ruby-ensembl-api 0.9.6 → 1.0

data/lib/ensembl/variation/activerecord.rb

@@ -4,14 +4,13 @@
 # Copyright::   Copyright (C) 2008 Francesco Strozzi <francesco.strozzi@gmail.com>
 # License::     The Ruby License
 #
+# @author Francesco Strozzi
 
 nil
 module Ensembl
-  # = DESCRIPTION
   # The Ensembl::Variation module covers the variation databases from
   # ensembldb.ensembl.org.
   module Variation
-    # = DESCRIPTION
     # The Allele class describes a single allele of a variation. In addition to
     # the nucleotide(s) (or absence of) that representing the allele frequency
     # and population information may be present.
@@ -28,6 +27,7 @@ module Ensembl
       belongs_to :sample
       belongs_to :variation
       belongs_to :population
+      belongs_to :subsnp_handle
     end
 
     # = DESCRIPTION
@@ -62,6 +62,71 @@ module Ensembl
       belongs_to :allele_group
     end
     
+    # = DESCRIPTION
+    # Store information on attributes types
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class AttribType < DBConnection
+      set_primary_key "attrib_type_id"
+    end 
+    
+    
+    # = DESCRIPTION
+    # 
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class ConsequenceMapping < DBConnection
+      
+    end
+
+    # = DESCRIPTION
+    # 
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class FailedDescription < DBConnection
+      set_primary_key "failed_description_id"
+      has_many :failed_variations
+    end
+    
+    # = DESCRIPTION
+    # 
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class FailedVariation < DBConnection
+      set_primary_key "failed_variation_id"
+      belongs_to :failed_description
+      belongs_to :variation
+    end    
+    
+    # = DESCRIPTION
+    # 
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class FeatureType < DBConnection
+      set_primary_key "feature_type_id"
+    end
+        
+    class Meta < DBConnection
+      set_primary_key "meta_id"
+    end
+    
+    class MetaCoord < DBConnection
+     
+    end
+    
+    class Phenotype < DBConnection
+      set_primary_key "phenotype_id"
+      has_many :variation_annotations
+    end
+    
+    
+    
     # = DESCRIPTION
     # The Sample class gives information about the biological samples stored in the database. 
     #
@@ -79,7 +144,6 @@ module Ensembl
       has_many :tagged_variation_features
     end
 
-    # = DESCRIPTION
     # The IndividualPopulation class is used to connect Individual and Population classes. 
     # Should not be used directly.
     #
@@ -87,8 +151,8 @@ module Ensembl
     # See the general documentation of the Ensembl module for
     # more information on what this means and what methods are available.    
     class IndividualPopulation < DBConnection
-      belongs_to :individual
-      belongs_to :population
+      belongs_to :individual, :foreign_key => "individual_sample_id"
+      belongs_to :population, :foreign_key => "population_sample_id"
     end
     
     # = DESCRIPTION
@@ -99,17 +163,27 @@ module Ensembl
     # See the general documentation of the Ensembl module for
     # more information on what this means and what methods are available.
     class Individual < DBConnection
+      set_primary_key "sample_id"
       belongs_to :sample
-      # FIXME
+      has_one :individual_type
+      has_many :individual_populations, :foreign_key => "individual_sample_id"
+      has_many :populations, :through => :individual_populations
     end
     
     class IndividualGenotypeMultipleBp < DBConnection
       belongs_to :sample
       belongs_to :variation
+      belongs_to :subsnp_handle
     end
+   
+    class IndividualType < DBConnection
+      set_primary_key "invidual_type_id"
+      belongs_to :individual
+    end    
+    
     
     class CompressedGenotypeSingleBp < DBConnection
-      belongs_to :sample
+      belongs_to :population_genotype, :foreign_key => "sample_id"
     end  
     
     class ReadCoverage < DBConnection
@@ -118,10 +192,19 @@ module Ensembl
     
     class Population < DBConnection
       belongs_to :sample
+      set_primary_key "sample_id"
+      has_many :population_genotypes, :foreign_key => "sample_id"
+      has_many :individual_populations, :foreign_key => "population_sample_id"
+      has_many :individuals, :through => :individual_populations
+      has_many :sample_synonyms
+      has_one :population_structure
+      has_many :tagged_variation_features
+      has_many :alleles
+      has_many :allele_groups
     end
     
     class PopulationStructure < DBConnection
-      # FIXME
+      
     end
     
     # = DESCRIPTION
@@ -135,6 +218,8 @@ module Ensembl
       set_primary_key "population_genotype_id"
       belongs_to :variation
       belongs_to :population
+      belongs_to :subsnp_handle
+      has_many :compressed_genotype_single_bps, :foreign_key => "sample_id"
     end
     
