Raw content of Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor
=head1 SYNOPSIS
my $dfa = $db->get_DitagFeatureAdaptor;
my $ditagFeatures = $dfa->fetch_all_by_Slice( $slice, "SME005" );
foreach my $ditagFeature (@$ditagFeatures) {
print $ditagFeature->ditag_id . " "
. $ditagFeature->slice . " "
. $ditagFeature->start . "-"
. $ditagFeature->end . " "
. $ditagFeature->strand;
}
=head1 DESCRIPTION
Provides database interaction for the Bio::EnsEMBL::Map::DitagFeature
object
=head1 METHODS
=cut
package Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor;
use strict;
use vars ('@ISA');
use Bio::EnsEMBL::Map::Ditag;
use Bio::EnsEMBL::Map::DitagFeature;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception qw( throw warning );
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
=head2 fetch_all
Arg [1] : none
Example : @all_tags = @{$ditagfeature_adaptor->fetch_all};
Description: Retrieves all ditagFeatures from the database;
Usually not a good idea, use fetch_all_by_Slice instead.
Returntype : listref of Bio::EnsEMBL::Map::DitagFeature
Caller : general
Status : At Risk
=cut
sub fetch_all {
my $self = shift;
my $sth = $self->prepare("SELECT df.ditag_feature_id, df.ditag_id, df.seq_region_id,
df.seq_region_start, df.seq_region_end, df.seq_region_strand,
df.analysis_id, df.hit_start, df.hit_end, df.hit_strand,
df.cigar_line, df.ditag_side, df.ditag_pair_id, d.tag_count
FROM ditag_feature df, ditag d
WHERE df.ditag_id=d.ditag_id" );
$sth->execute;
my $result = $self->_fetch($sth);
return $result;
}
=head2 fetch_by_dbID
Arg [1] : ditagFeature dbID
Example : @my_tags = @{$ditagfeature_adaptor->fetch_by_dbID($my_id)};
Description: Retrieves a ditagFeature from the database.
Returntype : Bio::EnsEMBL::Map::DitagFeature
Caller : general
Status : At Risk
=cut
sub fetch_by_dbID {
my ($self, $dbid) = @_;
my $sth = $self->prepare("SELECT df.ditag_feature_id, df.ditag_id, df.seq_region_id,
df.seq_region_start, df.seq_region_end, df.seq_region_strand,
df.analysis_id, df.hit_start, df.hit_end, df.hit_strand,
df.cigar_line, df.ditag_side, df.ditag_pair_id, d.tag_count
FROM ditag_feature df, ditag d
WHERE df.ditag_id=d.ditag_id AND df.ditag_feature_id = ?" );
$sth->execute($dbid);
my $result = $self->_fetch($sth);
return $result->[0];
}
=head2 fetch_all_by_ditagID
Arg [1] : ditag dbID
Arg [2] : (optional) ditag-pair dbID
Arg [3] : (optional) analysis ID
Example : @my_tags = @{$ditagfeature_adaptor->fetch_all_by_ditag_id($my_id)};
Description: Retrieves all ditagFeatures from the database linking to a specific ditag-id
Returntype : listref of Bio::EnsEMBL::Map::DitagFeature
Caller : general
Status : At Risk
=cut
sub fetch_all_by_ditagID {
my ($self, $ditag_id, $ditag_pair_id, $analysis_id) = @_;
my $arg = $ditag_id;
my $sql = "SELECT df.ditag_feature_id, df.ditag_id, df.seq_region_id,
df.seq_region_start, df.seq_region_end, df.seq_region_strand,
df.analysis_id, df.hit_start, df.hit_end, df.hit_strand,
