Bio::EnsEMBL::ExternalData::SNPSQL
SNPAdaptor
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Summary
Bio::EnsEMBL::ExternalData::SNPSQL::SNPAdaptor
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
A SNP adaptor which sits over a SNP database. Provides a means of getting
SNPs out of a SNP database as Bio::EnsEMBL::ExternalData::Variation objects.
Description
No description!
Methods
Methods description
Title : fetch_all_by_Slice
Usage : snpa->fetch_all_by_Slice($slice)
Function: return variation objects in the given slice
Example : snpa->fetch_all_by_Slice($slice)
Returns : a list of all variation objects in the given slice
Args : $slice |
Arg [1] : int refsnp_id
Arg [2] : (optional) string source
Example : none
Description: Retrieves a snp objcet from the SNP database but does not
populate the location information. This is necessary given
the current state of the snp database because location
information has to be retrieved differently for different
species!
Returntype : Bio::EnsEMBL::SNP
Exceptions : none
Caller : snpview |
Title : fetch_between_internal_ids
Usage :
Function:
Example :
Returns : a list of all snp info between start_internal_id and end_internal_id
Args : start_internal_id and end_internal_id |
Arg [1] : int $refsnpid
The refsnp identifier of the snp to retrieve
Arg [2] : string $source
The source string of the snp to retrieve
Example : @snps = @{$snp_adaptor->fetch_by_SNP_id($refsnpid, 'dbSNP')};
Description: Retreives a snp via its refsnp identifier and
datasource. One variation object is returned per mapped
location of the snp.
Returntype : Bio::EnsEMBL::Variation
Exceptions : none
Caller : internal |
Title : fetch_by_refsnpid
Usage :
Function:
Example :
Returns : a list of snp info by given refsnpid
Args : refsnpid, mouse_flag |
Arg 1 : int $refsnpid
Arg 2 : int population ID
Use refsnp identifier and population ID to retrieve the allele
frequencies
Example : @freqs = @{$snp_adaptor->fetch_freqs_by_pop_SNP_id($pop_id,$refsnpid)};
Description: Retreives frequency population objects for a given refSNP id
Returntype : Array ref of Bio::EnsEMBL::ExternalData::Frequency objects
Exceptions : none
Caller : internal |
Arg [1] : int $refsnpid
The refsnp identifier of the snp to retrieve genotypes
Example : @snps = @{$snp_adaptor->fetch_genotype_by_SNP_id($refsnpid)};
Description: Retreives a variation object via its refsnp identifier
One variation object is returned for genotype data
associated with that snp
Returntype : Bio::EnsEMBL::Variation
Exceptions : none
Caller : internal |
Title : fetch_genotyped_by_Slice
Usage : snpa->fetch_genotyped_by_Slice($slice)
Function: return variation objects in the given slice that have been genotyped
Example : snpa->fetch_genotyped_by_Slice($slice)
Returns : a list of genotyped variation objects in the given slice
Args : $slice |
Arg 1 : int $refsnpid
Use refsnp identifier of the snp to retrieve the populations
in which it has been genotyped.
