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Commit 49bf7bab authored by Dan Staines's avatar Dan Staines
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updated adaptors to handle analysis types for operons and their transcripts

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modules/Bio/EnsEMBL/DBSQL/OperonAdaptor.pm
+ 55
− 44
View file @ 49bf7bab
......@@ -63,8 +63,7 @@ use vars '@ISA';
# Status : Stable
sub _tables {
return ( [ 'operon', 'o' ],
[ 'operon_stable_id', 'osi' ]);
return ( [ 'operon', 'o' ], [ 'operon_stable_id', 'osi' ] );
}
# _columns
......@@ -87,8 +86,8 @@ sub _columns {
return ( 'o.operon_id', 'o.seq_region_id', 'o.seq_region_start',
'o.seq_region_end', 'o.seq_region_strand', 'o.display_label',
'osi.stable_id', 'osi.version', $created_date,
$modified_date );
'o.analysis_id', 'osi.stable_id', 'osi.version',
$created_date, $modified_date );
}
sub _left_join {
......@@ -199,11 +198,12 @@ sub fetch_by_stable_id {
Status : At Risk
=cut
sub fetch_all {
my ($self) = @_;
my $constraint = '';
my @operons = @{ $self->generic_fetch($constraint) };
my @operons = @{ $self->generic_fetch($constraint) };
return \@operons;
}
......@@ -342,8 +342,9 @@ sub fetch_all_by_Slice {
if ( $slice != $ext_slice ) {
$new_tr = $tr->transfer($slice);
if ( !defined($new_tr) ) {
throw( "Unexpected. "
. "Transcript could not be transfered onto operon slice." );
throw( "Unexpected. "
. "Transcript could not be transfered onto operon slice."
);
}
} else {
$new_tr = $tr;
......@@ -438,9 +439,9 @@ sub fetch_by_operon_transcript_stable_id {
}
sub fetch_by_operon_transcript {
my ( $self, $trans ) = @_;
assert_ref($trans,'Bio::EnsEMBL::OperonTranscript');
$self->fetch_by_operon_transcript_id($trans->dbID());
my ( $self, $trans ) = @_;
assert_ref( $trans, 'Bio::EnsEMBL::OperonTranscript' );
$self->fetch_by_operon_transcript_id( $trans->dbID() );
}
=head2 store
......@@ -471,7 +472,14 @@ sub store {
if ( $operon->is_stored($db) ) {
return $operon->dbID();
}
my $analysis = $operon->analysis();
throw("Operons must have an analysis object.") if(!defined($analysis));
my $analysis_id;
if ( $analysis->is_stored($db) ) {
$analysis_id = $analysis->dbID();
} else {
$analysis_id = $db->get_AnalysisAdaptor->store( $analysis );
}
# ensure coords are correct before storing
#$operon->recalculate_coordinates();
......@@ -485,17 +493,19 @@ sub store {
seq_region_start = ?,
seq_region_end = ?,
seq_region_strand = ?,
display_label = ?
display_label = ?,
analysis_id = ?
