1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
|
#
# = bio/db/fasta/fasta_to_biosequence.rb - Bio::FastaFormat to Bio::Sequence adapter module
#
# Copyright:: Copyright (C) 2008
# Naohisa Goto <ng@bioruby.org>,
# 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
|
