Patches applied to circular slice core DB

modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm

@@ -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 

modules/t/test-genome-DBs/circ/core/external_db.txt

@@ -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

modules/t/test-genome-DBs/circ/core/meta.txt

@@ -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