);
# column status is used from schema version 34 onwards (before it was
# confidence)
my $sth = $self->prepare($store_operon_sql);
$sth->bind_param(1,$seq_region_id,SQL_INTEGER);
$sth->bind_param( 2, $operon->start(), SQL_INTEGER );
$sth->bind_param( 3, $operon->end(), SQL_INTEGER );
$sth->bind_param( 4, $operon->strand(), SQL_TINYINT );
$sth->bind_param( 5, $operon->display_label(), SQL_VARCHAR );
$sth->bind_param( 1, $seq_region_id, SQL_INTEGER );
$sth->bind_param( 2, $operon->start(), SQL_INTEGER );
$sth->bind_param( 3, $operon->end(), SQL_INTEGER );
$sth->bind_param( 4, $operon->strand(), SQL_TINYINT );
$sth->bind_param( 5, $operon->display_label(), SQL_VARCHAR );
$sth->bind_param( 6, $analysis_id, SQL_INTEGER );
$sth->execute();
$sth->finish();
......@@ -595,9 +605,9 @@ sub remove {
$dbe_adaptor->remove_from_object( $dbe, $operon, 'Operon' );
}
# # remove the attributes associated with this transcript
# my $attrib_adaptor = $self->db->get_AttributeAdaptor;
# $attrib_adaptor->remove_from_Operon($operon);
# # remove the attributes associated with this transcript
# my $attrib_adaptor = $self->db->get_AttributeAdaptor;
# $attrib_adaptor->remove_from_Operon($operon);
# remove all of the transcripts associated with this operon
my $transcriptAdaptor = $self->db->get_OperonTranscriptAdaptor();
......@@ -650,23 +660,24 @@ sub _objs_from_sth {
#
my $sa = $self->db()->get_SliceAdaptor();
#my $aa = $self->db->get_AnalysisAdaptor();
my $aa = $self->db->get_AnalysisAdaptor();
my @operons;
my %analysis_hash;
my %slice_hash;
my %sr_name_hash;
my %sr_cs_hash;
my ( $stable_id, $version, $created_date, $modified_date );
my ( $stable_id, $version, $created_date, $modified_date, $analysis_id );
my ( $operon_id, $seq_region_id, $seq_region_start, $seq_region_end,
$seq_region_strand, $display_label );
my ( $operon_id, $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand, $display_label );
$sth->bind_columns( \$operon_id, \$seq_region_id,
\$seq_region_start, \$seq_region_end,
\$seq_region_strand, \$display_label,
\$stable_id, \$version,
\$created_date, \$modified_date );
\$analysis_id, \$stable_id,
\$version, \$created_date,
\$modified_date );
my $asm_cs;
my $cmp_cs;
......@@ -701,9 +712,10 @@ sub _objs_from_sth {
my $count = 0;
OPERON: while ( $sth->fetch() ) {
$count++;
# #get the analysis object
# my $analysis = $analysis_hash{$analysis_id} ||=
# $aa->fetch_by_dbID($analysis_id);
#get the analysis object
my $analysis = $analysis_hash{$analysis_id} ||=
$aa->fetch_by_dbID($analysis_id);
$analysis_hash{$analysis_id} = $analysis;
#need to get the internal_seq_region, if present
$seq_region_id = $self->get_seq_region_id_internal($seq_region_id);
#get the slice object
......@@ -774,21 +786,20 @@ sub _objs_from_sth {
$slice = $dest_slice;
} ## end if ($dest_slice)
push(
@operons,
Bio::EnsEMBL::Operon->new(
-START => $seq_region_start,
-END => $seq_region_end,
-STRAND => $seq_region_strand,
-SLICE => $slice,
-DISPLAY_LABEL => $display_label,
-ADAPTOR => $self,
-DBID => $operon_id,
-STABLE_ID => $stable_id,
-VERSION => $version,
-CREATED_DATE => $created_date || undef,
-MODIFIED_DATE => $modified_date || undef
));
push( @operons,
Bio::EnsEMBL::Operon->new(
-START => $seq_region_start,
-END => $seq_region_end,
-STRAND => $seq_region_strand,
-SLICE => $slice,
-DISPLAY_LABEL => $display_label,
-ADAPTOR => $self,
-DBID => $operon_id,
-STABLE_ID => $stable_id,
-VERSION => $version,
-CREATED_DATE => $created_date || undef,
-MODIFIED_DATE => $modified_date || undef,
-ANALYSIS => $analysis ) );
} ## end while ( $sth->fetch() )
......
modules/Bio/EnsEMBL/DBSQL/OperonTranscriptAdaptor.pm
+ 52
− 36
View file @ 49bf7bab
......@@ -92,8 +92,9 @@ sub _columns {
return ( 'o.operon_transcript_id', 'o.seq_region_id',
'o.seq_region_start', 'o.seq_region_end',
'o.seq_region_strand', 'o.display_label',
'osi.stable_id', 'osi.version',
$created_date, $modified_date );
'o.analysis_id', 'osi.stable_id',
'osi.version', $created_date,
$modified_date );
}
sub _left_join {
......@@ -194,6 +195,7 @@ sub fetch_by_name {
return $operon;
}
=head2 fetch_all
Example : $operon_transcripts = $operon_adaptor->fetch_all();
......@@ -203,6 +205,7 @@ sub fetch_by_name {
Status : At Risk
=cut
sub fetch_all {
my ($self) = @_;
......@@ -529,7 +532,15 @@ sub store {
( $operon_transcript, $seq_region_id ) =
$self->_pre_store($operon_transcript);
my $analysis = $operon_transcript->analysis();
throw("OperonTranscripts must have an analysis object.")