Example : @pops = @{$snp_adaptor->fetch_pop_by_SNP_id($refsnpid)};
Description: Retreives a population objects for a given refSNP id
Returntype : Array ref of Bio::EnsEMBL::ExternalData::Population objects
Exceptions : none
Caller : internal |
Arg 1 : int $ssid
Arg 2 : $slice
Use $ssid and $slice to retrieve the slice strand of
given $ssid
Example : my $slice_strand = $snp_adaptor->fetch_slice_strand_by_ssid($ssid,$slice)
Description: Retreives slice strand for a given SubSNP id
Returntype : int $slice_strand
Exceptions : none
Caller : internal |
Methods code
| _objFromHashref | description | prev | next | Top |
sub _objFromHashref
{ my ($self,$info) = @_;
my $acc_version = '';
my $acc = $info->{acc};
my $ver = $info->{version};
$acc_version .= uc $acc if $acc;
$acc_version .= ".$ver" if $ver;
my $snp = new Bio::EnsEMBL::ExternalData::Variation;
$snp->acc($info->{acc});
$snp->version($info->{version});
$snp->seqname($acc_version);
$snp->start($info->{start});
$snp->end($info->{end});
$snp->strand($info->{strand});
$snp->source_tag('dbSNP');
$snp->alleles($info->{observed});
$snp->upStreamSeq($info->{seq5});
$snp->dnStreamSeq($info->{seq3});
$snp->score($info->{mapweight});
$snp->snpid($info->{id});
$snp->snpclass($info->{snpclass});
$snp->unique_id($info->{chr_start},$info->{internal_id});
my $link = new Bio::Annotation::DBLink;
$link->database('dbSNP');
$link->primary_id($info->{id});
$snp->add_DBLink($link);
return $snp;
}
1;} | sub coordinate_systems
{ return ("CLONE");} | sub fetch_all_by_Clone
{ my ( $self, $clone, $start, $end ) = @_;
$self->fetch_by_clone_accession_version( $clone->embl_id(),
$clone->embl_version(),
$start,
$end); } | sub fetch_all_by_Slice
{ my ($self,$slice) = @_;
my ($query, @var_objs, %var_objs);
my $chr_start = $slice->start;
my $chr_end = $slice->end;
my $chr_name = $slice->seq_region_name;
$query = qq{
SELECT r.id, r.snpclass, r.mapweight, r.observed, r.seq5, r.seq3,
ch.physmap as start, ch.physmapstr as end , ch.physmapstrand as strand
FROM RefSNP as r, ContigHit as ch
WHERE r.snptype = "notwithdrawn"
and r.internal_id = ch.internal_id and ch.physmap between $chr_start and $chr_end
and ch.chr = "$chr_name"
};
my $sth=$self->prepare($query);
my $res=$sth->execute();
while (my $info = $sth->fetchrow_hashref()) {
if ($info) {
my $physmapstr = $info->{end};
my ($start, $end) = split /\^|\.\./, $physmapstr if ($info->{start} ne $info->{end});
$info->{start} = $start-$chr_start+1 if ($start);
$info->{end} = $end-$chr_start+1 if ($end);
$info->{start} = $info->{start}-$chr_start+1 if (!$start);
$info->{end} = $info->{end}-$chr_start+1 if (!$end);
my $var_obj = $self->_objFromHashref($info);
push (@var_objs, $var_obj);
}
}
return\@ var_objs;} | sub fetch_attributes_only
{ my $self = shift;
my $refsnp_id = shift;
my $source = shift || 'dbSNP';
my $sth = $self->prepare('
SELECT refsnp.internal_id, refsnp.snpclass, refsnp.snptype,
refsnp.observed, refsnp.seq5, refsnp.seq3,
refsnp.het, refsnp.hetse, refsnp.validated, refsnp.mapweight, refsnp.hapmap_snp,
ds.version
FROM RefSNP refsnp, DataSource ds
WHERE refsnp.id = ?
AND ds.id = refsnp.datasource
AND ds.datasource = ?');
$sth->execute("$refsnp_id", $source);
$sth->rows || $self->throw("snp with refsnp_id/src [$refsnp_id/$source]" .
