Class: Bio::EMBL
- Includes:
- Bio::EMBLDB::Common
- Defined in:
- lib/bio/db/embl/embl.rb
Constant Summary
Constants included from Bio::EMBLDB::Common
Bio::EMBLDB::Common::DELIMITER, Bio::EMBLDB::Common::RS, Bio::EMBLDB::Common::TAGSIZE
Instance Method Summary collapse
-
#cc ⇒ Object
returns comment text in the comments (CC) line.
-
#division ⇒ Object
returns DIVISION in the ID line.
-
#dt(key = nil) ⇒ Object
returns contents in the date (DT) line.
-
#each_cds ⇒ Object
iterates on CDS features in the FT lines.
-
#each_gene ⇒ Object
iterates on gene features in the FT lines.
-
#entry ⇒ Object
(also: #entry_name, #entry_id)
returns ENTRY_NAME in the ID line.
-
#fh ⇒ Object
returns feature table header (String) in the feature header (FH) line.
-
#ft ⇒ Object
(also: #features)
returns contents in the feature table (FT) lines.
-
#id_line(key = nil) ⇒ Object
returns contents in the ID line.
-
#molecule ⇒ Object
(also: #molecule_type)
returns MOLECULE_TYPE in the ID line.
-
#seq ⇒ Object
(also: #naseq, #ntseq)
returns the nucleotie sequence in this entry.
-
#sequence_length ⇒ Object
(also: #seqlen)
returns SEQUENCE_LENGTH in the ID line.
-
#sq(base = nil) ⇒ Object
returns sequence header information in the sequence header (SQ) line.
-
#sv ⇒ Object
returns the version information in the sequence version (SV) line.
- #version ⇒ Object
Methods included from Bio::EMBLDB::Common
#ac, #accession, #de, #dr, #initialize, #kw, #oc, #og, #os, #ref, #references
Methods inherited from EMBLDB
Methods inherited from DB
#exists?, #fetch, #get, open, #tags
Instance Method Details
#cc ⇒ Object
returns comment text in the comments (CC) line.
CC Line; comments of notes (>=0)
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# File 'lib/bio/db/embl/embl.rb', line 313 def cc get('CC') end |
#division ⇒ Object
returns DIVISION in the ID line.
-
Bio::EMBL#division -> String
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# File 'lib/bio/db/embl/embl.rb', line 125 def division id_line('DIVISION') end |
#dt(key = nil) ⇒ Object
returns contents in the date (DT) line.
-
Bio::EMBL#dt -> <DT Hash>
where <DT Hash> is:
{}
-
Bio::EMBL#dt(key) -> String
keys: ‘created’ and ‘updated’
DT Line; date (2/entry)
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# File 'lib/bio/db/embl/embl.rb', line 167 def dt(key=nil) unless @data['DT'] tmp = Hash.new dt_line = self.get('DT').split(/\n/) tmp['created'] = dt_line[0].sub(/\w{2} /,'').strip tmp['updated'] = dt_line[1].sub(/\w{2} /,'').strip @data['DT'] = tmp end if key @data['DT'][key] else @data['DT'] end end |
#each_cds ⇒ Object
iterates on CDS features in the FT lines.
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# File 'lib/bio/db/embl/embl.rb', line 292 def each_cds ft.each do |cds_feature| if cds_feature.feature == 'CDS' yield cds_feature end end end |
#each_gene ⇒ Object
iterates on gene features in the FT lines.
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# File 'lib/bio/db/embl/embl.rb', line 301 def each_gene ft.each do |gene_feature| if gene_feature.feature == 'gene' yield gene_feature end end end |
#entry ⇒ Object Also known as: entry_name, entry_id
returns ENTRY_NAME in the ID line.
-
Bio::EMBL#entry -> String
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# File 'lib/bio/db/embl/embl.rb', line 110 def entry id_line('ENTRY_NAME') end |
#fh ⇒ Object
returns feature table header (String) in the feature header (FH) line.
FH Line; feature table header (0 or 2)
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# File 'lib/bio/db/embl/embl.rb', line 236 def fh fetch('FH') end |
#ft ⇒ Object Also known as: features
returns contents in the feature table (FT) lines.
-
Bio::EMBL#ft -> Bio::Features
-
Bio::EMBL#ft {} -> {|Bio::Feature| }
same as features method in bio/db/genbank.rb
FT Line; feature table data (>=0)
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# File 'lib/bio/db/embl/embl.rb', line 247 def ft unless @data['FT'] @data['FT'] = Array.new ary = Array.new in_quote = false @orig['FT'].each_line do |line| next if line =~ /^FEATURES/ head = line[0,20].strip # feature key (source, CDS, ...) body = line[20,60].chomp # feature value (position, /qualifier=) if line =~ /^FT {3}(\S+)/ ary.push([ $1, body ]) # [ feature, position, /q="data", ... ] elsif body =~ /^ \// and not in_quote ary.last.push(body) # /q="data..., /q=data, /q if body =~ /=" / and body !~ /"$/ in_quote = true end else ary.last.last << body # ...data..., ...data..." if body =~ /"$/ in_quote = false end end end ary.map! do || parse_qualifiers() end @data['FT'] = Features.new(ary) end if block_given? @data['FT'].each do |feature| yield feature end else @data['FT'] end end |
#id_line(key = nil) ⇒ Object
returns contents in the ID line.