if ( !defined($analysis) );
my $analysis_id;
if ( $analysis->is_stored($db) ) {
$analysis_id = $analysis->dbID();
} else {
$analysis_id = $db->get_AnalysisAdaptor->store($analysis);
}
my $store_operon_transcript_sql = qq(
INSERT INTO operon_transcript
SET seq_region_id = ?,
......@@ -537,7 +548,8 @@ sub store {
seq_region_end = ?,
seq_region_strand = ?,
display_label = ?,
operon_id = ?
operon_id = ?,
analysis_id =?
);
# column status is used from schema version 34 onwards (before it was
# confidence)
......@@ -549,6 +561,7 @@ sub store {
$sth->bind_param( 4, $operon_transcript->strand(), SQL_TINYINT );
$sth->bind_param( 5, $operon_transcript->display_label(), SQL_VARCHAR );
$sth->bind_param( 6, $operon_id, SQL_INTEGER );
$sth->bind_param( 7, $analysis_id, SQL_INTEGER );
$sth->execute();
$sth->finish();
......@@ -557,18 +570,18 @@ sub store {
# store stable ids if they are available
if ( defined( $operon_transcript->stable_id() ) ) {
my $statement = sprintf(
"INSERT INTO operon_transcript_stable_id SET "
. "operon_transcript_id = ?, "
. "stable_id = ?, "
. "version = ?, "
. "created_date = %s, "
. "modified_date = %s",
$self->db()->dbc()->from_seconds_to_date(
my $statement = sprintf( "INSERT INTO operon_transcript_stable_id SET "
. "operon_transcript_id = ?, "
. "stable_id = ?, "
. "version = ?, "
. "created_date = %s, "
. "modified_date = %s",
$self->db()->dbc()->from_seconds_to_date(
$operon_transcript->created_date()
),
$self->db()->dbc()
->from_seconds_to_date( $operon_transcript->modified_date() ) );
),
$self->db()->dbc()->from_seconds_to_date(
$operon_transcript->modified_date()
) );
$sth = $self->prepare($statement);
$sth->bind_param( 1, $operon_transcript_dbID, SQL_INTEGER );
......@@ -674,9 +687,9 @@ sub remove {
'OperonTranscript' );
}
# # remove the attributes associated with this transcript
# my $attrib_adaptor = $self->db->get_AttributeAdaptor;
# $attrib_adaptor->remove_from_OperonTranscript($operon_transcript);
# # remove the attributes associated with this transcript
# my $attrib_adaptor = $self->db->get_AttributeAdaptor;
# $attrib_adaptor->remove_from_OperonTranscript($operon_transcript);
# remove the stable identifier
my $sth = $self->prepare(
......@@ -722,7 +735,7 @@ sub _objs_from_sth {
#
my $sa = $self->db()->get_SliceAdaptor();
#my $aa = $self->db->get_AnalysisAdaptor();
my $aa = $self->db->get_AnalysisAdaptor();
my @operons;
my %analysis_hash;
......@@ -732,13 +745,15 @@ sub _objs_from_sth {
my ( $stable_id, $version, $created_date, $modified_date );
my ( $operon_transcript_id, $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand, $display_label );
$seq_region_end, $seq_region_strand, $display_label,
$analysis_id );
$sth->bind_columns( \$operon_transcript_id, \$seq_region_id,
\$seq_region_start, \$seq_region_end,
\$seq_region_strand, \$display_label,
\$stable_id, \$version,
\$created_date, \$modified_date );
\$analysis_id, \$stable_id,
\$version, \$created_date,
\$modified_date );
my $asm_cs;
my $cmp_cs;
......@@ -774,8 +789,9 @@ sub _objs_from_sth {
OPERON: while ( $sth->fetch() ) {
$count++;
# #get the analysis object
# my $analysis = $analysis_hash{$analysis_id} ||=
# $aa->fetch_by_dbID($analysis_id);
my $analysis = $analysis_hash{$analysis_id} ||=