"not found in database");
my ($dbID, $snp_class, $snp_type, $alleles, $seq5, $seq3,
$het, $hetse, $confirmed, $mapweight, $hapmap_snp, $source_version) = $sth->fetchrow_array;
$sth->finish;
if ($confirmed eq 'no-info') {
$confirmed = "suspected";
} else {
$confirmed =~ s/-/ /;
$confirmed = "proven $confirmed";
}
$alleles =~ s/\//\|/g;
$seq5 = substr($seq5, -25, 25);
$seq3 = substr($seq3, 0, 25);
$seq3 .= 'N' x ( 25 - length $seq3 ) if length($seq3) < 25 ;
$seq5 = ('N' x ( 25 - length $seq5 ) ). $seq5 if length($seq5) < 25 ;
my $snp = Bio::EnsEMBL::SNP->new;
$snp->dbID($dbID);
$snp->source_tag($source);
$snp->source_version($source_version);
$snp->status($confirmed);
$snp->alleles($alleles);
$snp->upStreamSeq($seq5);
$snp->dnStreamSeq($seq3);
$snp->score($mapweight);
$snp->het($het);
$snp->hetse($hetse);
$snp->hapmap_snp($hapmap_snp);
my $link = new Bio::Annotation::DBLink;
$link->database('dbSNP');
$link->primary_id($refsnp_id);
$snp->add_DBLink($link);
$sth = $self->prepare("
SELECT subsnp.handle, subsnp.altid
FROM SubSNP as subsnp
WHERE subsnp.internal_id = ?");
$sth->execute($dbID);
while(my ($handle, $altid) = $sth->fetchrow_array) {
my $link = new Bio::Annotation::DBLink;
$link->database($handle);
$link->primary_id($altid);
$snp->add_DBLink($link);
}
eval {
foreach my $genotype (@{$self->fetch_genotype_by_SNP_id($snp->id)}){
$snp->add_genotype($genotype);
}
};
foreach my $pop (@{$self->fetch_pops_by_SNP_id($snp->id)}) {
my $freqs = undef;
eval {
$freqs = $self->fetch_freqs_by_pop_SNP_id($pop->pop_id, $snp->id);
};
next if $@;
next unless @$freqs;
foreach my $freq (@$freqs) {
$pop->add_frequency($freq);
}
$snp->add_population($pop);
}
return $snp;} | sub fetch_between_internal_ids
{ my ($self,$start_internal_id,$end_internal_id) = @_;
my ($query, @var_objs, %var_objs);
if (!$end_internal_id) {
$end_internal_id = $start_internal_id;
}
$query = qq{
SELECT r.id, r.snpclass, r.mapweight, r.observed, r.seq5, r.seq3,
h.acc, h.version, h.start, h.end, h.strand
FROM RefSNP as r left join Hit as h on r.internal_id = h.internal_id
WHERE snptype = "notwithdrawn"
and r.internal_id between $start_internal_id and $end_internal_id
};
my $sth=$self->prepare($query);
my $res=$sth->execute();
while (my $info = $sth->fetchrow_hashref()) {
if ($info) {
my $var_obj = $self->_objFromHashref($info);
push (@var_objs, $var_obj);
}
}
return\@ var_objs;} | sub fetch_by_SNP_id
{ my ($self, $refsnpid, $source) = @_;
unless($refsnpid && $source) {
die("Both refsnpid and source arguments are required");
}
my $sth = $self->prepare('
SELECT STRAIGHT_JOIN
refsnp.internal_id, refsnp.id, hit.acc, hit.version, hit.start,
hit.end, hit.type, hit.strand, refsnp.snpclass, refsnp.snptype,
refsnp.observed, refsnp.seq5, refsnp.seq3,
refsnp.het, refsnp.hetse, refsnp.validated, refsnp.mapweight,
ds.datasource
FROM RefSNP refsnp, DataSource ds left join Hit hit on hit.internal_id = refsnp.internal_id
WHERE ds.id = refsnp.datasource
AND refsnp.id = ?
AND ds.datasource = ?');
$sth->execute("$refsnpid", $source);
$sth->rows || $self->throw("$source $refsnpid not in database or not mapped to contig");
my $arr;
my @variations = ();
while ($arr = $sth->fetchrow_arrayref) {
my ($internal_id, $dbsnp_id, $acc, $ver, $begin, $end, $postype,
$strand, $class, $type, $alleles, $seq5, $seq3, $het, $hetse,
$confirmed, $mapweight, $source ) = @$arr;
$self->throw("SNP withdrawn. Reason: $type ")