     # = DESCRIPTION
@@ -166,6 +251,41 @@ module Ensembl
       has_many :variation_groups
       has_many :httags
       has_many :variation_synonyms
+      has_many :variation_annotations
+      has_many :structural_variations
+    end
+    
+    class StructuralVariation < DBConnection
+      set_primary_key "structural_variation_id"
+      belongs_to :source
+      belongs_to :seq_region
+      
+      class << self # Workaround for 'class' field, otherwise it creates a mess for AR
+        def instance_method_already_implemented?(method_name)
+          return true if method_name == 'class'
+          super
+        end
+      end
+      
+      def sv_class
+        self.attributes["class"]
+      end
+      
+    end
+    
+        
+    class SeqRegion < DBConnection
+      set_primary_key "seq_region_id"
+      has_many :variation_features
+      has_many :structural_variations
+    end
+    
+    class SubsnpHandle < DBConnection
+      set_primary_key "subsnp_id"
+      has_many :individual_genotype_multiple_bps, :foreign_key => "subsnp_id"
+      has_many :population_genotypes, :foreign_key => "subsnp_id"
+      has_many :alleles, :foreign_key => "subsnp_id"
+      has_many :variation_synonyms,:foreign_key => "subsnp_id"
     end
     
     # = DESCRIPTION
@@ -179,6 +299,7 @@ module Ensembl
       set_primary_key "variation_synonym_id"
       belongs_to :variation
       belongs_to :source
+      belongs_to :subsnp_handle
     end
         
     # = DESCRIPTION
@@ -221,6 +342,14 @@ module Ensembl
       belongs_to :variation_group
     end
     
+    class VariationAnnotation < DBConnection
+      set_primary_key "variation_annotation_id"
+      belongs_to :variation
+      belongs_to :phenotype
+      belongs_to :source
+    end
+    
+    
     # = DESCRIPTION
     # The FlankingSequence class gives information about the genomic coordinates 
     # of the flanking sequences, for a single VariationFeature. 
@@ -249,5 +378,6 @@ module Ensembl
       belongs_to :variation_group
       belongs_to :source
     end
+    
   end
 end

data/lib/ensembl/variation/variation.rb

@@ -4,13 +4,13 @@
 # Copyright::   Copyright (C) 2008 Francesco Strozzi <francesco.strozzi@gmail.com>
 # License::     The Ruby License
 #
+# @author Francesco Strozzi
+
 
-nil
 module Ensembl
   
   module Variation
     
-    # = DESCRIPTION
     # The Variation class represents single nucleotide polymorhisms (SNP) or variations 
     # and provides information like the names (IDs), the validation status and 
     # the allele information.
@@ -23,16 +23,16 @@ module Ensembl
     # See the general documentation of the Ensembl module for
     # more information on what this means and what methods are available.
     #
-    #= USAGE
-    # v = Variation.find_by_name('rs10111')
-    # v.alleles.each do |a|
-    #  puts a.allele, a.frequency
-    # end
+    # @example
+    #   v = Variation.find_by_name('rs10111')
+    #   v.alleles.each do |a|
+    #     puts a.allele, a.frequency
+    #   end
     #
-    # variations = Variation.fetch_all_by_source('dbSNP') (many records)
-    # variations.each do |v|
-    #   puts v.name
-    # end
+    #   variations = Variation.fetch_all_by_source('dbSNP') # many records
+    #   variations.each do |v|
+    #     puts v.name
+    #   end
     # 
     class Variation < DBConnection
       set_primary_key "variation_id"
@@ -47,6 +47,8 @@ module Ensembl
       has_many :variation_group_variations
       has_many :variation_groups, :through => :variation_group_variations
       has_many :individual_genotype_multiple_bps
+      has_many :failed_variations
+      has_many :failed_descriptions, :through => :failed_variations
       
       def self.fetch_all_by_source(source)
         variations = Source.find_by_name(source).variations
@@ -54,7 +56,6 @@ module Ensembl
     end
     
