Raw content of Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor
<![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::DBSQL::DnaAlignFeatureAdaptor - Adaptor for DnaAlignFeatures
=head1 SYNOPSIS
$dafa = $registry->get_adaptor( 'Human', 'Core', 'DnaAlignFeature' );
my @features = @{ $dafa->fetch_all_by_Slice($slice) };
$dafa->store(@features);
=head1 DESCRIPTION
This is an adaptor responsible for the retrieval and storage of
DnaDnaAlignFeatures from the database. This adaptor inherits most of its
functionality from the BaseAlignFeatureAdaptor and BaseFeatureAdaptor
superclasses.
=head1 METHODS
=cut
package Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor;
use vars qw(@ISA);
use strict;
use Data::Dumper;
use Bio::EnsEMBL::DnaDnaAlignFeature;
use Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor);
=head2 _tables
Args : none
Example : @tabs = $self->_tables
Description: PROTECTED implementation of the abstract method inherited from
BaseFeatureAdaptor. Returns list of [tablename, alias] pairs
Returntype : list of listrefs of strings
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::generic_fetch
Status : Stable
=cut
sub _tables {
my $self = shift;
return (['dna_align_feature', 'daf'],['external_db','exdb']);
}
sub _left_join{
return (['external_db',"exdb.external_db_id = daf.external_db_id"]);
}
=head2 _columns
Args : none
Example : @columns = $self->_columns
Description: PROTECTED implementation of abstract superclass method.
Returns a list of columns that are needed for object creation.
Returntype : list of strings
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::generic_fetch
Status : Stable
=cut
sub _columns {
my $self = shift;
#warning, implementation of _objs_from_sth method depends on order of list
return qw(daf.dna_align_feature_id
daf.seq_region_id
daf.analysis_id
daf.seq_region_start
daf.seq_region_end
daf.seq_region_strand
daf.hit_start
daf.hit_end
daf.hit_name
daf.hit_strand
daf.cigar_line
daf.evalue
daf.perc_ident
daf.score
daf.external_db_id
daf.hcoverage
daf.external_data
daf.pair_dna_align_feature_id
exdb.db_name
exdb.db_display_name);
}
=head2 store
Arg [1] : list of Bio::EnsEMBL::DnaAlignFeatures @feats
the features to store in the database
Example : $dna_align_feature_adaptor->store(@features);
Description: Stores a list of DnaAlignFeatures in the database
Returntype : none
Exceptions : throw if any of the provided features cannot be stored
which may occur if:
* The feature does not have an associate Slice
* The feature does not have an associated analysis
* The Slice the feature is associated with is on a seq_region
unknown to this database
A warning is given if:
* The feature has already been stored in this db
Caller : Pipeline
Status : Stable
=cut
sub store {
my ($self, @feats) = @_;
throw("Must call store with features") if( scalar(@feats) == 0 );
my @tabs = $self->_tables;
my ($tablename) = @{$tabs[0]};
my $db = $self->db();
my $analysis_adaptor = $db->get_AnalysisAdaptor();
my $sth = $self->prepare(
"INSERT INTO $tablename (seq_region_id, seq_region_start, seq_region_end,
seq_region_strand, hit_start, hit_end,
hit_strand, hit_name, cigar_line,
analysis_id, score, evalue, perc_ident, external_db_id,
hcoverage, pair_dna_align_feature_id)
VALUES (?,?,?,?,?,?,?,?,?,?,?, ?, ?, ?, ?, ?)");
FEATURE: foreach my $feat ( @feats ) {
if( !ref $feat || !$feat->isa("Bio::EnsEMBL::DnaDnaAlignFeature") ) {
throw("feature must be a Bio::EnsEMBL::DnaDnaAlignFeature,"
. " not a [".ref($feat)."].");
}
if($feat->is_stored($db)) {
warning("DnaDnaAlignFeature [".$feat->dbID."] is already stored" .
" in this database.");
next FEATURE;
}
my $hstart = $feat->hstart();
my $hend = $feat->hend();
my $hstrand = $feat->hstrand();
$self->_check_start_end_strand($hstart,$hend, $hstrand);
my $cigar_string = $feat->cigar_string();
if(!$cigar_string) {
$cigar_string = $feat->length() . 'M';
warning("DnaDnaAlignFeature does not define a cigar_string.\n" .