$aa->fetch_by_dbID($analysis_id);
$analysis_hash{$analysis_id} = $analysis;
#need to get the internal_seq_region, if present
$seq_region_id = $self->get_seq_region_id_internal($seq_region_id);
#get the slice object
......@@ -848,18 +864,18 @@ sub _objs_from_sth {
push( @operons,
Bio::EnsEMBL::OperonTranscript->new(
-START => $seq_region_start,
-END => $seq_region_end,
-STRAND => $seq_region_strand,
-SLICE => $slice,
-DISPLAY_LABEL => $display_label,
-ADAPTOR => $self,
-DBID => $operon_transcript_id,
-STABLE_ID => $stable_id,
-VERSION => $version,
-CREATED_DATE => $created_date || undef,
-MODIFIED_DATE => $modified_date || undef
) );
-START => $seq_region_start,
-END => $seq_region_end,
-STRAND => $seq_region_strand,
-SLICE => $slice,
-DISPLAY_LABEL => $display_label,
-ADAPTOR => $self,
-DBID => $operon_transcript_id,
-STABLE_ID => $stable_id,
-VERSION => $version,
-CREATED_DATE => $created_date || undef,
-MODIFIED_DATE => $modified_date || undef,
-ANALYSIS => $analysis ) );
} ## end while ( $sth->fetch() )
......
modules/t/operon.t
+ 6
− 1
View file @ 49bf7bab
......@@ -4,7 +4,7 @@ use warnings;
BEGIN {
$| = 1;
use Test;
plan tests => 12;
plan tests => 15;
}
use Bio::EnsEMBL::DBEntry;
use Bio::EnsEMBL::Operon;
......@@ -31,6 +31,7 @@ my $end = 31225946;
my $strand = 1;
my $display_label = "accBC";
my $analysis = $dba->get_AnalysisAdaptor->fetch_by_logic_name("Genscan");
ok(defined $analysis);
my $operon = Bio::EnsEMBL::Operon->new(
-START => $start,
-END => $end,
......@@ -49,6 +50,7 @@ ok( $display_label, $operon->display_label(), "Operon name" );
ok( $start, $operon->seq_region_start(), "Operon start" );
ok( $end, $operon->seq_region_end(), "Operon end" );
ok( $strand, $operon->seq_region_strand(), "Operon strand" );
ok( $analysis, $operon->analysis(), "Analysis" );
my $operon_adaptor = Bio::EnsEMBL::DBSQL::OperonAdaptor->new($dba);
......@@ -64,4 +66,7 @@ ok( $operon2->seq_region_end(), $operon->seq_region_end(), "Operon end" );
ok( $operon2->seq_region_strand(),
$operon->seq_region_strand(),
"Operon strand" );
ok( $operon2->analysis(),
$operon->analysis(),
"Analysis" );
modules/t/operon_fetch.t
+ 4
− 1
View file @ 49bf7bab
......@@ -2,7 +2,7 @@ use strict;
use warnings;
BEGIN { $| = 1;
use Test;
plan tests => 12;
plan tests => 17;
}
use Bio::EnsEMBL::Test::MultiTestDB;
......@@ -25,11 +25,13 @@ my $operon_adaptor = Bio::EnsEMBL::DBSQL::OperonAdaptor->new($dba);
my $operon = $operon_adaptor->fetch_by_name("16152-16153-4840");
ok(defined $operon);
debug("O ".$operon->dbID());
ok(defined $operon->analysis());
# iterate over its transcripts
my $transcripts = $operon->get_all_OperonTranscripts();
ok(defined $transcripts);
ok(scalar(@$transcripts)>0);
for my $ot (@$transcripts) {
ok(defined $ot->analysis());
debug("OT ".$ot->dbID());
for my $gene (@{$ot->get_all_Genes()}) {
debug("G ".$gene->dbID());
......@@ -43,6 +45,7 @@ my $operons = $operon_adaptor->fetch_all_by_Slice($slice);
ok(defined $operons);
ok(scalar(@$operons)>0);
for my $o (@$operons) {
ok(defined $o->analysis());
debug("O ".$o->dbID());
for my $ot (@{$o->get_all_OperonTranscripts()}) {
debug("OT ".$ot->dbID());
......