if ($type && $type ne 'notwithdrawn');
if ($confirmed eq 'no-info') {
$confirmed = "suspected";
} else {
$confirmed =~ s/-/ /;
$confirmed = "proven $confirmed";
}
$alleles =~ s/\//\|/g;
$seq5 = substr($seq5, -25, 25);
$seq3 = substr($seq3, 0, 25);
$seq3 .= 'N' x ( 25 - length $seq3 ) if length($seq3) < 25 ;
$seq5 = ('N' x ( 25 - length $seq5 ) ). $seq5 if length($seq5) < 25 ;
my $acc_version = '';
$acc_version .= uc $acc if $acc;
$acc_version .= ".$ver" if $ver;
my $snp = new Bio::EnsEMBL::ExternalData::Variation;
if ($acc_version) {
$snp->seqname($acc_version);
$snp->start($begin);
$snp->end($end);
$snp->strand($strand);
$snp->original_strand($strand);
}
$snp->source_tag($source);
$snp->status($confirmed);
$snp->alleles($alleles);
$snp->upStreamSeq($seq5);
$snp->dnStreamSeq($seq3);
$snp->score($mapweight);
$snp->het($het);
$snp->hetse($hetse);
my $link = new Bio::Annotation::DBLink;
$link->database('dbSNP');
$link->primary_id($dbsnp_id);
$snp->add_DBLink($link);
my $sth2 = $self->prepare("
SELECT subsnp.handle, subsnp.altid
FROM SubSNP as subsnp
WHERE subsnp.internal_id = ?");
$sth2->execute($internal_id);
while( (my $arr2 = $sth2->fetchrow_arrayref()) ) {
my ($handle, $altid) = @{$arr2};
my $link = new Bio::Annotation::DBLink;
$link->database($handle);
$link->primary_id($altid);
$snp->add_DBLink($link);
}
push @variations, $snp;
}
return\@ variations;} | sub fetch_by_clone_accession_version
{ my($self) = shift;
my ($acc, $ver, $start, $stop) = @_;
my @variations;
if ( ! defined $acc) {
$self->throw("Two arguments are requided: embl_accession number and version_number!");
}
if ( ! defined $ver) {
$self->throw("Two arguments are required: embl_accession number and version_number!");
}
if (defined $start) {
$start = 1 if $start eq "";
if ( $start !~ /^\d+$/ and $start > 0) {
$self->throw("$start is not a valid start");
}
}
if (defined $stop) {
$start = 1 if not defined $start;
if ( $stop !~ /^\d+$/ and $stop > 0 ) {
$self->throw("$stop is not a valid stop");
}
}
if (defined $start and defined $stop) {
if ($stop < $start) {
$self->throw("$stop is smaller than $start not a valid start");
}
}
my $acc_version = uc "$acc.$ver";
my $query = qq{
SELECT p1.start, p1.end, p1.type, p1.strand,
p2.id, p2.snpclass, p2.snptype,
p2.observed, p2.seq5, p2.seq3,
p2.het, p2.hetse,
p2.validated, p2.mapweight, p3.datasource, p2.internal_id
FROM Hit as p1, RefSNP as p2, DataSource as p3
WHERE p1.acc = "$acc" and p1.version = "$ver"
AND p3.id = p2.datasource
AND p1.internal_id = p2.internal_id
};
if($start) {
$query .= " AND p1.start >= $start";
}
if($stop) {
$query .= " AND p1.end <= $stop";
}
my $sth = $self->prepare($query);
my $res = $sth->execute();
while( (my $arr = $sth->fetchrow_arrayref()) ) {
my ($begin, $end, $hittype, $strand,
$snpuid, $class, $type,
$alleles, $seq5, $seq3, $het, $hetse,
$confirmed, $mapweight,
$source, $primid
) = @{$arr};
next if ($type && $type ne 'notwithdrawn');
next if $mapweight > 2;
if (defined $start) {
next if $begin < $start;
}
if (defined $stop) {
next if $end > $stop;
}
if ($confirmed eq 'no-info') {
$confirmed = "suspected";
} else {
$confirmed =~ s/-/ /;
$confirmed = "proven $confirmed";
}
$alleles =~ s/\//\|/g;
$seq5 = substr($seq5, -25, 25);
$seq3 = substr($seq3, 0, 25);
$seq3 .= 'N' x ( 25 - length $seq3 ) if length($seq3) < 25 ;
$seq5 = ('N' x ( 25 - length $seq5 ) ). $seq5 if length($seq5) < 25 ;
my $snp = new Bio::EnsEMBL::ExternalData::Variation
