Module: Bio::EMBLDB::Common
Constant Summary collapse
- DELIMITER =
"\n//\n"
- RS =
DELIMITER
- TAGSIZE =
5
Instance Method Summary collapse
-
#ac ⇒ Object
(also: #accessions)
returns a Array of accession numbers in the AC lines.
-
#accession ⇒ Object
returns the first accession number in the AC lines.
-
#de ⇒ Object
(also: #description, #definition)
returns a String int the DE line.
-
#dr ⇒ Object
returns contents in the DR line.
- #initialize(entry) ⇒ Object
-
#kw ⇒ Object
(also: #keywords)
returns keywords in the KW line.
-
#oc ⇒ Object
returns contents in the OC line.
-
#og ⇒ Object
returns contents in the OG line.
-
#os(num = nil) ⇒ Object
returns contents in the OS line.
-
#ref ⇒ Object
returns contents in the R lines.
-
#references ⇒ Object
returns Bio::Reference object from Bio::EMBLDB::Common#ref.
Instance Method Details
#ac ⇒ Object Also known as: accessions
returns a Array of accession numbers in the AC lines.
AC Line
"AC A12345; B23456;"
AC [AC1;]+
Accession numbers format:
1 2 3 4 5 6
[O,P,Q] [0-9] [A-Z, 0-9] [A-Z, 0-9] [A-Z, 0-9] [0-9]
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# File 'lib/bio/db/embl/common.rb', line 98 def ac unless @data['AC'] tmp = Array.new field_fetch('AC').split(/ /).each do |e| tmp.push(e.sub(/;/,'')) end @data['AC'] = tmp end @data['AC'] end |
#accession ⇒ Object
returns the first accession number in the AC lines
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# File 'lib/bio/db/embl/common.rb', line 112 def accession ac[0] end |
#de ⇒ Object Also known as: description, definition
returns a String int the DE line.
DE Line
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# File 'lib/bio/db/embl/common.rb', line 120 def de unless @data['DE'] @data['DE'] = fetch('DE') end @data['DE'] end |
#dr ⇒ Object
returns contents in the DR line.
-
Bio::EMBLDB::Common#dr -> [ <Database cross-reference Hash>* ]
where <Database cross-reference Hash> is:
-
Bio::EMBLDB::Common#dr {|k,v| }
DR Line; defabases cross-reference (>=0) a cross_ref pre one line
"DR database_identifier; primary_identifier; secondary_identifier."
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# File 'lib/bio/db/embl/common.rb', line 313 def dr unless @data['DR'] tmp = Hash.new self.get('DR').split(/\n/).each do |db| a = db.sub(/^DR /,'').sub(/.$/,'').strip.split(/;[ ]/) dbname = a.shift tmp[dbname] = Array.new unless tmp[dbname] tmp[dbname].push(a) end @data['DR'] = tmp end if block_given? @data['DR'].each do |k,v| yield(k, v) end else @data['DR'] end end |
#initialize(entry) ⇒ Object
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# File 'lib/bio/db/embl/common.rb', line 85 def initialize(entry) super(entry, TAGSIZE) end |
#kw ⇒ Object Also known as: keywords
returns keywords in the KW line.
-
Bio::EMBLDB::Common#kw -> [ <keyword>* ]
KW Line; keyword (>=1)
KW [Keyword;]+
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# File 'lib/bio/db/embl/common.rb', line 219 def kw unless @data['KW'] if get('KW').size > 0 tmp = fetch('KW').sub(/.$/,'') @data['KW'] = tmp.split(/;/).map {|e| e.strip } else @data['KW'] = [] end end @data['KW'] end |
#oc ⇒ Object
returns contents in the OC line.
-
Bio::EMBLDB::Common#oc -> [ <organism class String>* ]
OC Line; organism classification (>=1)
OC Eukaryota; Alveolata; Apicomplexa; Piroplasmida; Theileriidae;
OC Theileria.
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# File 'lib/bio/db/embl/common.rb', line 202 def oc unless @data['OC'] begin @data['OC'] = fetch('OC').sub(/.$/,'').split(/;/).map {|e| e.strip } rescue NameError nil end end @data['OC'] end |
#og ⇒ Object
returns contents in the OG line.
-
Bio::EMBLDB::Common#og -> [ <ogranella String>* ]
OG Line; organella (0 or 1/entry)
OG Plastid; Chloroplast.
OG Mitochondrion.