     
-    # = DESCRIPTION
     # The VariationFeature class gives information about the genomic position of 
     # each Variation, including also validation status and consequence type. 
     #
@@ -62,30 +63,56 @@ module Ensembl
     # See the general documentation of the Ensembl module for
     # more information on what this means and what methods are available.
     #
-    #= USAGE
-    # * SLOWER QUERY*
-    # vf = VariationFeature.find_by_variation_name('rs10111')
-    # * FASTER QUERY*
-    # vf = Variation.find_by_name('rs10111').variation_feature
-    #
-    # puts vf.seq_region_start, vf.seq_region_end, vf.allele_string
-    # puts vf.variation.ancestral_allele
-    # genomic_region = vf.fetch_region (returns an Ensembl::Core::Slice)
-    # genomic_region.genes
-    # up_region,down_region = vf.flanking_seq (returns two Ensembl::Core::Slice)
+    # @example
+    #   # SLOWER QUERY
+    #   vf = VariationFeature.find_by_variation_name('rs10111')
+    #   # FASTER QUERY
+    #   vf = Variation.find_by_name('rs10111').variation_feature
+    #   
+    #   puts vf.seq_region_start, vf.seq_region_end, vf.allele_string
+    #   puts vf.variation.ancestral_allele
+    #   genomic_region = vf.fetch_region (returns an Ensembl::Core::Slice)
+    #   genomic_region.genes
+    #   up_region,down_region = vf.flanking_seq (returns two Ensembl::Core::Slice)
     #
     class VariationFeature < DBConnection
       set_primary_key "variation_feature_id"
       belongs_to :variation
       has_many :tagged_variation_features
       has_many :samples, :through => :tagged_variation_features
-      has_many :transcript_variations
+      belongs_to :seq_region
+      validates_inclusion_of :consequence_type, :in => ['ESSENTIAL_SPLICE_SITE',
+                                                        'STOP_GAINED',
+                                                        'STOP_LOST',
+                                                        'COMPLEX_INDEL',
+                                                        'FRAMESHIFT_CODING',
+                                                        'NON_SYNONYMOUS_CODING',
+                                                        'SPLICE_SITE',
+                                                        'PARTIAL_CODON',
+                                                        'SYNONYMOUS_CODING',
+                                                        'REGULATORY_REGION',
+                                                        'WITHIN_MATURE_miRNA',
+                                                        '5PRIME_UTR',
+                                                        '3PRIME_UTR',
+                                                        'INTRONIC',
+                                                        'NMD_TRANSCRIPT',
+                                                        'UPSTREAM',
+                                                        'DOWNSTREAM',
+                                                        'WITHIN_NON_CODING_GENE',
+                                                        'HGMD_MUTATION'
+                                                        ], :message => "Consequence type not allowed!"      
       
+      def consequence_type # workaround as ActiveRecord do not parse SET field in MySQL
+        "#{attributes_before_type_cast['consequence_type']}" 
+      end 
       
-      #=DESCRIPTION
       # Based on Perl API 'get_all_Genes' method for Variation class. Get a genomic region
       # starting from the Variation coordinates, expanding the region upstream and
-      # downstream. Default values are -5000 and +5000.
+      # downstream.
+      #
+      # @param [Integer] up Length of upstream flanking region
+      # @param [Integer] down Length of downstream flanking region
+      # @return [Slice] Slice object containing the variation
       def fetch_region(up = 5000, down = 5000)
         sr = core_connection(self.seq_region_id)
         slice = Ensembl::Core::Slice.fetch_by_region(Ensembl::Core::CoordSystem.find(sr.coord_system_id).name,sr.name,self.seq_region_start-up,self.seq_region_end+down)
@@ -100,15 +127,24 @@ module Ensembl
         return slice_up,slice_down
       end
       
