Raw content of Bio::EnsEMBL::ExternalData::Glovar::GlovarBaseCompAdaptor
<![CDATA[=head1 NAME
Bio::EnsEMBL::ExternalData::Glovar::GlovarBaseCompAdaptor -
Object adaptor for Glovar base composition
=head1 SYNOPSIS
$db_adaptor = Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor->new(
-user => 'ensro',
-pass => 'secret',
-dbname => 'snp',
-host => 'go_host',
-driver => 'Oracle'
);
my $basecomp_adaptor = $db_adaptor->get_GlovarBaseCompAdaptor;
my $listref = $basecomp_adaptor->fetch_all_by_Slice($slice);
=head1 DESCRIPTION
This module is an entry point into a Glovar database. It allows you to retrieve
base composition data from the database.
=head1 LICENCE
This code is distributed under an Apache style licence:
Please see /code_licence.html for details
=head1 AUTHOR
Jody Clements <jc3@sanger.ac.uk>
=head1 CONTACT
Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk
=cut
package Bio::EnsEMBL::ExternalData::Glovar::GlovarBaseCompAdaptor;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::ExternalData::Glovar::BaseComposition;
use Bio::EnsEMBL::ExternalData::Glovar::GlovarAdaptor;
use Bio::EnsEMBL::Utils::Eprof qw(eprof_start eprof_end eprof_dump);
@ISA = qw(Bio::EnsEMBL::ExternalData::Glovar::GlovarAdaptor);
=head2 fetch_all_by_Slice
Arg [1] : Bio::EnsEMBL::Slice
Arg [2] : (optional) boolean $is_lite
Flag indicating if 'light weight' objects should be obtained
Example : @list = @{$basecomp_adaptor->fetch_all_by_Slice($slice)};
Description: Retrieves a list of base composition objects on a slice in
slice coordinates
Returntype : Listref of Bio::EnsEMBL::External::Glovar::BaseComposition
objects
Exceptions : none
Caller : Bio::EnsEMBL::Slice::get_all_ExternalFeatures
=cut
sub fetch_all_by_Slice {
my ($self, $slice, $is_light) = @_;
unless($slice->assembly_name() && $slice->assembly_version()){
warn("Cannot determine assembly name and version from Slice in GlovarAdaptor!\n");
return([]);
}
my @f = ();
if($is_light){
push @f, @{$self->fetch_Light_Base_Comp_by_chr_start_end($slice)};
} else {
push @f, @{$self->fetch_Base_Comp_by_chr_start_end($slice)};
}
return(\@f);
}
=head2 fetch_Light_Base_Comp_by_chr_start_end
Arg [1] : Bio::EnsEMBL::Slice
Example : @list = @{$basecomp_adaptor->fetch_Light_Base_Comp_by_chr_start_end($slice)};
Description: Retrieves a list of base composition objects on a slice in
slice coordinates
Returntype : Listref of Bio::EnsEMBL::External::Glovar::BaseComposition
objects. Returns lightweight objects for drawing purposes
Exceptions : none
Caller : $self->fetch_all_by_Slice
=cut
sub fetch_Light_Base_Comp_by_chr_start_end {
my ($self, $slice) = @_;
my $slice_chr = $slice->chr_name();
my $slice_start = $slice->chr_start();
my $slice_end = $slice->chr_end();
my $slice_strand = $slice->strand();
my $ass_name = $slice->assembly_name();
my $ass_version = $slice->assembly_version();
&eprof_start('glovar_basecomp');
## NOTE:
## all code here assumes that ssm.contig_orientation is always 1!
my $q = qq(
SELECT
(rp.position + ssm.start_coordinate -1) as position,
rp.genomic_base as genomic_base,
COUNT(decode (sp.base,'A',1
,'G',NULL
,'T',NULL
,'C',NULL)) as A,
COUNT(decode (sp.base,'A',NULL
,'G',1
,'T',NULL
,'C',NULL)) as G,
COUNT(decode (sp.base,'A',NULL
,'G',NULL
,'T',NULL
,'C',1)) as C,
COUNT(decode (sp.base,'A',NULL
,'G',NULL
,'T',1
,'C',NULL)) as T,
COUNT(decode (ed.id_dict,0,1
,1,NULL
,2,NULL
,3,NULL)) as E0,
COUNT(decode (ed.id_dict,0,NULL
,1,1
,2,NULL
,3,NULL)) as E1,
COUNT(decode (ed.id_dict,0,NULL
,1,NULL
,2,1
,3,NULL)) as E2,
COUNT(decode (ed.id_dict,0,NULL
,1,NULL
,2,NULL
,3,1)) as E3
FROM chrom_seq cs,
seq_seq_map ssm,
snp_sequence ss,
reference_position rp,
sequence_position sp,
snp_read sr,
individual i,
ethnicitydict ed
WHERE cs.database_seqname = '$slice_chr'
AND cs.is_current = 1
AND cs.id_chromseq = ssm.id_chromseq
AND ssm.sub_sequence = ss.id_sequence
AND ss.id_sequence = rp.id_sequence
AND rp.id_sequence = sp.repo_id_sequence
AND sp.repo_position = rp.position
AND sp.is_nqs = 1
AND sp.seq_content = sr.id_read
AND sr.dna_content = i.id_ind
AND i.ethnicity = ed.id_dict
AND rp.position
BETWEEN
($slice_start - ssm.start_coordinate + 1)
AND
($slice_end - ssm.start_coordinate + 1)
GROUP BY
(rp.position + ssm.start_coordinate),
rp.genomic_base
ORDER by position
);
my $sth;
eval {
$sth = $self->prepare($q);
$sth->execute();
};
if ($@){
warn("ERROR: SQL failed in GlovarAdaptor->fetch_Light_Base_Comp_by_chr_start_end()!\n$@");
return([]);
}
my @bases = ();
my $refs = $sth->fetchall_arrayref();
for my $ref(@$refs){
my($position,$genomic_base,$A_count,$G_count,$C_count,$T_count,$e0,$e1,$e2,$e3) = @$ref;
my $basecomp = Bio::EnsEMBL::ExternalData::Glovar::BaseComposition->new_fast({
'position' => $position - $slice_start + 1,
'genomic_base' => $genomic_base,
'alleles' => {
'T' => $T_count,
'G' => $G_count,
'A' => $A_count,
'C' => $C_count,
},
'ethnicity' => {
'unknown' => $e0,
'Caucasian' => $e1,
'Asian' => $e2,
'African-American' => $e3,
},
'_gsf_strand' => 1,
});
push (@bases, $basecomp);
}
&eprof_end('glovar_basecomp');
return (\@bases);
}
=head2 fetch_Base_Comp_by_chr_start_end
Arg [1] : Bio::EnsEMBL::Slice
Example : @list = @{$basecomp_adaptor->fetch_Base_Comp_by_chr_start_end($slice)};
Description: Retrieves a list of base composition objects on a slice in
slice coordinates
Returntype : Listref of Bio::EnsEMBL::External::Glovar::BaseComposition
objects
Exceptions : none
Caller : $self->fetch_all_by_Slice
=cut
sub fetch_Base_Comp_by_chr_start_end {
my ($self,$slice) = @_;
my @vars = ();
## to be implemented
return(\@vars);
}
=head2 track_name
Arg[1] : none
Example : my $track_name = $basecomp_adaptor->track_name;
Description : returns the track name
Return type : String - track name
Exceptions : none
Caller : Bio::EnsEMBL::Slice,
Bio::EnsEMBL::ExternalData::ExternalFeatureAdaptor
=cut
sub track_name {
my ($self) = @_;
return("GlovarBaseComp");
}
1;
]]>