-
Bio::EMBL#id_line -> <ID Hash>
where <ID Hash> is:
{'ENTRY_NAME' => String, 'MOLECULE_TYPE' => String, 'DIVISION' => String,
'SEQUENCE_LENGTH' => Int, 'SEQUENCE_VERSION' => Int}
ID Line
"ID ENTRY_NAME DATA_CLASS; MOLECULE_TYPE; DIVISION; SEQUENCE_LENGTH BP."
DATA_CLASS = [‘standard’]
MOLECULE_TYPE: DNA RNA XXX
Code ( DIVISION )
EST (ESTs)
PHG (Bacteriophage)
FUN (Fungi)
GSS (Genome survey)
HTC (High Throughput cDNAs)
HTG (HTGs)
HUM (Human)
INV (Invertebrates)
ORG (Organelles)
MAM (Other Mammals)
VRT (Other Vertebrates)
PLN (Plants)
PRO (Prokaryotes)
ROD (Rodents)
SYN (Synthetic)
STS (STSs)
UNC (Unclassified)
VRL (Viruses)
Rel 89- ID CD789012; SV 4; linear; genomic DNA; HTG; MAM; 500 BP. ID <1>; SV <2>; <3>; <4>; <5>; <6>; <7> BP.
-
Primary accession number
-
Sequence version number
-
Topology: ‘circular’ or ‘linear’
-
Molecule type (see note 1 below)
-
Data class (see section 3.1)
-
Taxonomic division (see section 3.2)
-
Sequence length (see note 2 below)
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# File 'lib/bio/db/embl/embl.rb', line 82 def id_line(key=nil) unless @data['ID'] tmp = Hash.new idline = fetch('ID').split(/; +/) tmp['ENTRY_NAME'], tmp['DATA_CLASS'] = idline.shift.split(/ +/) if idline.first =~ /^SV/ tmp['SEQUENCE_VERSION'] = idline.shift.split(' ').last tmp['TOPOLOGY'] = idline.shift tmp['MOLECULE_TYPE'] = idline.shift tmp['DATA_CLASS'] = idline.shift else tmp['MOLECULE_TYPE'] = idline.shift end tmp['DIVISION'] = idline.shift tmp['SEQUENCE_LENGTH'] = idline.shift.strip.split(' ').first.to_i @data['ID'] = tmp end if key @data['ID'][key] else @data['ID'] end end |
#molecule ⇒ Object Also known as: molecule_type
returns MOLECULE_TYPE in the ID line.
-
Bio::EMBL#molecule -> String
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# File 'lib/bio/db/embl/embl.rb', line 118 def molecule id_line('MOLECULE_TYPE') end |
#seq ⇒ Object Also known as: naseq, ntseq
returns the nucleotie sequence in this entry.
-
Bio::EMBL#seq -> Bio::Sequence::NA
@orig as sequence bb Line; (blanks) sequence data (>=1)
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# File 'lib/bio/db/embl/embl.rb', line 357 def seq Sequence::NA.new( fetch('').gsub(/ /,'').gsub(/\d+/,'') ) end |
#sequence_length ⇒ Object Also known as: seqlen
returns SEQUENCE_LENGTH in the ID line.
-
Bio::EMBL#sequencelength -> String
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# File 'lib/bio/db/embl/embl.rb', line 131 def sequence_length id_line('SEQUENCE_LENGTH') end |
#sq(base = nil) ⇒ Object
returns sequence header information in the sequence header (SQ) line.
-
Bio::EMBL#sq -> <SQ Hash>
where <SQ Hash> is:
{'ntlen' => Int, 'other' => Int,
'a' => Int, 'c' => Int, 'g' => Int, 't' => Int}
-
Bio::EMBL#sq(base) -> <base content in Int>
-
Bio::EMBL#sq -> <base content in Int>
SQ Line; sequence header (1/entry)
SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
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# File 'lib/bio/db/embl/embl.rb', line 334 def sq(base = nil) unless @data['SQ'] fetch('SQ') =~ \ /(\d+) BP\; (\d+) A; (\d+) C; (\d+) G; (\d+) T; (\d+) other;/ @data['SQ'] = {'ntlen' => $1.to_i, 'other' => $6.to_i, 'a' => $2.to_i, 'c' => $3.to_i , 'g' => $4.to_i, 't' => $5.to_i} else @data['SQ'] end if base @data['SQ'][base.downcase] else @data['SQ'] end end |
#sv ⇒ Object
returns the version information in the sequence version (SV) line.
-
Bio::EMBL#sv -> Accession.Version in String
-
Bio::EMBL#version -> accession in Int
SV Line; sequence version (1/entry)
SV Accession.Version
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# File 'lib/bio/db/embl/embl.rb', line 147 def sv if (v = field_fetch('SV').sub(/;/,'')) == "" [id_line['ENTRY_NAME'], id_line['SEQUENCE_VERSION']].join('.') else v end end |
#version ⇒ Object
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# File 'lib/bio/db/embl/embl.rb', line 154 def version (sv.split(".")[1] || id_line['SEQUENCE_VERSION']).to_i end |