+      def transcript_variations
+        tvs = TranscriptVariation.find_all_by_variation_feature_id(self.variation_feature_id)
+        if tvs[0].nil? then # the variation is not stored in the database, so run the calculations
+          sr = core_connection(self.seq_region_id)
+          return custom_transcript_variation(self,sr)
+        else
+          return tvs # the variation is already present in the database
+        end  
+      end
+      
       private 
       
       def core_connection(seq_region_id) 
         if !Ensembl::Core::DBConnection.connected? then  
-          host,user,password,db_name,port = Ensembl::Variation::DBConnection.get_info
-          if db_name =~/(\w+_\w+)_\w+_(\d+)_\S+/ then
-            species,release = $1,$2
+          host,user,password,db_name,port,species,release = Ensembl::Variation::DBConnection.get_info
+          begin
             Ensembl::Core::DBConnection.connect(species,release.to_i,:username => user, :password => password,:host => host, :port => port)
-          else
+          rescue
             raise NameError, "Can't derive Core database name from #{db_name}. Are you using non conventional names?"
           end
         end
@@ -123,9 +159,186 @@ module Ensembl
         return seq_region
       end
       
+      # Calculate a consequence type for a user-defined variation
+      def custom_transcript_variation(vf,sr)
+                
+        @variation_name = vf.variation_name
+        @seq_region = sr
+
+        downstream = 5000
+        upstream = 5000
+        tvs = [] # store all the calculated TranscriptVariations
+         # retrieve the slice of the genomic region where the variation is located
+         region = Ensembl::Core::Slice.fetch_by_region(Ensembl::Core::CoordSystem.find(sr.coord_system_id).name,sr.name,vf.seq_region_start-upstream,vf.seq_region_end+downstream-1)
+         # iterate through all the transcripts present in the region
+        genes = region.genes(inclusive = true)
+         if genes[0] != nil
+          genes.each do |g|
+            g.transcripts.each do |t|
+              tv = TranscriptVariation.new() # create a new TranscriptVariation object for every transcript present
+              # do the calculations
+              
+              # check if the variation is intergenic for this transcript (no effects)
+              tv.consequence_type = check_intergenic(vf,t)
+              
+              # check if the variation is upstram or downstram the transcript
+              tv.consequence_type = check_upstream_downstream(vf,t) if tv.consequence_type == ""
+              
+              # if no consequence type is found, then the variation is inside the transcript         
+              # check for non coding gene
+              tv.consequence_type = check_non_coding(vf,t) if tv.consequence_type == "" and t.biotype != 'protein_coding'
+
+              # if no consequence type is found, then check intron / exon boundaries
+              tv.consequence_type = check_splice_site(vf,t) if tv.consequence_type == ""
+
+              # if no consequence type is found, check if the variation is inside UTRs
+              tv.consequence_type = check_utr(vf,t) if tv.consequence_type == ""    
+                        
+              # if no consequence type is found, then variation is inside an exon. 
+              # Check the codon change
+              (tv.consequence_type,tv.peptide_allele_string) = check_aa_change(vf,t) if tv.consequence_type == ""
+                
+              
+              begin # this changed from release 58
+                 tv.transcript_stable_id = t.stable_id
+              rescue NoMethodError
+                 tv.transcript_id = t.id
+              end
+              
+              tv.consequence_type = "INTERGENIC" if tv.consequence_type == ""
+              tvs << tv 
+            end   
+          end
+         end
+         # if there are no transcripts/genes within 5000 bases upstream and downstream set the variation as INTERGENIC (no effects)
+         if tvs.size == 0 then
+          tv = TranscriptVariation.new()
+          tv.consequence_type = "INTERGENIC"
+          tvs << tv
+         end
+
+         return tvs
+       end
+      
+      ## CONSEQUENCE CALCULATION FUNCTIONS ##
+      
+      def check_intergenic(vf,t)
+        if vf.seq_region_end < t.seq_region_start and ((t.seq_region_start - vf.seq_region_end) +1) > 5000 then
+           return "INTERGENIC"
+        elsif vf.seq_region_start > t.seq_region_end and ((vf.seq_region_start - t.seq_region_end) +1) > 5000 then
+           return "INTERGENIC"      
+        end
+        return nil        
+      end
+      
+      def check_upstream_downstream(vf,t)
+        if vf.seq_region_end < t.seq_region_start and ((t.seq_region_start - vf.seq_region_end) +1) <= 5000 then
+           return (t.strand == 1) ? "UPSTREAM" : "DOWNSTREAM"
+        elsif vf.seq_region_start > t.seq_region_end and ((vf.seq_region_start - t.seq_region_end)+1) <= 5000 then
+           return (t.strand == 1) ? "DOWNSTREAM" : "UPSTREAM"
+        
+        # check if it's an InDel and if overlaps the transcript start / end   
+        elsif t.seq_region_start > vf.seq_region_start and t.seq_region_start < vf.seq_region_end then
+            return "COMPLEX_INDEL"
+        elsif t.seq_region_end > vf.seq_region_start and t.seq_region_end < vf.seq_region_end then
+            return "COMPLEX_INDEL"                
+        end
+        return nil
+      end
+      
+      def check_non_coding(vf,t)
+          if t.biotype == "miRNA" then 
+             return (vf.seq_region_start == vf.seq_region_end) ? "WITHIN_MATURE_miRNA" : "COMPLEX_INDEL"
+          elsif t.biotype == "nonsense_mediated_decay"
+             return (vf.seq_region_start == vf.seq_region_end) ? "NMD_TRANSCRIPT" : "COMPLEX_INDEL"
+          else
+             return (vf.seq_region_start == vf.seq_region_end) ? "WITHIN_NON_CODING_GENE" : "COMPLEX_INDEL"
+          end
+          return nil
+      end
+      
+      def check_utr(vf,t)
+          if vf.seq_region_start > t.seq_region_start and vf.seq_region_end < t.coding_region_genomic_start then
+             return (t.strand == 1) ? "5PRIME_UTR" : "3PRIME_UTR"
+          elsif vf.seq_region_start > t.coding_region_genomic_end and vf.seq_region_end < t.seq_region_end then
+             return (t.strand == 1) ? "3PRIME_UTR" : "5PRIME_UTR"   
+          end
+          return nil   
+      end
+      
+      def check_splice_site(vf,t)
+          exon_up = t.exon_for_genomic_position(vf.seq_region_start)
+          exon_down = t.exon_for_genomic_position(vf.seq_region_end)
+          if exon_up.nil? and exon_down.nil? # we are inside an intron
+             # checking boundaries
+             near_exon_up_2bp = t.exon_for_genomic_position(vf.seq_region_start-2)
+             near_exon_down_2bp = t.exon_for_genomic_position(vf.seq_region_end+2)
+             near_exon_up_8bp = t.exon_for_genomic_position(vf.seq_region_start-8)
+             near_exon_down_8bp = t.exon_for_genomic_position(vf.seq_region_end+8)
+             if near_exon_up_2bp or near_exon_down_2bp then
+                return "ESSENTIAL_SPLICE_SITE"
+             elsif near_exon_up_8bp or near_exon_down_8bp then
+                return "SPLICE_SITE"
+             else
+                return "INTRONIC"   
+             end
+          elsif exon_up and exon_down # the variation is inside an exon
+                # check if it is a splice site
+                if (vf.seq_region_start-exon_up.seq_region_start) <= 3 or (exon_down.seq_region_end-vf.seq_region_end) <= 3 then
+                    return "SPLICE_SITE"                   
+                end
+          else # a complex indel spanning intron/exon boundary
+               return "COMPLEX_INDEL"
+          end
+          return nil      
+      end
+      
+      def check_aa_change(vf,t)
+          alleles = vf.allele_string.split('/') # get the different alleles for this variation          
+          # if the variation is an InDel then it produces a frameshift
+          if vf.seq_region_start != vf.seq_region_end or alleles.include?("-") then
+            return "FRAMESHIFT_CODING",nil
+          end
+
+          # Find the position inside the CDS
+          
+          mutation_position = t.genomic2cds(vf.seq_region_start)
+          
+          mutation_base = Bio::Sequence::NA.new(alleles[1])
+          if t.seq_region_strand == -1
+             mutation_base.reverse_complement!
+          end
+          # The rank of the codon 
+          target_codon = (mutation_position)/3 + 1
+          cds_sequence = nil
+          cds_sequence = t.cds_seq
+          mut_sequence = cds_sequence.dup
+          # Replace base with the variant allele
+          mut_sequence[mutation_position] = mutation_base.seq
+          refcodon =  cds_sequence[(target_codon*3 -3)..(target_codon*3-1)]
+          mutcodon =  mut_sequence[(target_codon*3 -3)..(target_codon*3-1)]
+          codontable = Bio::CodonTable[1]
+          refaa = codontable[refcodon]
+          mutaa = codontable[mutcodon.downcase]
+          if mutaa == nil
+            raise RuntimeError "Codon #{mutcodon.downcase} wasn't recognized."
+          end
+          pep_string = refaa+"/"+mutaa
+          if mutaa == "*" and refaa != "*"
+            return "STOP_GAINED",pep_string
+          elsif mutaa != "*" and refaa == "*"
+            return "STOP_LOST",pep_string
+          elsif mutaa != refaa
+            return "NON_SYNONYMOUS_CODING",pep_string 
+          elsif mutaa == refaa
+            return "SYNONYMOUS_CODING",pep_string 
+          end
+           
+       end
+      
+      
     end # VariationFeature
     
