Class: Bio::GenBank

Class

Bio::GenBank

In:

lib/bio/db/genbank/genbank.rb

Parent:

Description

Parses a GenBank formatted database entry

Example

  # entry is a string containing only one entry contents
  gb = Bio::GenBank.new(entry)

Methods

basecount circular classification date date_modified division each_cds each_gene entry_id length locus nalen naseq natype seq seq_len strand strandedness to_biosequence

Included Modules

Bio::NCBIDB::Common

Classes and Modules

Class Bio::GenBank::Locus

Public Instance methods

basecount(base = nil)

BASE COUNT (this field is obsoleted after GenBank release 138.0) — Returns the BASE COUNT as a Hash. When the base is specified, returns count of the base as a Fixnum. The base can be one of ‘a’, ‘t’, ‘g’, ‘c’, and ‘o’ (others).

     # File lib/bio/db/genbank/genbank.rb, line 99
 99:   def basecount(base = nil)
100:     unless @data['BASE COUNT']
101:       hash = Hash.new(0)
102:       get('BASE COUNT').scan(/(\d+) (\w)/).each do |c, b|
103:         hash[b] = c.to_i
104:       end
105:       @data['BASE COUNT'] = hash
106:     end
107: 
108:     if base
109:       base.downcase!
110:       @data['BASE COUNT'][base]
111:     else
112:       @data['BASE COUNT']
113:     end
114:   end

    # File lib/bio/db/genbank/genbank.rb, line 68
68:   def circular;  locus.circular;  end

classification()

Taxonomy classfication. Returns an array of strings.

     # File lib/bio/db/genbank/genbank.rb, line 142
142:   def classification
143:     self.taxonomy.to_s.sub(/\.\z/, '').split(/\s*\;\s*/)
144:   end

    # File lib/bio/db/genbank/genbank.rb, line 70
70:   def date;      locus.date;      end

date_modified()

modified date. Returns Date object, String or nil.

     # File lib/bio/db/genbank/genbank.rb, line 133
133:   def date_modified
134:     begin
135:       Date.parse(self.date)
136:     rescue ArgumentError, TypeError, NoMethodError, NameError
137:       self.date
138:     end
139:   end

    # File lib/bio/db/genbank/genbank.rb, line 69
69:   def division;  locus.division;  end

each_cds() {|feature| ...}

FEATURES — Iterate only for the ‘CDS’ portion of the Bio::Features.

    # File lib/bio/db/genbank/genbank.rb, line 77
77:   def each_cds
78:     features.each do |feature|
79:       if feature.feature == 'CDS'
80:         yield(feature)
81:       end
82:     end
83:   end

each_gene() {|feature| ...}

FEATURES — Iterate only for the ‘gene’ portion of the Bio::Features.

    # File lib/bio/db/genbank/genbank.rb, line 86
86:   def each_gene
87:     features.each do |feature|
88:       if feature.feature == 'gene'
89:         yield(feature)
90:       end
91:     end
92:   end

    # File lib/bio/db/genbank/genbank.rb, line 66
66:   def entry_id;  locus.entry_id;  end

    # File lib/bio/db/genbank/genbank.rb, line 67
67:   def length;    locus.length;    end

Accessor methods for the contents of the LOCUS record.

    # File lib/bio/db/genbank/genbank.rb, line 62
62:   def locus
63:     @data['LOCUS'] ||= Locus.new(get('LOCUS'))
64:   end

nalen()

Alias for length

naseq()

Alias for seq

    # File lib/bio/db/genbank/genbank.rb, line 73
73:   def natype;    locus.natype;    end

ORIGIN — Returns DNA sequence in the ORIGIN record as a Bio::Sequence::NA object.

     # File lib/bio/db/genbank/genbank.rb, line 118
118:   def seq
119:     unless @data['SEQUENCE']
120:       origin
121:     end
122:     Bio::Sequence::NA.new(@data['SEQUENCE'])
123:   end

(obsolete???) length of the sequence

     # File lib/bio/db/genbank/genbank.rb, line 128
128:   def seq_len
129:     seq.length
130:   end

    # File lib/bio/db/genbank/genbank.rb, line 72
72:   def strand;    locus.strand;    end

Strandedness. Returns one of ‘single’, ‘double’, ‘mixed’, or nil.

     # File lib/bio/db/genbank/genbank.rb, line 147
147:   def strandedness
148:     case self.strand.to_s.downcase
149:     when 'ss-'; 'single'
150:     when 'ds-'; 'double'
151:     when 'ms-'; 'mixed'
152:     else nil; end
153:   end

to_biosequence()

converts Bio::GenBank to Bio::Sequence

Arguments:

Returns:

Bio::Sequence object

     # File lib/bio/db/genbank/genbank.rb, line 159
159:   def to_biosequence
160:     Bio::Sequence.adapter(self, Bio::Sequence::Adapter::GenBank)
161:   end