modules/t/operon_transcript.t
+ 11
− 5
View file @ 49bf7bab
......@@ -4,7 +4,7 @@ use warnings;
BEGIN {
$| = 1;
use Test;
plan tests => 40;
plan tests => 46;
}
use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Test::TestUtils;
......@@ -34,11 +34,13 @@ my $start = 3403162;
my $end = 3405288;
my $strand = 1;
my $display_label = "accBC";
my $analysis = $dba->get_AnalysisAdaptor->fetch_by_logic_name("Genscan");
my $operon = Bio::EnsEMBL::Operon->new( -START => $start,
-END => $end,
-STRAND => $strand,
-SLICE => $slice,
-DISPLAY_LABEL => $display_label, -STABLE_ID=>"op1" );
-DISPLAY_LABEL => $display_label, -STABLE_ID=>"op1", -ANALYSIS=>$analysis );
ok( $analysis, $operon->analysis(), "Analysis" );
my $gene_name = "accB";
my $gene_start = 31225346;
......@@ -54,7 +56,6 @@ my $gene = Bio::EnsEMBL::Gene->new();
my $transcript = Bio::EnsEMBL::Transcript->new();
my $exon = Bio::EnsEMBL::Exon->new();
my $translation = Bio::EnsEMBL::Translation->new();
my $analysis = $dba->get_AnalysisAdaptor->fetch_by_logic_name("Genscan");
ok( defined $analysis );
for my $feature ( $gene, $transcript, $exon ) {
$feature->start($gene_start);
......@@ -117,18 +118,20 @@ my $operon_transcript =
Bio::EnsEMBL::OperonTranscript->new( -START => $start,
-END => $end,
-STRAND => $strand,
-SLICE => $slice, -STABLE_ID=>"opt1" );
-SLICE => $slice, -STABLE_ID=>"opt1", -ANALYSIS=>$analysis );
$operon_transcript->add_gene($gene);
$operon_transcript->add_gene($gene2);
$operon->add_OperonTranscript($operon_transcript);
ok( $analysis, $operon_transcript->analysis(), "Analysis" );
my $operon_transcript2 =
Bio::EnsEMBL::OperonTranscript->new( -START => $start,
-END => $gene_start2,
-STRAND => $strand,
-SLICE => $slice, -STABLE_ID=>"opt2" );
-SLICE => $slice, -STABLE_ID=>"opt2", -ANALYSIS=>$analysis );
$operon_transcript2->add_gene($gene);
$operon->add_OperonTranscript($operon_transcript2);
ok( $analysis, $operon_transcript->analysis(), "Analysis" );
# store the lot
# store operon
......@@ -144,6 +147,7 @@ ok( $operon2->seq_region_end(), $operon->seq_region_end(), "Operon end" );
ok( $operon2->seq_region_strand(),
$operon->seq_region_strand(),
"Operon strand" );
ok( $operon2->analysis(), $operon->analysis(), "Analysis" );
my @operon_transcripts = @{ $operon2->get_all_OperonTranscripts() };
# check operon transcript
ok( scalar @operon_transcripts, 2, "Expected number of transcripts" );
......@@ -160,6 +164,7 @@ ok( $operon_transcript_r->seq_region_end(),
ok( $operon_transcript_r->seq_region_strand(),
$operon_transcript->seq_region_strand(),
"Operon transcript strand" );
ok( $operon_transcript->analysis(), $operon_transcript_r->analysis(), "Analysis" );
# check genes
my @ogenes = @{ $operon_transcript_r->get_all_Genes() };
......@@ -188,6 +193,7 @@ ok( $operon_transcript_r2->seq_region_end(),
ok( $operon_transcript_r2->seq_region_strand(),
$operon_transcript2->seq_region_strand(),
"Operon transcript strand" );
ok( $operon_transcript2->analysis(), $operon_transcript_r2->analysis(), "Analysis" );
# check genes
@ogenes = @{ $operon_transcript_r2->get_all_Genes() };
......
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