-    #= DESCRIPTION
     # The TranscriptVariation class gives information about the position of 
     # a VariationFeature, mapped on an annotated transcript.
     #
@@ -133,31 +346,56 @@ module Ensembl
     # See the general documentation of the Ensembl module for
     # more information on what this means and what methods are available.
     #
-    #= USAGE 
-    # vf = Variation.find_by_name('rs10111').variation_feature
-    # vf.transcript_variations.each do |tv|
-    #   puts tv.peptide_allele_string, tv.transcript.stable_id    
-    # end
+    # @example 
+    #   vf = Variation.find_by_name('rs10111').variation_feature
+    #   vf.transcript_variations.each do |tv|
+    #     puts tv.peptide_allele_string, tv.transcript.stable_id    
+    #   end
     #
     class TranscriptVariation < DBConnection
       set_primary_key "transcript_variation_id"
       belongs_to :variation_feature
+      validates_inclusion_of :consequence_type, :in => ['ESSENTIAL_SPLICE_SITE',
+                                                        'STOP_GAINED',
+                                                        'STOP_LOST',
+                                                        'COMPLEX_INDEL',
+                                                        'FRAMESHIFT_CODING',
+                                                        'NON_SYNONYMOUS_CODING',
+                                                        'SPLICE_SITE',
+                                                        'PARTIAL_CODON',
+                                                        'SYNONYMOUS_CODING',
+                                                        'REGULATORY_REGION',
+                                                        'WITHIN_MATURE_miRNA',
+                                                        '5PRIME_UTR',
+                                                        '3PRIME_UTR',
+                                                        'INTRONIC',
+                                                        'NMD_TRANSCRIPT',
+                                                        'UPSTREAM',
+                                                        'DOWNSTREAM',
+                                                        'WITHIN_NON_CODING_GENE',
+                                                        'HGMD_MUTATION'
+                                                        ], :message => "Consequence type not allowed!"
+                                                        
+      def consequence_type # workaround as ActiveRecord do not parse SET field in MySQL
+        "#{attributes_before_type_cast['consequence_type']}" 
+      end                                                  
       
       def transcript
-        if !Ensembl::Core::DBConnection.connected? then
-          host,user,password,db_name,port = Ensembl::Variation::DBConnection.get_info
-          if db_name =~/(\w+_\w+)_\w+_(\d+)_\S+/ then
-            species,release = $1,$2
-            Ensembl::Core::DBConnection.connect(species,release.to_i,:username => user, :password => password,:host => host, :port => port)
-          else
-            raise NameError, "Can't get Core database name from #{db_name}. Pheraps you are using non conventional names"
-          end
+        host,user,password,db_name,port,species,release = Ensembl::Variation::DBConnection.get_info
+        if !Ensembl::Core::DBConnection.connected? then     
+            Ensembl::Core::DBConnection.connect(species,release.to_i,:username => user, :password => password,:host => host, :port => port)    
+        end
+        
+        begin # this changed from release 58
+          return Ensembl::Core::Transcript.find_by_stable_id(self.transcript_stable_id)
+        rescue NoMethodError  
+          return Ensembl::Core::Transcript.find(self.transcript_id)
         end
-        Ensembl::Core::Transcript.find(self.transcript_id)
+        
       end
       
     end
     
   end
   
-end
+end