From cc9bc6f9692b87519bf1862782a44d994d8b6114 Mon Sep 17 00:00:00 2001
From: Alessandro Vullo <avullo@ebi.ac.uk>
Date: Thu, 5 Dec 2013 16:09:37 +0000
Subject: [PATCH] fetch_all_by_biotype as in GeneAdaptor, which implies the
inclusion of method biotype_contraint Added method count_all_by_biotype as in
GeneAdaptor.
---
.../Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm | 129 +++++++-----------
1 file changed, 52 insertions(+), 77 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
index 06818b65ad..362d37bc61 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
@@ -706,100 +706,75 @@ sub fetch_all_by_exon_stable_id {
return \@trans;
}
-=head2 fetch_all_by_source
-
- Arg [1] : String $source
- listref of $sources
- The source of the transcript to retrieve. You can also have a reference
- to a list of sources in the event of needing several.
- Example : $transcript = $transcript_adaptor->fetch_all_by_source('ensembl');
- $transcript = $transcript_adaptor->fetch_all_by_source(['ensembl','another_source']);
- Description: Retrieves an array reference of transcript objects from the
- database via its source or sources.
- The transcript will be retrieved in its native coordinate system
- (i.e. in the coordinate system it is stored in the database).
- It may be converted to a different coordinate system through a
- call to transform() or transfer(). If the transcript is not found
+
+=head2 fetch_all_by_biotype
+
+ Arg [1] : String $biotype
+ listref of $biotypes
+ The biotype of the transcript to retrieve. You can have as an argument a reference
+ to a list of biotypes
+ Example : $gene = $transcript_adaptor->fetch_all_by_biotype('protein_coding');
+ $gene = $transcript_adaptor->fetch_all_by_biotypes(['protein_coding', 'sRNA', 'miRNA']);
+ Description: Retrieves an array reference of transcript objects from the database via its biotype or biotypes.
+ The transcript will be retrieved in its native coordinate system (i.e.
+ in the coordinate system it is stored in the database). It may
+ be converted to a different coordinate system through a call to
+ transform() or transfer(). If the gene or exon is not found
undef is returned instead.
- Returntype : listref of Bio::EnsEMBL::Transcript
- Exceptions : if we cant get the transcript in given coord system
+ Returntype : listref of Bio::EnsEMBL::Transcript
+ Exceptions : if we cant get the gene in given coord system
Caller : general
Status : Stable
=cut
-sub fetch_all_by_source {
- my ($self, $source) = @_;
-
- if (!defined $source){
- throw("Source or listref of sources expected");
- }
- my $constraint;
- if (ref($source) eq 'ARRAY'){
- $constraint = "t.source IN (";
- foreach my $s (@{$source}){
- $constraint .= "?,";
- $self->bind_param_generic_fetch($s,SQL_VARCHAR);
- }
- chop($constraint); #remove last , from expression
- $constraint .= ") and t.is_current = 1";
-
- }
- else{
- $constraint = "t.source = ? and t.is_current = 1";
- $self->bind_param_generic_fetch($source,SQL_VARCHAR);
- }
- my @transcripts = @{ $self->generic_fetch($constraint) };
- return \@transcripts ;
+sub fetch_all_by_biotype {
+ my ($self, $biotype) = @_;
+ my @transcripts = @{$self->generic_fetch($self->biotype_constraint($biotype))};
+ return \@transcripts;
}
-=head2 fetch_all_by_biotype
+=head2 biotype_constraint
- Arg [1] : String $biotype
+ Arg [1] : String $biotypes
listref of $biotypes
- The biotype of the gene to retrieve. You can also have a reference
- to a list of biotypes in the event of needing several.
- Example : $transcript = $transcript_adaptor->fetch_all_by_biotype('pseudogene');
- $transcript = $transcript_adaptor->fetch_all_by_biotype(['protein_coding','ambiguous_orf']);
- Description: Retrieves an array reference of transcript objects from the
- database via its biotype or biotypes.
- The transcript will be retrieved in its native coordinate system
- (i.e. in the coordinate system it is stored in the database).
- It may be converted to a different coordinate system through a
- call to transform() or transfer(). If the transcript is not found
- undef is returned instead.
- Returntype : listref of Bio::EnsEMBL::Transcript
- Exceptions : if we cant get the transcript in given coord system
+ The biotype of the transcript to retrieve. You can have as an argument a reference
+ to a list of biotypes
+ Description: Used internally to generate a SQL constraint to restrict a transcript query by biotype
+ Returntype : String
+ Exceptions : If biotype is not supplied
Caller : general
Status : Stable
=cut
-sub fetch_all_by_biotype {
- my ($self, $biotype) = @_;
-
- if (!defined $biotype){
- throw("Biotype or listref of biotypes expected");
- }
- my $constraint;
- if (ref($biotype) eq 'ARRAY'){
- $constraint = "t.biotype IN (";
- foreach my $b (@{$biotype}){
- $constraint .= "?,";
- $self->bind_param_generic_fetch($b,SQL_VARCHAR);
- }
- chop($constraint); #remove last , from expression
- $constraint .= ") and t.is_current = 1";
-
- }
- else{
- $constraint = "t.biotype = ? and t.is_current = 1";
- $self->bind_param_generic_fetch($biotype,SQL_VARCHAR);
- }
- my @transcripts = @{ $self->generic_fetch($constraint) };
- return \@transcripts ;
+sub biotype_constraint {
+ my ($self, $biotypes, $inline_variables) = @_;
+ my $constraint = "t.is_current = 1";
+ my $in_statement = $self->generate_in_constraint($biotypes, 't.biotype', SQL_VARCHAR, $inline_variables);
+ $constraint .= " and $in_statement";
+ return $constraint;
}
+=head2 count_all_by_biotype
+
+ Arg [1] : String $biotype
+ listref of $biotypes
+ The biotype of the transcript to retrieve. You can have as an argument a reference
+ to a list of biotypes
+ Example : $cnt = $transcript_adaptor->count_all_by_biotype('protein_coding');
+ $cnt = $transcript_adaptor->count_all_by_biotypes(['protein_coding', 'sRNA', 'miRNA']);
+ Description : Retrieves count of transcript objects from the database via its biotype or biotypes.
+ Returntype : integer
+ Caller : general
+ Status : Stable
+
+=cut
+
+sub count_all_by_biotype {
+ my ($self, $biotype) = @_;
+ return $self->generic_count($self->biotype_constraint($biotype));
+}
=head2 store
--
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