"Assuming ungapped block with cigar_line=$cigar_string .");
}
my $hseqname = $feat->hseqname();
if(!$hseqname) {
throw("DnaDnaAlignFeature must define an hseqname.");
}
if(!defined($feat->analysis)) {
throw("An analysis must be attached to the features to be stored.");
}
#store the analysis if it has not been stored yet
if(!$feat->analysis->is_stored($db)) {
$analysis_adaptor->store($feat->analysis());
}
my $original = $feat;
my $seq_region_id;
($feat, $seq_region_id) = $self->_pre_store($feat);
$sth->bind_param(1,$seq_region_id,SQL_INTEGER);
$sth->bind_param(2,$feat->start,SQL_INTEGER);
$sth->bind_param(3,$feat->end,SQL_INTEGER);
$sth->bind_param(4,$feat->strand,SQL_TINYINT);
$sth->bind_param(5,$hstart,SQL_INTEGER);
$sth->bind_param(6,$hend,SQL_INTEGER);
$sth->bind_param(7,$hstrand,SQL_TINYINT);
$sth->bind_param(8,$hseqname,SQL_VARCHAR);
$sth->bind_param(9,$cigar_string,SQL_LONGVARCHAR);
$sth->bind_param(10,$feat->analysis->dbID,SQL_INTEGER);
$sth->bind_param(11,$feat->score,SQL_DOUBLE);
$sth->bind_param(12,$feat->p_value,SQL_DOUBLE);
$sth->bind_param(13,$feat->percent_id,SQL_FLOAT);
$sth->bind_param(14,$feat->external_db_id,SQL_INTEGER);
$sth->bind_param(15,$feat->hcoverage,SQL_DOUBLE);
$sth->bind_param(16,$feat->pair_dna_align_feature_id, SQL_INTEGER);
$sth->execute();
$original->dbID($sth->{'mysql_insertid'});
$original->adaptor($self);
}
$sth->finish();
}
sub save {
my ($self, $features) = @_;
my @feats = @$features;
throw("Must call store with features") if( scalar(@feats) == 0 );
my @tabs = $self->_tables;
my ($tablename) = @{$tabs[0]};
my $db = $self->db();
my $analysis_adaptor = $db->get_AnalysisAdaptor();
my $sql = qq{INSERT INTO $tablename (seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_start, hit_end, hit_strand, hit_name, cigar_line, analysis_id, score, evalue, perc_ident, external_db_id, hcoverage, pair_dna_align_feature_id, external_data) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)};
my %analyses = ();
my $sth = $self->prepare($sql);
FEATURE: foreach my $feat ( @feats ) {
if( !ref $feat || !$feat->isa("Bio::EnsEMBL::DnaDnaAlignFeature") ) {
throw("feature must be a Bio::EnsEMBL::DnaDnaAlignFeature,"
. " not a [".ref($feat)."].");
}
if($feat->is_stored($db)) {
warning("DnaDnaAlignFeature [".$feat->dbID."] is already stored" .
" in this database.");
next FEATURE;
}
my $hstart = $feat->hstart || 0; # defined $feat->hstart ? $feat->hstart : $feat->start ;
my $hend = $feat->hend || 0; # defined $feat->hend ? $feat->hend : $feat->end;
my $hstrand = $feat->hstrand|| 0; # defined $feat->hstrand ? $feat->hstrand : $feat->strand;
if( $hstart && $hend ) {
if($hend < $hstart) {
throw("Invalid Feature start/end [$hstart/$hend]. Start must be less than or equal to end.");
}
}
my $cigar_string = $feat->cigar_string();
if(!$cigar_string) {
$cigar_string = $feat->length() . 'M';
warning("DnaDnaAlignFeature does not define a cigar_string.\n" .
"Assuming ungapped block with cigar_line=$cigar_string .");
}
my $hseqname = $feat->hseqname();
if(!$hseqname) {
throw("DnaDnaAlignFeature must define an hseqname.");
}
if(!defined($feat->analysis)) {
throw("An analysis must be attached to the features to be stored.");
}
#store the analysis if it has not been stored yet
if(!$feat->analysis->is_stored($db)) {
$analysis_adaptor->store($feat->analysis());
}
$analyses{ $feat->analysis->dbID }++;
my $original = $feat;
my $seq_region_id;
($feat, $seq_region_id) = $self->_pre_store_userdata($feat);
my $extra_data = $feat->extra_data ? $self->dump_data($feat->extra_data) : '';
$sth->bind_param(1,$seq_region_id,SQL_INTEGER);
$sth->bind_param(2,$feat->start,SQL_INTEGER);
$sth->bind_param(3,$feat->end,SQL_INTEGER);
$sth->bind_param(4,$feat->strand,SQL_TINYINT);
$sth->bind_param(5,$hstart,SQL_INTEGER);
$sth->bind_param(6,$hend,SQL_INTEGER);
$sth->bind_param(7,$hstrand,SQL_TINYINT);
$sth->bind_param(8,$hseqname,SQL_VARCHAR);
$sth->bind_param(9,$cigar_string,SQL_LONGVARCHAR);
$sth->bind_param(10,$feat->analysis->dbID,SQL_INTEGER);
$sth->bind_param(11,$feat->score,SQL_DOUBLE);
# $sth->bind_param(11,$feat->score); # if the above statement does not work it means you need to upgrade DBD::mysql, meantime you can replace it with this line
$sth->bind_param(12,$feat->p_value,SQL_DOUBLE);
$sth->bind_param(13,$feat->percent_id,SQL_FLOAT);
$sth->bind_param(14,$feat->external_db_id,SQL_INTEGER);
$sth->bind_param(15,$feat->hcoverage,SQL_DOUBLE);
$sth->bind_param(16,$feat->pair_dna_align_feature_id,SQL_INTEGER);
$sth->bind_param(17,$extra_data,SQL_LONGVARCHAR);
$sth->execute();
$original->dbID($sth->{'mysql_insertid'});
$original->adaptor($self);
}
$sth->finish();
## js5 hack to update meta_coord table...
if( keys %analyses ) {
my $sth = $self->prepare( 'select sr.coord_system_id, max(daf.seq_region_end-daf.seq_region_start) from seq_region as sr, dna_align_feature as daf where daf.seq_region_id=sr.seq_region_id and analysis_id in ('.join(',',keys %analyses).') group by coord_system_id' );
$sth->execute;
foreach( @{ $sth->fetchall_arrayref } ) {
my $sth2 = $self->prepare( qq(insert ignore into meta_coord values("dna_align_feature",$_->[0],$_->[1])) );
$sth2->execute;
$sth2->finish;
$sth2 = $self->prepare( qq(update meta_coord set max_length = $_->[1] where coord_system_id = $_->[0] and table_name="dna_align_feature" and max_length < $_->[1]) );
$sth2->execute;
$sth2->finish;
}
$sth->finish;
}
}
=head2 _objs_from_sth
Arg [1] : DBI statement handle $sth
an exectuted DBI statement handle generated by selecting
the columns specified by _columns() from the table specified
by _table()
Example : @dna_dna_align_feats = $self->_obj_from_hashref
Description: PROTECTED implementation of superclass abstract method.
Creates DnaDnaAlignFeature objects from a DBI hashref
Returntype : listref of Bio::EnsEMBL::DnaDnaAlignFeatures
Exceptions : none
Caller : Bio::EnsEMBL::BaseFeatureAdaptor::generic_fetch
Status : Stable
=cut
sub _objs_from_sth {
my ($self, $sth, $mapper, $dest_slice) = @_;
#
# This code is ugly because an attempt has been made to remove as many
# function calls as possible for speed purposes. Thus many caches and
# a fair bit of gymnastics is used.
#
# in case of userdata we need the features on the dest_slice
# in case of get_all_supporting_features dest_slice is not provided ..
my $sa = $dest_slice ? $dest_slice->adaptor() : $self->db()->get_SliceAdaptor();
my $aa = $self->db->get_AnalysisAdaptor();
my @features;
my %analysis_hash;
my %slice_hash;
my %sr_name_hash;
my %sr_cs_hash;
my($dna_align_feature_id, $seq_region_id, $analysis_id, $seq_region_start,
$seq_region_end, $seq_region_strand, $hit_start, $hit_end, $hit_name,
$hit_strand, $cigar_line, $evalue, $perc_ident, $score,
$external_db_id, $hcoverage, $extra_data, $pair_dna_align_feature_id,
$external_db_name, $external_display_db_name);
$sth->bind_columns(
\$dna_align_feature_id, \$seq_region_id, \$analysis_id, \$seq_region_start,
\$seq_region_end, \$seq_region_strand, \$hit_start, \$hit_end, \$hit_name,
\$hit_strand, \$cigar_line, \$evalue, \$perc_ident, \$score,
\$external_db_id, \$hcoverage, \$extra_data, \$pair_dna_align_feature_id,
\$external_db_name, \$external_display_db_name);
my $asm_cs;
my $cmp_cs;
my $asm_cs_vers;
my $asm_cs_name;
my $cmp_cs_vers;
my $cmp_cs_name;
if($mapper) {
$asm_cs = $mapper->assembled_CoordSystem();
$cmp_cs = $mapper->component_CoordSystem();
$asm_cs_name = $asm_cs->name();
$asm_cs_vers = $asm_cs->version();
$cmp_cs_name = $cmp_cs->name();
$cmp_cs_vers = $cmp_cs->version();
}
my $dest_slice_start;
my $dest_slice_end;
my $dest_slice_strand;
my $dest_slice_length;
my $dest_slice_sr_name;
my $dest_slice_seq_region_id;
if($dest_slice) {
$dest_slice_start = $dest_slice->start();
$dest_slice_end = $dest_slice->end();
$dest_slice_strand = $dest_slice->strand();
$dest_slice_length = $dest_slice->length();
$dest_slice_sr_name = $dest_slice->seq_region_name();
$dest_slice_seq_region_id = $dest_slice->get_seq_region_id();
}
FEATURE: while($sth->fetch()) {
#get the analysis object
my $analysis = $analysis_hash{$analysis_id} ||=
$aa->fetch_by_dbID($analysis_id);
#get the slice object
my $slice = $slice_hash{"ID:".$seq_region_id};
if(!$slice) {
$slice = $sa->fetch_by_seq_region_id($seq_region_id);
$slice_hash{"ID:".$seq_region_id} = $slice;
$sr_name_hash{$seq_region_id} = $slice->seq_region_name();
$sr_cs_hash{$seq_region_id} = $slice->coord_system();
}
my $sr_name = $sr_name_hash{$seq_region_id};
my $sr_cs = $sr_cs_hash{$seq_region_id};
#
# remap the feature coordinates to another coord system
# if a mapper was provided
#
if($mapper) {
($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
$mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs);
#skip features that map to gaps or coord system boundaries
next FEATURE if(!defined($seq_region_id));
#get a slice in the coord system we just mapped to
if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
$slice = $slice_hash{"ID:".$seq_region_id} ||=
$sa->fetch_by_seq_region_id($seq_region_id);
} else {
$slice = $slice_hash{"ID:".$seq_region_id} ||=
$sa->fetch_by_seq_region_id($seq_region_id);
}
}
#
# If a destination slice was provided convert the coords
# If the dest_slice starts at 1 and is foward strand, nothing needs doing
#
if($dest_slice) {
if($dest_slice_start != 1 || $dest_slice_strand != 1) {
if($dest_slice_strand == 1) {
$seq_region_start = $seq_region_start - $dest_slice_start + 1;
$seq_region_end = $seq_region_end - $dest_slice_start + 1;
} else {
my $tmp_seq_region_start = $seq_region_start;
$seq_region_start = $dest_slice_end - $seq_region_end + 1;
$seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
$seq_region_strand *= -1;
}
#throw away features off the end of the requested slice
if($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
( $dest_slice_seq_region_id ne $seq_region_id )) {
next FEATURE;
}
}
$slice = $dest_slice;
}
# Finally, create the new DnaAlignFeature.
push( @features,
$self->_create_feature_fast(
'Bio::EnsEMBL::DnaDnaAlignFeature', {
'slice' => $slice,
'start' => $seq_region_start,
'end' => $seq_region_end,
'strand' => $seq_region_strand,
'hseqname' => $hit_name,
'hstart' => $hit_start,
'hend' => $hit_end,
'hstrand' => $hit_strand,
'score' => $score,
'p_value' => $evalue,
'percent_id' => $perc_ident,
'cigar_string' => $cigar_line,
'analysis' => $analysis,
'adaptor' => $self,
'dbID' => $dna_align_feature_id,
'external_db_id' => $external_db_id,
'hcoverage' => $hcoverage,
'extra_data' => $extra_data ? $self->get_dumped_data($extra_data) : '',
'dbname' => $external_db_name,
'db_display_name' => $external_display_db_name,
'pair_dna_align_feature_id' => $pair_dna_align_feature_id
} ) );
}
return \@features;
}
=head2 list_dbIDs
Arg [1] : none
Example : @feature_ids = @{$dna_align_feature_adaptor->list_dbIDs()};
Description: Gets an array of internal ids for all dna align features in
the current db
Arg[1] : <optional> int. not 0 for the ids to be sorted by the seq_region.
Returntype : list of ints
Exceptions : none
Caller : ?
Status : Stable
=cut
sub list_dbIDs {
my ($self, $ordered) = @_;
return $self->_list_dbIDs("dna_align_feature",undef, $ordered);
}
1;
]]>