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Summary

Bio::EnsEMBL::ExternalData::SNPSQL::WebAdaptor - Web accelerated (light objects) for SNPs

Package variables

Included modules

Inherit

Bio::EnsEMBL::ExternalData::SNPSQL::DBAdaptor

Synopsis

Give standard usage here

Description

This object is derived from SNPSQL::DBAdaptor.
Method get_Ensembl_SeqFeatures_clone_web() is there only to speed up
Web work. It loads only minimal set of sequence features into
Variation objects . To get a fullset of Variation attributes method
get_SeqFeature_by_id() is call on select objects, only. Additionally
it needs an attribute determined by the display resolution on how far
apart the features have to be to be drawn.

Methods

Methods description

 Title   : get_Ensembl_SeqFeatures_clone_web
 Usage   :
 Function:
 Example :
 Returns : a list of lightweight Variation features.
 Args    : scalar in nucleotides (should default to 50)
           array of accession.version numbers

Methods code

sub get_Ensembl_SeqFeatures_clone_web {

    my ($self,$glob,@acc) = @_;
    
    if (! defined $glob) {
        $self->throw("Need to call get_Ensembl_SeqFeatures_clone_web with a globbing parameter and a list of clones");
    }
    if (scalar(@acc) == 0) {
        $self->throw("Calling get_Ensembl_SeqFeatures_clone_web with empty list of clones!\n");
    }
    
    #lists of variations to be returned
    my @variations;
    my %hash;
    my $string;
    foreach my $a (@acc) {
        $a =~ /(\S+)\.(\d+)/;
        $string .= "'$1',";
        $hash{$1}=$2;
    }
    $string =~ s/,$//;
    my $inlist = "($string)";
    
    # db query to return all variation information in current GoldenPath; confidence attribute is gone!!
    # data are preprocessed to contain only relevent information (RefSNP.mapweight  is not needed)
    # denormalized SubSNP in

    my $query = qq{

        SELECT   start, end, strand,
                 acc, version, refsnpid,
                 tcsid, hgbaseid
        FROM   	 GPHit
        WHERE  	 acc in $inlist
	ORDER BY acc,start    

              };

    &eprof_start('snp-sql-query');

    my $sth = $self->prepare($query);
    my $res = $sth->execute();

    &eprof_end('snp-sql-query');

    my $snp;
    my $cl;

    &eprof_start('snp-sql-object');

  SNP:
    while( (my $arr = $sth->fetchrow_arrayref()) ) {
        
        my ($begin, $end, $strand,
            $acc, $ver, $snpuid,
            $tscid, $hgbaseid
           ) = @{$arr};
        
        my $acc_version="$acc.$ver";
	if ( defined $snp && $snp->end+$glob >= $begin && $acc_version eq $cl) {
            #ignore snp within glob area
            next SNP;
        }
        
        next SNP if $hash{$acc} != $ver;
        #
        # prepare the output objects
        #
        
        ### mega dodginess here: ideally, a Variation should be allowed to
        ### have several Locations. However, a Variation is-a SeqFeature,
        ### which can only have one. So instead, we'll return a list of
        ### Varations, each with a separate single location, but otherwise
        ### identical. That's clean-room engineering for you :-) 
        
        my $key=$snpuid.$acc;           # for purpose of filtering duplicates
        my %seen;                       # likewise
        
        
        if ( ! $seen{$key} )  {
            ## we're grabbing all the necessary stuff from the db in one
            ## SQL statement for speed purposes, so we have to do some
            ## duplicate filtering here.

            $seen{$key}++;
            
            #Variation
            $snp = new Bio::EnsEMBL::ExternalData::Variation
              (-start => $begin,
               -end => $end,
               -strand => $strand,
               -original_strand => $strand,
               -score => 1,
               -source_tag => 'dbSNP',
              );
            
            my $link = new Bio::Annotation::DBLink;
            $link->database('dbSNP');
            $link->primary_id($snpuid);
            $link->optional_id($acc_version);
            #add dbXref to Variation
            $snp->add_DBLink($link);
	    if ($hgbaseid) {
	      my $link2 = new Bio::Annotation::DBLink;
	      $link2->database('HGBASE');
	      $link2->primary_id($hgbaseid);
	      $link2->optional_id($acc_version);
	      $snp->add_DBLink($link2);
	    }
	    if ($tscid) {
	      my $link3 = new Bio::Annotation::DBLink;
	      $link3->database('TSC-CSHL');
	      $link3->primary_id($tscid);
	      $link3->optional_id($acc_version);
	      #add dbXref to Variation
	      $snp->add_DBLink($link3);
	    }
            $cl=$acc_version;
            # set for compatibility to Virtual Contigs
            $snp->seqname($acc_version);
            #add SNP to the list
            push(@variations, $snp);
        }                               # if ! $seen{$key}
      }                                    # while a row from select statement

    &eprof_end('snp-sql-object');
    
    return @variations;

}

General documentation

This modules is part of the Ensembl project
Email birney@ebi.ac.uk
Describe contact details here

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _