Contents

#
# = bio/db/fasta/fasta_to_biosequence.rb - Bio::FastaFormat to Bio::Sequence adapter module
#
# Copyright::   Copyright (C) 2008
#               Naohisa Goto <[e-mail]>,
# License::     The Ruby License
#
# $Id:$
#

require 'bio/sequence'
require 'bio/sequence/adapter'

# Internal use only. Normal users should not use this module.
#
# Bio::FastaFormat to Bio::Sequence adapter module.
# It is internally used in Bio::FastaFormat#to_biosequence.
#
module Bio::Sequence::Adapter::FastaFormat

  extend Bio::Sequence::Adapter

  private

  def_biosequence_adapter :seq

  # primary accession
  def_biosequence_adapter :primary_accession do |orig|
    orig.identifiers.accessions.first or orig.identifiers.entry_id
  end

  # secondary accessions
  def_biosequence_adapter :secondary_accessions do |orig|
    orig.identifiers.accessions[1..-1]
  end

  # entry_id
  def_biosequence_adapter :entry_id do |orig|
    orig.identifiers.locus or orig.identifiers.accessions.first or
      orig.identifiers.entry_id
  end

  # NCBI GI is stored on other_seqids
  def_biosequence_adapter :other_seqids do |orig|
    other = []
    if orig.identifiers.gi then
      other.push Bio::Sequence::DBLink.new('GI', orig.identifiers.gi)
    end
    other.empty? ? nil : other
  end

  # definition
  def_biosequence_adapter :definition do |orig|
    if orig.identifiers.accessions.empty? and
        !(orig.identifiers.gi) then
      orig.definition
    else
      orig.identifiers.description
    end
  end

end #module Bio::Sequence::Adapter::FastaFormat

Version data entries

29 entries across 29 versions & 4 rubygems

Version	Path
bio-2.0.5	lib/bio/db/fasta/fasta_to_biosequence.rb
bio-2.0.4	lib/bio/db/fasta/fasta_to_biosequence.rb
bio-2.0.3	lib/bio/db/fasta/fasta_to_biosequence.rb
bio-2.0.2	lib/bio/db/fasta/fasta_to_biosequence.rb
bio-2.0.1	lib/bio/db/fasta/fasta_to_biosequence.rb
bio-2.0.0	lib/bio/db/fasta/fasta_to_biosequence.rb
bio-1.6.0.pre.20181210	lib/bio/db/fasta/fasta_to_biosequence.rb
bio-1.5.2	lib/bio/db/fasta/fasta_to_biosequence.rb
bio-1.5.1	lib/bio/db/fasta/fasta_to_biosequence.rb
bio-1.5.0	lib/bio/db/fasta/fasta_to_biosequence.rb
bioruby-bio-1.2.9.9001	lib/bio/db/fasta/fasta_to_biosequence.rb
bioruby-bio-1.2.9.9501	lib/bio/db/fasta/fasta_to_biosequence.rb
bioruby-bio-1.3.0.5000	lib/bio/db/fasta/fasta_to_biosequence.rb
bioruby-bio-1.3.0.9901	lib/bio/db/fasta/fasta_to_biosequence.rb
bioruby-bio-1.3.0	lib/bio/db/fasta/fasta_to_biosequence.rb
bioruby-bio-1.3.1.5000	lib/bio/db/fasta/fasta_to_biosequence.rb
ngoto-bio-1.2.9.9001	lib/bio/db/fasta/fasta_to_biosequence.rb
ngoto-bio-1.2.9.9501	lib/bio/db/fasta/fasta_to_biosequence.rb
ngoto-bio-1.3.0.5000	lib/bio/db/fasta/fasta_to_biosequence.rb
ngoto-bio-1.3.0	lib/bio/db/fasta/fasta_to_biosequence.rb