Class: GFFDB

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

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(gff_file_path) ⇒ GFFDB

Returns a new instance of GFFDB.


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# File 'lib/protk/gffdb.rb', line 9

def initialize(gff_file_path)
  @database = gff_file_path
  @id_to_records_map={}
  @id_to_cds_map={}
end

Instance Attribute Details

#id_to_records_mapObject

Returns the value of attribute id_to_records_map


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# File 'lib/protk/gffdb.rb', line 7

def id_to_records_map
  @id_to_records_map
end

Class Method Details

.create(gff_file_path) ⇒ Object


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# File 'lib/protk/gffdb.rb', line 15

def self.create(gff_file_path)
  db = GFFDB.new(gff_file_path)
  db.make_index(gff_file_path)
  db
end

Instance Method Details

#get_by_id(entry_id) ⇒ Object


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# File 'lib/protk/gffdb.rb', line 21

def get_by_id(entry_id)
  @id_to_records_map[entry_id]
end

#get_cds_by_parent_id(entry_id) ⇒ Object


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# File 'lib/protk/gffdb.rb', line 25

def get_cds_by_parent_id(entry_id)
  @id_to_cds_map[entry_id]
end

#make_index(input_gff) ⇒ Object


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# File 'lib/protk/gffdb.rb', line 30

def make_index(input_gff)
  env=Constants.instance

  io = File.open(input_gff, "r")
  env.log "Parsing Input GFF",:info
  gffdb = Bio::GFF::GFF3.new(io)  #parses the entire db

  num_records = gffdb.records.length
  env.log "Indexing #{num_records}", :info

  # Now create the mapping from ids to records
  gffdb.records.each do |record| 

    @id_to_records_map[record.id] = [] if @id_to_records_map[record.id].nil?
    @id_to_records_map[record.id] << record

    begin
      # puts record.feature_type.match(/CDS/)
      if record.feature_type.to_s =~ /CDS/i
        # puts record.feature_type
        parent_id=record.attributes_to_hash['Parent']
        # puts parent_id
        if parent_id
          @id_to_cds_map[parent_id] = [] if @id_to_cds_map[parent_id].nil?
          @id_to_cds_map[parent_id] << record
        end
      end

    rescue
      puts "Problem initializing cds map for #{record}"
    end
  end

end