Class: SwissprotDatabase

Inherits:
Object
  • Object
show all
Defined in:
lib/protk/swissprot_database.rb

Overview

Provides fast indexed access to a swissprot database in a flat .dat file

Instance Method Summary collapse

Constructor Details

#initialize(env = nil, database = "swissprot") ⇒ SwissprotDatabase

Returns a new instance of SwissprotDatabase.



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# File 'lib/protk/swissprot_database.rb', line 10

def initialize(env=nil,database="swissprot")
  if ( env!=nil)
    @genv=env
  else
    @genv=Constants.new
  end


  dbpath=Pathname.new(database)

  if ( dbpath.exist? )
#      require 'debugger';debugger
    dbclass=Bio::SPTR
    parser = Bio::FlatFileIndex::Indexer::Parser.new(dbclass, nil, nil)
    Bio::FlatFileIndex::Indexer::makeindexFlat(dbpath.realpath.dirname.to_s, parser, {}, dbpath.realpath.to_s)
    @db_object=Bio::FlatFileIndex.new("#{dbpath.realpath.dirname.to_s}")
  elsif ( database=="swissprot")
    @db_object=Bio::FlatFileIndex.new("#{@genv.protein_database_root}/#{@genv.uniprot_sprot_annotation_database}")
  else
    @db_object=Bio::FlatFileIndex.new("#{@genv.protein_database_root}/#{@genv.uniprot_trembl_annotation_database}")
  end
  
  @db_object.always_check_consistency=false
end

Instance Method Details

#get_entry_for_name(name) ⇒ Object 



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# File 'lib/protk/swissprot_database.rb', line 36

def get_entry_for_name(name)
  result=@db_object.get_by_id(name)
  if result==""
    if ( @genv!=nil)
      @genv.log("Failed to find UniProt entry for protein named #{name} in database",:warn)
    end
    return nil
  else
    Bio::SPTR.new(result)
  end
end