Class: Bio::GenBank
- Includes:
- NCBIDB::Common
- Defined in:
- lib/bio/db/genbank/genbank.rb
Overview
Defined Under Namespace
Classes: Locus
Constant Summary
Constants included from NCBIDB::Common
NCBIDB::Common::DELIMITER, NCBIDB::Common::TAGSIZE
Instance Method Summary collapse
-
#basecount(base = nil) ⇒ Object
BASE COUNT (this field is obsoleted after GenBank release 138.0) – Returns the BASE COUNT as a Hash.
- #circular ⇒ Object
- #date ⇒ Object
- #division ⇒ Object
-
#each_cds ⇒ Object
FEATURES – Iterate only for the ‘CDS’ portion of the Bio::Features.
-
#each_gene ⇒ Object
FEATURES – Iterate only for the ‘gene’ portion of the Bio::Features.
- #entry_id ⇒ Object
- #length ⇒ Object (also: #nalen)
-
#locus ⇒ Object
Accessor methods for the contents of the LOCUS record.
- #natype ⇒ Object
-
#seq ⇒ Object
(also: #naseq)
ORIGIN – Returns DNA sequence in the ORIGIN record as a Bio::Sequence::NA object.
- #seq_len ⇒ Object
- #strand ⇒ Object
Methods included from NCBIDB::Common
#acc_version, #accession, #accessions, #comment, #common_name, #definition, #features, #gi, #initialize, #keywords, #nid, #organism, #origin, #references, #segment, #source, #taxonomy, #version, #versions
Methods inherited from NCBIDB
Methods inherited from DB
#exists?, #fetch, #get, open, #tags
Instance Method Details
#basecount(base = nil) ⇒ Object
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).
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# File 'lib/bio/db/genbank/genbank.rb', line 96 def basecount(base = nil) unless @data['BASE COUNT'] hash = Hash.new(0) get('BASE COUNT').scan(/(\d+) (\w)/).each do |c, b| hash[b] = c.to_i end @data['BASE COUNT'] = hash end if base base.downcase! @data['BASE COUNT'][base] else @data['BASE COUNT'] end end |
#circular ⇒ Object
65 |
# File 'lib/bio/db/genbank/genbank.rb', line 65 def circular; locus.circular; end |
#date ⇒ Object
67 |
# File 'lib/bio/db/genbank/genbank.rb', line 67 def date; locus.date; end |
#division ⇒ Object
66 |
# File 'lib/bio/db/genbank/genbank.rb', line 66 def division; locus.division; end |
#each_cds ⇒ Object
FEATURES – Iterate only for the ‘CDS’ portion of the Bio::Features.
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# File 'lib/bio/db/genbank/genbank.rb', line 74 def each_cds features.each do |feature| if feature.feature == 'CDS' yield(feature) end end end |
#each_gene ⇒ Object
FEATURES – Iterate only for the ‘gene’ portion of the Bio::Features.
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# File 'lib/bio/db/genbank/genbank.rb', line 83 def each_gene features.each do |feature| if feature.feature == 'gene' yield(feature) end end end |
#entry_id ⇒ Object
63 |
# File 'lib/bio/db/genbank/genbank.rb', line 63 def entry_id; locus.entry_id; end |
#length ⇒ Object Also known as: nalen
64 |
# File 'lib/bio/db/genbank/genbank.rb', line 64 def length; locus.length; end |
#locus ⇒ Object
Accessor methods for the contents of the LOCUS record.
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# File 'lib/bio/db/genbank/genbank.rb', line 59 def locus @data['LOCUS'] ||= Locus.new(get('LOCUS')) end |
#natype ⇒ Object
70 |
# File 'lib/bio/db/genbank/genbank.rb', line 70 def natype; locus.natype; end |
#seq ⇒ Object Also known as: naseq
ORIGIN – Returns DNA sequence in the ORIGIN record as a Bio::Sequence::NA object.
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# File 'lib/bio/db/genbank/genbank.rb', line 115 def seq unless @data['SEQUENCE'] origin end Bio::Sequence::NA.new(@data['SEQUENCE']) end |
#seq_len ⇒ Object
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# File 'lib/bio/db/genbank/genbank.rb', line 124 def seq_len seq.length end |
#strand ⇒ Object
69 |
# File 'lib/bio/db/genbank/genbank.rb', line 69 def strand; locus.strand; end |