OG Plasmid sym pNGR234a.
OG Plastid; Cyanelle.
OG Plasmid pSymA (megaplasmid 1).
OG Plasmid pNRC100, Plasmid pNRC200, and Plasmid pHH1.
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# File 'lib/bio/db/embl/common.rb', line 179 def og unless @data['OG'] og = Array.new if get('OG').size > 0 ogstr = fetch('OG') ogstr.sub!(/\.$/,'') ogstr.sub!(/ and/,'') ogstr.sub!(/;/, ',') ogstr.split(',').each do |tmp| og.push(tmp.strip) end end @data['OG'] = og end @data['OG'] end |
#os(num = nil) ⇒ Object
returns contents in the OS line.
-
Bio::EMBLDB#os -> Array of <OS Hash>
where <OS Hash> is:
[{'name'=>'Human', 'os'=>'Homo sapiens'},
{'name'=>'Rat', 'os'=>'Rattus norveticus'}]
-
Bio::SPTR#os[‘name’] => “Human”
-
Bio::SPTR#os => ‘os’=>‘Homo sapiens’
-
Bio::STPR#os(0) => “Homo sapiens (Human)”
OS Line; organism species (>=1)
"OS Trifolium repens (white clover)"
OS Genus species (name).
OS Genus species (name0) (name1).
OS Genus species (name0) (name1).
OS Genus species (name0), G s0 (name0), and G s (name1).
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# File 'lib/bio/db/embl/common.rb', line 147 def os(num = nil) unless @data['OS'] os = Array.new fetch('OS').split(/, and|, /).each do |tmp| if tmp =~ /([A-Z][a-z]* *[\w\d \:\'\+\-]+[\w\d])/ org = $1 tmp =~ /(\(.+\))/ os.push({'name' => $1, 'os' => org}) else raise "Error: OS Line. #{$!}\n#{fetch('OS')}\n" end end @data['OS'] = os end if num # EX. "Trifolium repens (white clover)" "#{@data['OS'][num]['os']} {#data['OS'][num]['name']" end @data['OS'] end |
#ref ⇒ Object
returns contents in the R lines.
-
Bio::EMBLDB::Common#ref -> [ <refernece information Hash>* ]
where <reference information Hash> is:
{'RN' => '', 'RC' => '', 'RP' => '', 'RX' => '',
'RA' => '', 'RT' => '', 'RL' => '', 'RG' => ''}
R Lines
-
RN RC RP RX RA RT RL RG
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# File 'lib/bio/db/embl/common.rb', line 241 def ref unless @data['R'] ary = Array.new get('R').split(/\nRN /).each do |str| raw = {'RN' => '', 'RC' => '', 'RP' => '', 'RX' => '', 'RA' => '', 'RT' => '', 'RL' => '', 'RG' => ''} str = 'RN ' + str unless /^RN / =~ str str.split("\n").each do |line| if /^(R[NPXARLCTG]) (.+)/ =~ line raw[$1] += $2 + ' ' else raise "Invalid format in R lines, \n[#{line}]\n" end end raw.each_value {|v| v.strip! v.sub!(/^"/,'') v.sub!(/;$/,'') v.sub!(/"$/,'') } ary.push(raw) end @data['R'] = ary end @data['R'] end |
#references ⇒ Object
returns Bio::Reference object from Bio::EMBLDB::Common#ref.
-
Bio::EMBLDB::Common#ref -> Bio::References
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# File 'lib/bio/db/embl/common.rb', line 270 def references unless @data['references'] ary = self.ref.map {|ent| hash = Hash.new('') ent.each {|key, value| case key when 'RA' hash['authors'] = value.split(/, /) when 'RT' hash['title'] = value when 'RL' if /(.*) (\d+) *(\(([^\)]+)\))?(\, |\:)([a-zA-Z\d]+\-[a-zA-Z\d]+) *\((\d+)\)\.?\z/ =~ value.to_s hash['journal'] = $1.rstrip hash['volume'] = $2 hash['issue'] = $4 hash['pages'] = $6 hash['year'] = $7 else hash['journal'] = value end when 'RX' # PUBMED, MEDLINE value.split(/\. /).each {|item| tag, xref = item.split(/\; /).map {|i| i.strip.sub(/\.\z/, '') } hash[ tag.downcase ] = xref } end } Reference.new(hash) } @data['references'] = References.new(ary) end @data['references'] end |