(-start => $begin,
-end => $end,
-strand => $strand,
-original_strand => $strand,
-source_tag => $source,
-score => $mapweight,
-status => $confirmed,
-alleles => $alleles,
);
$snp->upStreamSeq($seq5);
$snp->dnStreamSeq($seq3);
$snp->het($het);
$snp->hetse($hetse);
$snp->seqname($acc_version);
my $link = new Bio::Annotation::DBLink;
$link->database('dbSNP');
$link->primary_id($snpuid);
$link->optional_id($acc_version);
$snp->add_DBLink($link);
my $query2 = qq{
SELECT p1.handle, p1.altid
FROM SubSNP as p1
WHERE p1.internal_id = "$primid"
};
my $sth2 = $self->prepare($query2);
my $res2 = $sth2->execute();
while( (my $arr2 = $sth2->fetchrow_arrayref()) ) {
my ($handle, $altid) = @{$arr2};
my $link = new Bio::Annotation::DBLink;
$link->database($handle);
$link->primary_id($altid);
$snp->add_DBLink($link);
}
push(@variations, $snp);
}
return\@ variations;} | sub fetch_by_refsnpid
{
my ($self,$refsnpid,$mouse) = @_;
my (@infos,$query,%var_objs);
if ($mouse) {
$query = qq{
SELECT t1.id, t1.snpclass, t1.snptype, t1.observed, t1.seq5, t1.seq3
FROM RefSNP as t1
WHERE t1.id = "$refsnpid"
};
}
else {
$query = qq{
SELECT t1.id, t1.snpclass, t1.snptype, t1.observed, t1.seq5, t1.seq3,
t2.acc, t2.version, t2.start, t2.end, t2.strand
FROM RefSNP as t1 left join Hit as t2 on t1.internal_id = t2.internal_id
WHERE t1.mapweight <=2 and t1.id = "$refsnpid"
};
}
my $sth=$self->prepare($query);
my $res=$sth->execute();
while (my $info = $sth->fetchrow_hashref()) {
if ($info) {
my $var_obj = $self->_objFromHashref($info);
return $var_obj if $var_obj;
}
}} | sub fetch_freqs_by_pop_SNP_id
{ my ($self, $pop_id, $refsnpid) = @_;
my $sth = $self->prepare('
SELECT straight_join f.snpallele, f.otherallele, f.freq, f.count, f.ssid, f.batchid
FROM RefSNP rs, SubSNP ss, Freq f
WHERE rs.internal_id = ss.internal_id
AND ss.id=f.ssid
AND f.type="ALE" AND rs.id=? AND f.popid=?
ORDER BY f.batchid;');
$sth->execute($refsnpid, $pop_id);
$sth->rows || $self->throw("$refsnpid not in database or don't have frequency data");
my $arr;
my @freqs = ();
while ($arr = $sth->fetchrow_arrayref) {
my ($snpallele, $otherallele, $frequency, $count, $ssid,$batch_id) = @$arr;
my $freq = new Bio::EnsEMBL::ExternalData::Frequency;
my $allele = $snpallele || $otherallele;
$freq->allele($allele);
$freq->frequency($frequency);
$freq->count($count);
$freq->ssid($ssid);
$freq->batch_id($batch_id);
push @freqs, $freq;
}
return\@ freqs;} | sub fetch_genotype_by_SNP_id
{
my ($self, $refsnpid) = @_;
my $sth = $self->prepare('
SELECT refsnp.id, Strain.ssid, Strain.name, Strain.allele,
GTInd.sex, GTInd.source, GTInd.source_ind_id
FROM RefSNP refsnp, Strain Strain, GTInd GTInd
WHERE refsnp.internal_id = Strain.internal_id and Strain.ind_id = GTInd.ind_id
AND refsnp.id = ?');
$sth->execute("$refsnpid") || $self->throw("$refsnpid not in database or don't have genotype data");
my $arr;
my @snps = ();
while ($arr = $sth->fetchrow_arrayref) {
my ($refsnpid, $ssid, $strain_name, $strain_alleles, $sex, $gt_source, $gt_source_ind_id ) = @$arr;
my $snp = new Bio::EnsEMBL::ExternalData::Variation;
$snp->snpid($refsnpid);
$snp->ssid($ssid);
$snp->strain_name($strain_name);
$snp->strain_alleles($strain_alleles);
$snp->sex($sex);
$snp->gt_source($gt_source);
$snp->gt_source_ind_id($gt_source_ind_id);
push @snps, $snp;
}
return\@ snps;} | sub fetch_genotyped_by_Slice
{ my ($self, $slice) = @_;
