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Commit cc9bc6f9 authored by Alessandro Vullo's avatar Alessandro Vullo
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fetch_all_by_biotype as in GeneAdaptor, which implies the inclusion of method biotype_contraint 

Added method count_all_by_biotype as in GeneAdaptor.
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modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+ 52
− 77
View file @ cc9bc6f9
......@@ -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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