df.cigar_line, df.ditag_side, df.ditag_pair_id, d.tag_count
FROM ditag_feature df, ditag d
WHERE df.ditag_id=d.ditag_id AND df.ditag_id = ? ";
if($ditag_pair_id){
$sql .= "AND df.ditag_pair_id = ? ";
$arg .= ", $ditag_pair_id";
}
if($analysis_id){
$sql .= "AND df.analysis_id = ? ";
$arg .= ", $analysis_id";
}
$sql .= "ORDER BY df.ditag_pair_id";
my $sth = $self->prepare($sql);
$sth->execute(split(",",$arg));
my $result = $self->_fetch($sth);
return $result;
}
=head2 fetch_all_by_type
Arg [1] : ditag type
Example : @my_tags = @{$ditagfeature_adaptor->fetch_all_by_type($type)};
Description: Retrieves all ditagFeatures from the database linking to a specific ditag-type
Returntype : listref of Bio::EnsEMBL::Map::DitagFeature
Caller : general
Status : At Risk
=cut
sub fetch_all_by_type {
my ($self, $ditag_type) = @_;
my $sth = $self->prepare("SELECT df.ditag_feature_id, df.ditag_id, df.seq_region_id,
df.seq_region_start, df.seq_region_end, df.seq_region_strand,
df.analysis_id, df.hit_start, df.hit_end, df.hit_strand,
df.cigar_line, df.ditag_side, df.ditag_pair_id, d.tag_count
FROM ditag_feature df, ditag d
WHERE df.ditag_id=d.ditag_id AND d.type = ?
ORDER BY df.ditag_id, df.ditag_pair_id" );
$sth->execute($ditag_type);
my $result = $self->_fetch($sth);
return $result;
}
=head2 fetch_all_by_Slice
Arg [1] : Bio::EnsEMBL::Slice
Arg [2] : (optional) ditag type name (specific library) or an aray ref with multiple type names
Arg [3] : (optional) analysis logic_name
Example : $tags = $ditagfeature_adaptor->fetch_all_by_Slice($slice, "SME005");
Description: Retrieves ditagFeatures from the database overlapping a specific region
and (optional) of a specific ditag type or analysis.
Start & end locations are returned in slice coordinates, now.
Returntype : listref of Bio::EnsEMBL::Map::DitagFeatures
Caller : general
Status : At Risk
=cut
sub fetch_all_by_Slice {
my ($self, $slice, $tagtype, $logic_name) = @_;
my @result;
my $moresql;
if(!ref($slice) || !$slice->isa("Bio::EnsEMBL::Slice")) {
throw("Bio::EnsEMBL::Slice argument expected not $slice.");
}
#get affected ditag_feature_ids
my $sql = "SELECT df.ditag_feature_id, df.ditag_id, df.seq_region_id, df.seq_region_start,
df.seq_region_end, df.seq_region_strand, df.analysis_id, df.hit_start, df.hit_end,
df.hit_strand, df.cigar_line, df.ditag_side, df.ditag_pair_id,
d.tag_count
FROM ditag_feature df, ditag d
WHERE df.ditag_id=d.ditag_id";
if($tagtype){
my $tagtypes = '';
#check if array
if(ref $tagtype eq 'ARRAY'){
my @arraytype_mod;
foreach my $arraytype (@$tagtype){ push @arraytype_mod, '"'.$arraytype.'"' }
$tagtypes = join(", ", @arraytype_mod);
}
else{
$tagtypes = '"'.$tagtype.'"';
}
$sql .= " AND d.type IN(".$tagtypes.")";
}
if($logic_name){
my $analysis = $self->db->get_AnalysisAdaptor->fetch_by_logic_name($logic_name);
if(!$analysis) {
return undef;
}
$sql .= " AND df.analysis_id = ".$analysis->dbID();
}
$sql .= " AND df.seq_region_id = ".$slice->get_seq_region_id.
" AND df.seq_region_start <= ".$slice->end.
