Class | Bio::GenBank |
In: |
lib/bio/db/genbank/genbank.rb
|
Parent: | NCBIDB |
Parses a GenBank formatted database entry
# entry is a string containing only one entry contents gb = Bio::GenBank.new(entry)
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
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
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
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
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
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
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