
Kathryn Beal
kbeal at ebi.ac.uk
Thu Apr 18 09:39:27 BST 2013
Hi Nathalie,
I've amended your script a little and added a simple method to get the coordinates you wish. This should be fine if you only have a few regions of interest but might not scale lots of regions. Feel free to get back to me if this is becomes a problem.
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 17 Apr 2013, at 22:11, Nathalie Conte wrote:
>
>
>> Hi,
>>
>> I would like your help to select the more appropriate method to answer my question
>> From a set of mouse coordinates (chromosome start end), i would like to be able to find the equivalent orthologous coordinates in human and then find genes around (+- 2kb) and related SNPs +other variation information.
>> This is the start of my script below, I am parsing a mouse location file: MouseLoctest.txt which contain my mouse coordinates I have selected first the core API and get a slice object then I found a tutorial for getting genomic blocks from this slice- I would like to get the human coordinates (ch start end )from this block and I am not sure which method to use for this? Thanks for any suggestion-
>> Nathalie
>>
>> my script so far
>> #!/usr/bin/perl
>> use warnings;
>> use strict;
>> use Bio::EnsEMBL::Registry;
>> use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
>>
>> my $registry = "Bio::EnsEMBL::Registry";
>> $registry->load_registry_from_db(-host => 'ensembldb.ensembl.org', -user => 'anonymous');
>> #input file with chromosome coordinates, open and read:
>> my $file = "MouseLoctest.txt";
>>
>> unless (open(REGIONS, $file)){
>> print "Cannot open file \"$file\"\n\n";
>> }
>>
>> my @regions = <REGIONS>;
>>
>> close REGIONS;
>> open(OUT,">test_output.txt");
>>
>> # Getting the Slice adaptor:
>> my $slice_adaptor = $registry->get_adaptor('Mouse', 'Core', 'Slice');
>>
>>
>> #slice obejct containing chr start and end
>> foreach my $region(@regions){
>> chomp $region;
>>
>> my @coordinates = split(/\t/, $region);
>>
>> my $seq_region = $coordinates[0];
>> my $seq_region_start = $coordinates[4];
>> my $seq_region_end = $coordinates[5];
>> };
>> my $query_slice =
>> $slice_adaptor->fetch_by_region('chromosome',$seq_region,
>> $seq_region_start, $seq_region_end);
>> throw("No Slice can be created with coordinates
>> $seq_region:$seq_region_start-".
>> "$seq_region_end") if (!$query_slice);
>>
>> #now go wit this splice to compara and fetch the corresponding human sequence from this slice
>>
>> # Getting the GenomicAlignBlock adaptor:
>> my $genomic_align_block_adaptor = Bio::EnsEMBL::Registry->get_adaptor(
>> 'Multi', 'compara', 'GenomicAlignBlock');
>> # Fetching all the GenomicAlignBlock corresponding to this Slice:
>> my $genomic_align_blocks =
>> $genomic_align_block_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice(
>> $human_mouse_blastz_net_mlss,
>> $query_slice);
>>
>> I am stuck here and would like the coordinates ??
>>
>>
>
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