" AND df.seq_region_end >= ".$slice->start;
my $sth = $self->prepare($sql);
$sth->execute();
my $result = $self->_fetch($sth, $slice);
push(@result, @$result);
return \@result;
}
=head2 fetch_pairs_by_Slice
Arg [1] : Bio::EnsEMBL::Slice
Arg [2] : (optional) ditag type (specific library)
Arg [3] : (optional) analysis logic_name
Example : my $ditagfeatures = $dfa->fetch_pairs_by_Slice($slice);
foreach my $ditagfeature (@$ditagfeatures){
$minstart = $$ditagfeature2{'start'};
$maxend = $$ditagfeature2{'end'};
$bothstrand = $$ditagfeature2{'strand'};
$tag_count = $$ditagfeature2{'tag_count'};
print "$minstart, $maxend, $bothstrand, $tag_count\n";
}
Description: Retrieves ditagFeature information in pairs from the database overlapping a specific region
and (optional) of a specific ditag type or analysis. The absotute start and end points are
fetched.
Slices should be SMALL!
Returntype : array ref with hash ref of artifical DitagFeature object
Caller : general
Status : At Risk
=cut
sub fetch_pairs_by_Slice {
my ($self, $slice, $tagtype, $logic_name) = @_;
my ($tag_id, $pair_id, $seq_region_id, $start, $end, $strand, $analysis_id, $tag_count);
my @result;
my $sql = "SELECT df.ditag_id, df.ditag_pair_id, df.seq_region_id, MIN(df.seq_region_start), ".
"MAX(df.seq_region_end), df.seq_region_strand, df.analysis_id, d.tag_count ".
"FROM ditag_feature df, ditag d ".
"WHERE df.ditag_id=d.ditag_id ";
if($tagtype){
$sql .= "AND d.type = \"".$tagtype."\"";
}
$sql .= " AND df.seq_region_id = ".$slice->get_seq_region_id.
" AND df.seq_region_start <= ".$slice->end.
" AND df.seq_region_end >= ".$slice->start;
if($logic_name){
my $analysis = $self->db->get_AnalysisAdaptor->fetch_by_logic_name($logic_name);
if(!$analysis) {
return undef;
}
$sql .= " AND df.analysis_id = ".$analysis->dbID();
}
$sql .= " GROUP BY df.ditag_id, df.ditag_pair_id;";
my $sth = $self->prepare($sql);
$sth->execute();
$sth->bind_columns( \$tag_id, \$pair_id, \$seq_region_id, \$start, \$end, \$strand, \$analysis_id ,\$tag_count);
while ( $sth->fetch ) {
#convert into relative slice coordinates
if($slice->strand == 1) {
$start = $start - $slice->start + 1;
$end = $end - $slice->start + 1;
}
else{
$start = $slice->end - $end + 1;
$end = $slice->end - $start + 1;
$strand *= -1;
}
my %ditag_feature_pair = (
ditag => $tag_id,
pair_id => $pair_id,
region => $seq_region_id,
start => $start,
end => $end,
strand => $strand,
analysis => $analysis_id,
tag_count => $tag_count
);
push(@result, \%ditag_feature_pair);
}
return \@result;
}
=head2 _fetch
Arg [1] : statement handler
Arg [2] : (optional) target-slice for the feature
Description: generic sql-fetch function for the DitagFeature fetch methods
Returntype : listref of Bio::EnsEMBL::Map::DitagFeatures
Caller : private
Status : At Risk
=cut
sub _fetch {
my ($self, $sth, $dest_slice) = @_;