warn ("ERROR: No slice object passed to $0") if !$slice;
my ($query, @var_objs, %var_objs);
my $chr_start = $slice->start;
my $chr_end = $slice->end;
my $chr_name = $slice->seq_region_name;
$query = qq{
SELECT distinct(r.id), r.snpclass, r.mapweight, r.observed, r.seq5,
r.seq3, ch.physmap as start, ch.physmapstr as end,
ch.physmapstrand as strand, r.internal_id as internal_id
FROM RefSNP as r, ContigHit as ch, Strain as s
WHERE r.snptype = "notwithdrawn"
and r.internal_id = s.internal_id
and r.internal_id = ch.internal_id
and s.allele != ""
and ch.physmap between $chr_start
and $chr_end and ch.chr = "$chr_name"
};
my $sth=$self->prepare($query);
my $res=$sth->execute();
while (my $info = $sth->fetchrow_hashref()) {
if ($info) {
my $physmapstr = $info->{end};
my ($start, $end) = split /\^|\.\./, $physmapstr if ($info->{start} ne $info->{end});
$info->{chr_start} = $start || $info->{start};
$info->{start} = $start-$chr_start+1 if ($start);
$info->{end} = $end-$chr_start+1 if ($end);
$info->{start} = $info->{start}-$chr_start+1 if (!$start);
$info->{end} = $info->{end}-$chr_start+1 if (!$end);
my $var_obj = $self->_objFromHashref($info);
push (@var_objs, $var_obj);
}
}
return\@ var_objs;} | sub fetch_pops_by_SNP_id
{ my ($self, $refsnpid) = @_;
my $sth = $self->prepare('
SELECT straight_join sp.id, sp.name, sp.class, sp.samplesize
FROM RefSNP rs, SubSNP ss, SubPop sp
WHERE rs.internal_id = ss.internal_id
AND ss.id=sp.ssid
AND sp.batchtype="ALE"
AND rs.id = ?');
$sth->execute($refsnpid) || $self->throw("$refsnpid not in database or don't have genotype data");
my $arr;
my @pops = ();
while ($arr = $sth->fetchrow_arrayref) {
my ($pop_id, $name, $region, $sample_size) = @$arr;
my $pop = new Bio::EnsEMBL::ExternalData::Population;
$pop->pop_id($pop_id);
$pop->name($name);
$pop->region($region);
$pop->sample_size($sample_size);
push @pops, $pop;
}
return\@ pops;} | sub fetch_slice_strand_by_ssid
{ my ($self, $ssid, $slice) = @_;
my $slice_name = $slice->name;
my @names = split /\:/, $slice_name;
my $slice_strand = $names[-1];
my $sth = $self->prepare('
SELECT ch.strand as ref_strand, ss.strand_to_rs as ss_strand
FROM ContigHit ch, SubSNP ss
WHERE ch.internal_id = ss.internal_id and ss.id = ?;');
$sth->execute($ssid)|| $self->throw("The SubSNP table don't have strand_to_rs column?");
my ($ref_strand, $ss_strand) = $sth->fetchrow;
my $ssid_slice_strand = $slice_strand * $ref_strand * $ss_strand;
return $ssid_slice_strand;} | General documentation
| fetch_by_clone_accession_vesion | Top |
Title : fetch_by_clone_accession_version
Usage : fetch_by_clone_accession_version($embl_accession_number,
$sequence_version,$start,$end);
Function:
The semantics of this method is as follows:
$sequence_version - embl/genbank sequence version
$embl_accession_number - the embl/genbank accession number
The $start/$end can be ignored, but methods can take advantage of it.
This is so that ensembl can ask for features only on a region of DNA,
and if desired, the external database can respond with features only
in this region, rather than the entire sequence.
The hope is that the second method could potentially have a very
complex set of mappings of other embl_accession numbers to one
embl_accession number and provide the complex mapping.
Example :
Returns : list of Bio::SeqFeature::Variation objects
Args : $embl_accession_number,
$sequence_version,
$start of range, optional
$end of range, optional