class Ensembl::Variation::TranscriptVariation
The TranscriptVariation
class gives information about the position of a VariationFeature
, mapped on an annotated transcript.
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.
@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
The TranscriptVariation
class gives information about the position of a VariationFeature
, mapped on an annotated transcript.
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.
@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
Public Instance Methods
consequence_type()
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# File lib/bio-ensembl/variation/variation_feature.rb, line 354 def consequence_type # workaround as ActiveRecord do not parse SET field in MySQL "#{attributes_before_type_cast['consequence_type']}" end
consequence_types()
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# File lib/bio-ensembl/variation/variation_feature62.rb, line 428 def consequence_types # workaround as ActiveRecord do not parse SET field in MySQL "#{attributes_before_type_cast['consequence_types']}" end
transcript()
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# File lib/bio-ensembl/variation/variation_feature.rb, line 358 def transcript 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 end