my ( $tag_id, $mothertag_id, $seqreg, $seqstart, $seqend, $strand, $analysis_id, $hit_start,
$hit_end, $hit_strand, $cigar_line, $ditag_side, $ditag_pair_id, $tag_count );
$sth->bind_columns( \$tag_id, \$mothertag_id, \$seqreg,
\$seqstart, \$seqend, \$strand,
\$analysis_id, \$hit_start, \$hit_end,
\$hit_strand, \$cigar_line, \$ditag_side,
\$ditag_pair_id, \$tag_count );
my @ditag_features;
my $dest_slice_start;
my $dest_slice_end;
my $dest_slice_strand;
if($dest_slice) {
$dest_slice_start = $dest_slice->start();
$dest_slice_end = $dest_slice->end();
$dest_slice_strand = $dest_slice->strand();
}
while ( $sth->fetch ) {
my $analysis_obj = $self->db->get_AnalysisAdaptor->fetch_by_dbID($analysis_id);
my $slice = $self->db->get_SliceAdaptor->fetch_by_seq_region_id($seqreg);
if($dest_slice) {
if($dest_slice_start != 1 || $dest_slice_strand != 1) {
if($dest_slice_strand == 1) {
$seqstart = $seqstart - $dest_slice_start + 1;
$seqend = $seqend - $dest_slice_start + 1;
} else {
my $tmp_seq_region_start = $seqstart;
$seqstart = $dest_slice_end - $seqend + 1;
$seqend = $dest_slice_end - $tmp_seq_region_start + 1;
$strand *= -1;
}
$slice = $dest_slice;
}
}
push @ditag_features,
Bio::EnsEMBL::Map::DitagFeature->new( -dbid => $tag_id,
-slice => $slice,
-start => $seqstart,
-end => $seqend,
-strand => $strand,
-analysis => $analysis_obj,
-hit_start => $hit_start,
-hit_end => $hit_end,
-hit_strand => $hit_strand,
-ditag_id => $mothertag_id,
-cigar_line => $cigar_line,
-ditag_side => $ditag_side,
-ditag_pair_id => $ditag_pair_id,
-ditag => undef,
-tag_count => $tag_count,
-adaptor => $self,
);
}
return \@ditag_features;
}
=head2 sequence
Arg [1] : dbID of DitagFeature
Example : $ditagfeature_adaptor->get_sequence($ditagFeature->dbID)
Description: get the part of the sequence of a ditag,
that is actully aligned to the genome.
Returntype : string
Exceptions : thrown if not all data needed for storing is populated in the
ditag features
Caller : Bio::EnsEMBL::Map::DitagFeature
Status : At Risk
=cut
sub sequence {
my ($self, $dbID) = @_;
my $sequence = undef;
my $db = $self->db() or throw "Couldn t get database connection.";
my $sql = "SELECT d.sequence, df.hit_start, df.hit_end, df.hit_strand ".
"FROM ditag d, ditag_feature df ".
"WHERE df.ditag_id=d.ditag_id and df.ditag_feature_id = ?";
my $sth = $db->dbc->prepare($sql);
$sth->execute( $dbID );
my ($seq, $start, $end, $strand) = $sth->fetchrow_array();
if($seq and $start and $end and $strand){
$sequence = substr($seq, ($start-1), ($end-$strand));
if($strand == -1) {
$sequence =~ tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/;
}
}
return $sequence;
}
=head2 store
Arg [1] : (Array ref of) Bio::EnsEMBL::Map::DitagFeature
Example : $ditagfeature_adaptor->store(@ditag_features);
Description: Stores a single ditagFeature or
a list of ditagFeatures in this database.
