Module: Bio::NCBIDB::Common

    # File lib/bio/db/genbank/common.rb, line 30
30:   def initialize(entry)
31:     super(entry, TAGSIZE)
32:   end

acc_version()

Returns the first part of the VERSION record as "ACCESSION.VERSION" String.

[Source]

    # File lib/bio/db/genbank/common.rb, line 57
57:   def acc_version
58:     versions.first.to_s
59:   end

accession()

Returns the ACCESSION part of the acc_version.

[Source]

    # File lib/bio/db/genbank/common.rb, line 62
62:   def accession
63:     acc_version.split(/\./).first.to_s
64:   end

accessions()

ACCESSION — Returns contents of the ACCESSION record as an Array.

[Source]

    # File lib/bio/db/genbank/common.rb, line 46
46:   def accessions
47:     field_fetch('ACCESSION').strip.split(/\s+/)
48:   end

comment()

COMMENT — Returns contents of the COMMENT record as a String.

[Source]

     # File lib/bio/db/genbank/common.rb, line 197
197:   def comment
198:     str = get('COMMENT').to_s.sub(/\ACOMMENT     /, '')
199:     str.gsub!(/^ {12}/, '')
200:     str.chomp!
201:     str
202:   end

common_name()

[Source]

     # File lib/bio/db/genbank/common.rb, line 120
120:   def common_name
121:     source['common_name']
122:   end

definition()

DEFINITION — Returns contents of the DEFINITION record as a String.

[Source]

    # File lib/bio/db/genbank/common.rb, line 40
40:   def definition
41:     field_fetch('DEFINITION')
42:   end

features() {|f| ...}

FEATURES — Returns contents of the FEATURES record as an array of Bio::Feature objects.

[Source]

     # File lib/bio/db/genbank/common.rb, line 207
207:   def features
208:     unless @data['FEATURES']
209:       ary = []
210:       in_quote = false
211:       get('FEATURES').each_line do |line|
212:         next if line =~ /^FEATURES/
213: 
214:         # feature type  (source, CDS, ...)
215:         head = line[0,20].to_s.strip
216: 
217:         # feature value (position or /qualifier=)
218:         body = line[20,60].to_s.chomp
219: 
220:         # sub-array [ feature type, position, /q="data", ... ]
221:         if line =~ /^ {5}\S/
222:           ary.push([ head, body ])
223: 
224:         # feature qualifier start (/q="data..., /q="data...", /q=data, /q)
225:         elsif body =~ /^ \// and not in_quote           # gb:IRO125195
226:           ary.last.push(body)
227:           
228:           # flag for open quote (/q="data...)
229:           if body =~ /="/ and body !~ /"$/
230:             in_quote = true
231:           end
232: 
233:         # feature qualifier continued (...data..., ...data...")
234:         else
235:           ary.last.last << body
236: 
237:           # flag for closing quote (/q="data... lines  ...")
238:           if body =~ /"$/
239:             in_quote = false
240:           end
241:         end
242:       end
243: 
244:       ary.collect! do |subary|
245:         parse_qualifiers(subary)
246:       end
247: 
248:       @data['FEATURES'] = ary.extend(Bio::Features::BackwardCompatibility)
249:     end
250:     if block_given?
251:       @data['FEATURES'].each do |f|
252:         yield f
253:       end
254:     else
255:       @data['FEATURES']
256:     end
257:   end

gi()

Returns the second part of the VERSION record as a "GI:#######" String.

[Source]

    # File lib/bio/db/genbank/common.rb, line 72
72:   def gi
73:     versions.last
74:   end

keywords()

KEYWORDS — Returns contents of the KEYWORDS record as an Array of Strings.

[Source]

    # File lib/bio/db/genbank/common.rb, line 84
84:   def keywords
85:     @data['KEYWORDS'] ||= fetch('KEYWORDS').chomp('.').split(/; /)
86:   end

locus()

LOCUS — Locus class must be defined in child classes.

[Source]

    # File lib/bio/db/genbank/common.rb, line 35
35:   def locus
36:     # must be overrided in each subclass
37:   end

nid()

NID — Returns contents of the NID record as a String.

[Source]

    # File lib/bio/db/genbank/common.rb, line 78
78:   def nid
79:     field_fetch('NID')
80:   end

organism()

[Source]

     # File lib/bio/db/genbank/common.rb, line 125
125:   def organism
126:     source['organism']
127:   end

origin()

ORIGIN — Returns contents of the ORIGIN record as a String.

[Source]

     # File lib/bio/db/genbank/common.rb, line 261
261:   def origin
262:     unless @data['ORIGIN']
263:       ori, seqstr = get('ORIGIN').split("\n", 2)
264:       seqstr ||= ""
265:       @data['ORIGIN'] = truncate(tag_cut(ori))
266:       @data['SEQUENCE'] = seqstr.tr("0-9 \t\n\r\/", '')
267:     end
268:     @data['ORIGIN']
269:   end

references() {|r| ...}

REFERENCE — Returns contents of the REFERENCE records as an Array of Bio::Reference objects.

