Commit b817ba79 authored by Alessandro Vullo's avatar Alessandro Vullo
Browse files

Patches applied to circular slice core DB

parent f0207d65
......@@ -706,6 +706,53 @@ 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 = $transcript_adaptor->fetch_all_by_source(['ensembl','another_source']);
Description: Retrieves an array reference of transcript objects from the
database via its source or sources.
The transcript will be retrieved in its native coordinate system
(i.e. in the coordinate system it is stored in the database).
It may be converted to a different coordinate system through a
call to transform() or transfer(). If the transcript is not found
undef is returned instead.
Returntype : listref of Bio::EnsEMBL::Transcript
Exceptions : if we cant get the transcript in given coord system
Caller : general
Status : Stable
=cut
sub fetch_all_by_source {
my ($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 ;
}
=head2 fetch_all_by_biotype
Arg [1] : String $biotype
......
......@@ -494,7 +494,9 @@
50681 Ens_Ac_transcript \N XREF 40 Ensembl Anole Lizard Transcript MISC \N \N \N
50682 BGI_Gene 1 XREF 50 BGI_2005_indica_Gene MISC \N \N BGI gene identifier
50683 GeneIndex 1 XREF 50 GeneIndex MISC \N \N \N
50684 EO 1 XREF 0 Environment Ontology MISC \N \N Plant environmental conditions ontology terms. \nMore information in there: \nhttp://www.gramene.org/plant_ontology/ontology_browse.html#eo
50684 EO 1 XREF 0 Environment Ontology MISC \N \N Plant environmental conditions ontology terms. \
More information in there: \
http://www.gramene.org/plant_ontology/ontology_browse.html#eo
50685 Ens_Rn_transcript \N XREF 5 Ensembl Rat Transcript MISC \N \N \N
50686 Ens_Rn_translation \N XREF 5 Ensembl Rat Translation MISC \N \N \N
50687 Uppsala University \N KNOWN 5 Uppsala University MISC \N \N \N
......@@ -541,7 +543,8 @@
50731 Turkey Genome Consortium \N KNOWN 5 Turkey Genome Consortium MISC \N \N Turkey Genome Consortium
50732 Yutaka_Satou_Kyoto_University \N KNOWN 5 Yutaka Satou Kyoto University MISC \N \N Yutaka Satou Kyoto University
50733 Chicken_Genome_Consortium \N KNOWN 5 International Chicken Genome Consortium MISC \N \N \N
50734 TAIR_TRANSLATION 1 XREF 1 TAIR Translation identifiers MISC \N \N TAIR identifiers to link to Ensembl Translation identifiers. \nThe main requirement behind this entry, is to be able to link TAIR GO annotations to Ensembl Translations.
50734 TAIR_TRANSLATION 1 XREF 1 TAIR Translation identifiers MISC \N \N TAIR identifiers to link to Ensembl Translation identifiers. \
The main requirement behind this entry, is to be able to link TAIR GO annotations to Ensembl Translations.
50735 AGI_GENE 1 XREF 1 AGI Gene MISC \N \N annotation provided by Arizona Genome Institute
50736 AGI_TRANSCRIPT 1 XREF 1 AGI Transcript MISC \N \N annotation provided by Arizona Genome Institute
50737 CGNC \N KNOWNXREF 100 CGNC Symbol PRIMARY_DB_SYNONYM \N \N \N
......
......@@ -8,8 +8,12 @@
64 \N patch patch_73_74_d.sql|remove_qtl
65 \N patch patch_73_74_e.sql|remove_canonical_annotation
66 \N patch patch_73_74_f.sql|remove_pair_dna_align
67 \N patch patch_73_74_g.sql|add_transcript_idx_tise
68 \N patch patch_73_74_h.sql|alt_allele_unique_gene_idx
69 \N patch patch_74_75_a.sql|schema_version
70 \N patch patch_74_75_b.sql|transcript_source
1 \N schema_type core
2 \N schema_version 74
2 \N schema_version 75
8 1 assembly.accession GCA_000292705.1
10 1 assembly.date 2012-08
7 1 assembly.default GCA_000292705.1
......
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