Returntype : none
Exceptions : thrown if not all data needed for storing is populated in the
ditag features
Caller : general
Status : At Risk
=cut
sub store {
my ( $self, $ditag_features ) = @_;
if ( ref $ditag_features eq 'ARRAY' ) {
if ( scalar(@$ditag_features) == 0 ) {
throw( "Must call store with ditag_feature or list ref of ditags_features" );
}
} elsif ($ditag_features) {
my @ditag_features;
push @ditag_features, $ditag_features;
$ditag_features = \@ditag_features;
} else {
throw( "Must call store with ditag_feature or list ref of ditag_features." );
}
my $db = $self->db() or throw "Couldn t get database connection.";
my $sth1 = $self->prepare( "INSERT INTO ditag_feature( ditag_id, seq_region_id, seq_region_start,
seq_region_end, seq_region_strand, analysis_id, hit_start, hit_end,
hit_strand, cigar_line, ditag_side, ditag_pair_id )
VALUES( ?,?,?,?,?,?,?,?,?,?,?,? )" );
my $sth2 = $self->prepare( "INSERT INTO ditag_feature( ditag_feature_ID, ditag_id, seq_region_id,
seq_region_start, seq_region_end, seq_region_strand, analysis_id, hit_start,
hit_end, hit_strand, cigar_line, ditag_side, ditag_pair_id )
VALUES( ?,?,?,?,?,?,?,?,?,?,?,?,? )" );
# my $sth3 = $self->prepare( "SELECT COUNT(*) FROM ditag_feature
# WHERE ditag_id = ?" );
TAG:
foreach my $ditag_feature (@$ditag_features) {
if ( !ref $ditag_feature || !$ditag_feature->isa("Bio::EnsEMBL::Map::DitagFeature") ) {
throw( "Object must be an Ensembl DitagFeature, "
. "not a " . ref($ditag_feature) );
}
if ( $ditag_feature->is_stored($db) ) {
warning( "DitagFeature " . $ditag_feature->dbID .
" is already stored in this database,".
" maybe you need to use the update() method?" );
next TAG;
}
if(!$ditag_feature->ditag_id or !($self->db->get_DitagAdaptor->fetch_by_dbID($ditag_feature->ditag_id))){
throw("DitagFeature must be supplied with the id of a corresponding Ditag object.");
}
if(!$ditag_feature->ditag or !$ditag_feature->ditag->isa("Bio::EnsEMBL::Map::Ditag")){
throw("DitagFeature must be linked to a valid Ditag object.");
}
# #check if more than x tags with this ditag id exist
# $sth3->execute( $ditag_feature->ditag_id );
# my ($num) = $sth3->fetchrow_array();
# if ( ($num) and ($num > 1) ) {
# warning( "There are already at least 2 DitagFeatures relating to Ditag ".
# $ditag->ditag_id." stored in this database." );
# if ( $num > 4 ) {
# warning( "not storing" );
# next TAG;
# }
# }
if ( $ditag_feature->dbID ) {
$sth2->bind_param( 1, $ditag_feature->dbID, SQL_INTEGER );
$sth2->bind_param( 2, $ditag_feature->ditag_id, SQL_INTEGER );
$sth2->bind_param( 3, ($ditag_feature->slice->get_seq_region_id), SQL_INTEGER );
$sth2->bind_param( 4, $ditag_feature->start, SQL_INTEGER );
$sth2->bind_param( 5, $ditag_feature->end, SQL_INTEGER );
$sth2->bind_param( 6, $ditag_feature->strand, SQL_VARCHAR );
$sth2->bind_param( 7, $ditag_feature->analysis->dbID, SQL_INTEGER );
$sth2->bind_param( 8, $ditag_feature->hit_start, SQL_INTEGER );
$sth2->bind_param( 9, $ditag_feature->hit_end, SQL_INTEGER );
$sth2->bind_param( 10, $ditag_feature->hit_strand, SQL_VARCHAR );
$sth2->bind_param( 11, $ditag_feature->cigar_line, SQL_VARCHAR );
$sth2->bind_param( 12, $ditag_feature->ditag_side, SQL_VARCHAR );
$sth2->bind_param( 13, $ditag_feature->ditag_pair_id, SQL_VARCHAR );
$sth2->execute();
}
else{
$sth1->bind_param( 1, $ditag_feature->ditag_id, SQL_INTEGER );
$sth1->bind_param( 2, ($ditag_feature->slice->get_seq_region_id), SQL_INTEGER );
$sth1->bind_param( 3, $ditag_feature->start, SQL_INTEGER );
$sth1->bind_param( 4, $ditag_feature->end, SQL_INTEGER );
$sth1->bind_param( 5, $ditag_feature->strand, SQL_VARCHAR );
$sth1->bind_param( 6, $ditag_feature->analysis->dbID, SQL_INTEGER );
$sth1->bind_param( 7, $ditag_feature->hit_start, SQL_INTEGER );
$sth1->bind_param( 8, $ditag_feature->hit_end, SQL_INTEGER );
$sth1->bind_param( 9, $ditag_feature->hit_strand, SQL_VARCHAR );
$sth1->bind_param( 10, $ditag_feature->cigar_line, SQL_VARCHAR );
$sth1->bind_param( 11, $ditag_feature->ditag_side, SQL_VARCHAR );
$sth1->bind_param( 12, $ditag_feature->ditag_pair_id, SQL_VARCHAR );
$sth1->execute();
my $dbID = $sth1->{'mysql_insertid'};
$ditag_feature->dbID($dbID);
$ditag_feature->adaptor($self);
}
}
}
=head2 batch_store
Arg [1] : (Array ref of) Bio::EnsEMBL::Map::DitagFeatures
Arg [2] : bool have_dbIDs
Example : $ditagfeature_adaptor->batch_store(\@ditag_features);
Description: Stores a list of ditagFeatures in this database.