[Source]

     # File lib/bio/db/genbank/common.rb, line 136
136:   def references
137:     unless @data['REFERENCE']
138:       ary = []
139:       toptag2array(get('REFERENCE')).each do |ref|
140:         hash = Hash.new
141:         subtag2array(ref).each do |field|
142:           case tag_get(field)
143:           when /REFERENCE/
144:             if /(\d+)(\s*\((.+)\))?/m =~ tag_cut(field) then
145:               hash['embl_gb_record_number'] = $1.to_i
146:               if $3 and $3 != 'sites' then
147:                 seqpos = $3
148:                 seqpos.sub!(/\A\s*bases\s+/, '')
149:                 seqpos.gsub!(/(\d+)\s+to\s+(\d+)/, "\\1-\\2")
150:                 seqpos.gsub!(/\s*\;\s*/, ', ')
151:                 hash['sequence_position'] = seqpos
152:               end
153:             end
154:           when /AUTHORS/
155:             authors = truncate(tag_cut(field))
156:             authors = authors.split(/, /)
157:             authors[-1] = authors[-1].split(/\s+and\s+/) if authors[-1]
158:             authors = authors.flatten.map { |a| a.sub(/,/, ', ') }
159:             hash['authors']     = authors
160:           when /TITLE/
161:             hash['title']       = truncate(tag_cut(field)) + '.'
162:           when /JOURNAL/
163:             journal = truncate(tag_cut(field))
164:             if journal =~ /(.*) (\d+) \((\d+)\), (\d+-\d+) \((\d+)\)$/
165:         hash['journal']  = $1
166:         hash['volume']   = $2
167:         hash['issue']    = $3
168:         hash['pages']    = $4
169:         hash['year']     = $5
170:             else
171:         hash['journal'] = journal
172:             end
173:           when /MEDLINE/
174:             hash['medline']     = truncate(tag_cut(field))
175:           when /PUBMED/
176:             hash['pubmed']      = truncate(tag_cut(field))
177:           when /REMARK/
178:             hash['comments'] ||= []
179:             hash['comments'].push truncate(tag_cut(field))
180:           end
181:         end
182:         ary.push(Reference.new(hash))
183:       end
184:       @data['REFERENCE'] = ary.extend(Bio::References::BackwardCompatibility)
185:     end
186:     if block_given?
187:       @data['REFERENCE'].each do |r|
188:         yield r
189:       end
190:     else
191:       @data['REFERENCE']
192:     end
193:   end

segment()

SEGMENT — Returns contents of the SEGMENT record as a "m/n" form String.

[Source]

    # File lib/bio/db/genbank/common.rb, line 90
90:   def segment
91:     @data['SEGMENT'] ||= fetch('SEGMENT').scan(/\d+/).join("/")
92:   end

source()

SOURCE — Returns contents of the SOURCE record as a Hash.

[Source]

     # File lib/bio/db/genbank/common.rb, line 96
 96:   def source
 97:     unless @data['SOURCE']
 98:       name, org = get('SOURCE').split('ORGANISM')
 99:       org ||= ""
100:       if org[/\S+;/]
101:         organism = $`
102:         taxonomy = $& + $'
103:       elsif org[/\S+\./]                                # rs:NC_001741
104:         organism = $`
105:         taxonomy = $& + $'
106:       else
107:         organism = org
108:         taxonomy = ''
109:       end
110:       @data['SOURCE'] = {
111:         'common_name'   => truncate(tag_cut(name)),
112:         'organism'      => truncate(organism),
113:         'taxonomy'      => truncate(taxonomy),
114:       }
115:       @data['SOURCE'].default = ''
116:     end
117:     @data['SOURCE']
118:   end

taxonomy()

[Source]

     # File lib/bio/db/genbank/common.rb, line 129
129:   def taxonomy
130:     source['taxonomy']
131:   end

vernacular_name()

Alias for common_name

version()

Returns the VERSION part of the acc_version as a Fixnum

[Source]

    # File lib/bio/db/genbank/common.rb, line 67
67:   def version
68:     acc_version.split(/\./).last.to_i
69:   end

versions()

VERSION — Returns contents of the VERSION record as an Array of Strings.

[Source]

    # File lib/bio/db/genbank/common.rb, line 52
52:   def versions
53:     @data['VERSION'] ||= fetch('VERSION').split(/\s+/)
54:   end

Description

References

Methods

Constants

Public Class methods

Public Instance methods

DELIMITER	=	RS = "\n//\n"
TAGSIZE	=	12