DitagFeatures are expected to have no dbID yet unless flag "have_dbIDs" is true.
They are inserted in one combined INSERT for better performance.
Returntype : none
Exceptions : thrown if not all data needed for storing is given for the
ditag features
Caller : general
Status : At Risk
=cut
sub batch_store {
my ( $self, $ditag_features, $have_dbIDs ) = @_;
my @good_ditag_features;
my ($sql, $sqladd);
my $inserts = 0;
if ( ref $ditag_features eq 'ARRAY' ) {
if ( scalar(@$ditag_features) == 0 ) {
throw( "Must call store with ditag_feature or list ref of ditag_features." );
}
} elsif ($ditag_features) {
my @ditag_features;
push @ditag_features, $ditag_features;
$ditag_features = \@ditag_features;
} else {
throw( "Must call store with ditag_feature or list ref of ditag_features." );
}
my $db = $self->db() or throw "Couldn t get database connection.";
#check whether it s a DitagFeature object and is not stored already
foreach my $ditag_feature (@$ditag_features) {
if ( !ref $ditag_feature || !$ditag_feature->isa("Bio::EnsEMBL::Map::DitagFeature") ) {
throw( "Object must be an Ensembl DitagFeature, "
. "not a " . ref($ditag_feature) );
}
if(!$ditag_feature->ditag_id or !($self->db->get_DitagAdaptor->fetch_by_dbID($ditag_feature->ditag_id))){
throw("DitagFeature must be supplied with the id of a corresponding Ditag object.");
}
if(!$ditag_feature->ditag or !$ditag_feature->ditag->isa("Bio::EnsEMBL::Map::Ditag")){
throw("DitagFeature must be linked to a valid Ditag object.");
}
if ( $ditag_feature->is_stored($db) ) {
warning( "DitagFeature " . $ditag_feature->dbID
. " is already stored in this database." );
next;
}
push(@good_ditag_features, $ditag_feature);
}
$ditag_features = undef;
#create batch INSERT
if($have_dbIDs){
$sql = "INSERT INTO ditag_feature ( ditag_feature_id, ditag_id, seq_region_id, seq_region_start, ".
"seq_region_end, seq_region_strand, analysis_id, hit_start, hit_end, ".
"hit_strand, cigar_line, ditag_side, ditag_pair_id ) VALUES ";
foreach my $ditag_feature (@good_ditag_features) {
$sqladd = "";
if($inserts){ $sqladd = ", " }
$sqladd .= "(". $ditag_feature->ditag_feature_id.", ".$ditag_feature->ditag_id.", ".
($ditag_feature->slice->get_seq_region_id).", ". $ditag_feature->start.", ".
$ditag_feature->end.", '".$ditag_feature->strand."', ".$ditag_feature->analysis->dbID.", ".
$ditag_feature->hit_start.", ".$ditag_feature->hit_end.", '".$ditag_feature->hit_strand.
"', '".$ditag_feature->cigar_line."', '".$ditag_feature->ditag_side."', ".
$ditag_feature->ditag_pair_id.")";
$sql .= $sqladd;
$inserts++;
}
}
else{
$sql = "INSERT INTO ditag_feature ( ditag_id, seq_region_id, seq_region_start, ".
"seq_region_end, seq_region_strand, analysis_id, hit_start, hit_end, ".
"hit_strand, cigar_line, ditag_side, ditag_pair_id ) VALUES ";
foreach my $ditag_feature (@good_ditag_features) {
$sqladd = "";
if($inserts){ $sqladd = ", " }
$sqladd .= "(". $ditag_feature->ditag_id.", ".($ditag_feature->slice->get_seq_region_id).", ".
$ditag_feature->start.", ".$ditag_feature->end.", '".$ditag_feature->strand."', ".
$ditag_feature->analysis->dbID.", ".$ditag_feature->hit_start.", ".$ditag_feature->hit_end.
", '".$ditag_feature->hit_strand."', '".$ditag_feature->cigar_line."', '".
$ditag_feature->ditag_side."', ".$ditag_feature->ditag_pair_id.")";
$sql .= $sqladd;
$inserts++;
}
}
#STORE
if($inserts){
print STDERR "\nHave $inserts Features.\n";
eval{
$db->dbc->do($sql);
};
if($@){
warning("Problem inserting ditag feature batch!".$@."\n");
}
}
else{
warn "Nothing stored!";
}
}
=head2 update
Arg [1] : ditagFeature to update
Description: update an existing ditagFeature with new values
Returntype : 1 on success
Status : At Risk
=cut
sub update {
my ($self, $ditagFeature) = @_;
my $sth = $self->prepare( "UPDATE ditag_feature
SET ditag_id=?, seq_region_id=?, seq_region_start=?, seq_region_end=?,
seq_region_strand=?, analysis_id=?, hit_start=?, hit_end=?, hit_strand=?,
cigar_line=?, ditag_side=?, ditag_pair_id=?
where ditag_feature_id=?;" );
$sth->bind_param(1, $ditagFeature->ditag_id, SQL_INTEGER);
$sth->bind_param(1, $ditagFeature->seq_region_id, SQL_INTEGER);
$sth->bind_param(1, $ditagFeature->seq_region_start, SQL_INTEGER);
$sth->bind_param(1, $ditagFeature->seq_region_end, SQL_INTEGER);
$sth->bind_param(1, $ditagFeature->seq_region_strand, SQL_TINYINT);
$sth->bind_param(1, $ditagFeature->hit_start, SQL_INTEGER);
$sth->bind_param(1, $ditagFeature->hit_end, SQL_INTEGER);
$sth->bind_param(1, $ditagFeature->hit_strand, SQL_TINYINT);
$sth->bind_param(1, $ditagFeature->cigar_line, SQL_LONGVARCHAR);
$sth->bind_param(1, $ditagFeature->ditag_side, SQL_VARCHAR);
$sth->bind_param(1, $ditagFeature->ditag_pair_id, SQL_INTEGER);
$sth->bind_param(1, $ditagFeature->dbID, SQL_INTEGER);
my $result =$sth->execute();
return $result;
}
=head2 list_dbIDs
Args : None
Example : my @feature_ids = @{$dfa->list_dbIDs()};
Description: Gets an array of internal IDs for all DitagFeature objects in
the current database.
Arg[1] : <optional> int. not 0 for the ids to be sorted by the seq_region.
Returntype : List of ints
Exceptions : None
Status : Stable
=cut
sub list_dbIDs {
my ($self, $ordered) = shift;
return $self->_list_dbIDs('ditag_feature', undef, $ordered);
}
1;
]]>