Class: Bio::FastaDefline
Overview
Parsing FASTA Defline, and extract IDs and other informations. IDs are NSIDs (NCBI standard FASTA sequence identifiers) or “:”-separated IDs.
specs are described in: ftp.ncbi.nih.gov/blast/documents/README.formatdb blast.wustl.edu/doc/FAQ-Indexing.html#Identifiers
Examples
rub = Bio::FastaDefline.new('>gi|671595|emb|CAA85678.1| rubisco large subunit [Perovskia abrotanoides]')
rub.entry_id ==> 'gi|671595'
rub.get('emb') ==> 'CAA85678.1'
rub.emb ==> 'CAA85678.1'
rub.gi ==> '671595'
rub.accession ==> 'CAA85678'
rub.accessions ==> [ 'CAA85678' ]
rub.acc_version ==> 'CAA85678.1'
rub.locus ==> nil
rub.list_ids ==> [["gi", "671595"],
["emb", "CAA85678.1", nil],
["Perovskia abrotanoides"]]
ckr = Bio::FastaDefline.new(">gi|2495000|sp|Q63931|CCKR_CAVPO CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)\001gi|2147182|pir||I51898 cholecystokinin A receptor - guinea pig\001gi|544724|gb|AAB29504.1| cholecystokinin A receptor; CCK-A receptor [Cavia]")
ckr.entry_id ==> "gi|2495000"
ckr.sp ==> "CCKR_CAVPO"
ckr.pir ==> "I51898"
ckr.gb ==> "AAB29504.1"
ckr.gi ==> "2495000"
ckr.accession ==> "AAB29504"
ckr.accessions ==> ["Q63931", "AAB29504"]
ckr.acc_version ==> "AAB29504.1"
ckr.locus ==> nil
ckr.description ==>
"CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)"
ckr.descriptions ==>
["CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)",
"cholecystokinin A receptor - guinea pig",
"cholecystokinin A receptor; CCK-A receptor [Cavia]"]
ckr.words ==>
["cavia", "cck-a", "cck-ar", "cholecystokinin", "guinea", "pig",
"receptor", "type"]
ckr.id_strings ==>
["2495000", "Q63931", "CCKR_CAVPO", "2147182", "I51898",
"544724", "AAB29504.1", "Cavia"]
ckr.list_ids ==>
[["gi", "2495000"], ["sp", "Q63931", "CCKR_CAVPO"],
["gi", "2147182"], ["pir", nil, "I51898"], ["gi", "544724"],
["gb", "AAB29504.1", nil], ["Cavia"]]
References
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Fasta format description (NCBI) www.ncbi.nlm.nih.gov/BLAST/fasta.shtml
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Frequently Asked Questions: Indexing of Sequence Identifiers (by Warren R. Gish.) (Dead link. Please find in web.archive.org/ ). blast.wustl.edu/doc/FAQ-Indexing.html#Identifiers
-
Program Parameters for formatdb and fastacmd (by Tao Tao) www.ncbi.nlm.nih.gov/staff/tao/URLAPI/formatdb_fastacmd.html#t1.1
-
Formatdb README ftp.ncbi.nih.gov/blast/documents/formatdb.html
Constant Summary collapse
- NSIDs =
{ # NCBI and WU-BLAST 'gi' => [ 'gi' ], # NCBI GI 'gb' => [ 'acc_version', 'locus' ], # GenBank 'emb' => [ 'acc_version', 'locus' ], # EMBL 'dbj' => [ 'acc_version', 'locus' ], # DDBJ 'sp' => [ 'accession', 'entry_id' ], # SWISS-PROT 'tr' => [ 'accession', 'entry_id' ], # TREMBL 'pdb' => [ 'entry_id', 'chain' ], # PDB 'bbs' => [ 'number' ], # GenInfo Backbone Id 'gnl' => [ 'database' , 'entry_id' ], # General database identifier 'ref' => [ 'acc_version' , 'locus' ], # NCBI Reference Sequence 'lcl' => [ 'entry_id' ], # Local Sequence identifier # WU-BLAST and NCBI 'pir' => [ 'accession', 'entry_id' ], # PIR 'prf' => [ 'accession', 'entry_id' ], # Protein Research Foundation 'pat' => [ 'country', 'number', 'serial' ], # Patents # WU-BLAST only 'bbm' => [ 'number' ], # NCBI GenInfo Backbone database identifier 'gim' => [ 'number' ], # NCBI GenInfo Import identifier 'gp' => [ 'acc_version', 'locus' ], # GenPept 'oth' => [ 'accession', 'name', 'release' ], # Other (user-definable) identifier 'tpd' => [ 'accession', 'name' ], # Third party annotation, DDBJ 'tpe' => [ 'accession', 'name' ], # Third party annotation, EMBL 'tpg' => [ 'accession', 'name' ], # Third party annotation, GenBank # Original 'ri' => [ 'entry_id', 'rearray_id', 'len' ], # RIKEN FANTOM DB }
- KillWords =
[ 'an', 'the', 'this', 'that', 'is', 'are', 'were', 'was', 'be', 'can', 'may', 'might', 'as', 'at', 'by', 'for', 'in', 'of', 'on', 'to', 'with', 'from', 'and', 'or', 'not', 'dna', 'rna', 'mrna', 'cdna', 'orf', 'aa', 'nt', 'pct', 'id', 'ec', 'sp', 'subsp', 'similar', 'involved', 'identical', 'identity', 'cds', 'clone', 'library', 'contig', 'contigs', 'homolog', 'homologue', 'homologs', 'homologous', 'protein', 'proteins', 'gene', 'genes', 'product', 'products', 'sequence', 'sequences', 'strain', 'strains', 'region', 'regions', ]
- KillWordsHash =
{}
- KillRegexpArray =
[ /\A\d{1,3}\%?\z/, /\A[A-Z][A-Za-z0-9\_]*[0-9]+[A-Za-z0-9\_]+\z/, /\A[A-Z][A-Z0-9]*\_[A-Z0-9\_]+\z/ ]
Instance Attribute Summary collapse
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#entry_id ⇒ Object
readonly
Shows a possibly unique identifier.
-
#list_ids ⇒ Object
readonly
Shows array that contains IDs (or ID-like strings).
Instance Method Summary collapse
-
#acc_version ⇒ Object
Shows accession with version number.
-
#accession ⇒ Object
Shows an accession number.
-
#accessions ⇒ Object
Shows accession numbers.
-
#add_defline(str) ⇒ Object
Parses given string and adds parsed data.
-
#description ⇒ Object
Shows description.
-
#descriptions ⇒ Object
Returns descriptions.
-
#get(dbname) ⇒ Object
Returns identifires by a database name.
-
#get_all_by_type(*type_strarg) ⇒ Object
Returns identifiers by given type.
-
#get_by_type(type_str) ⇒ Object
Returns an identifier by given type.
-
#gi ⇒ Object
Shows GI.
-
#id_strings ⇒ Object
Shows ID-like strings.
-
#initialize(str) ⇒ FastaDefline
constructor
Parses given string.
-
#locus ⇒ Object
Shows locus.
- #method_missing(name, *args) ⇒ Object
-
#to_s ⇒ Object
Shows original string.
-
#words(case_sensitive = nil, kill_regexp = self.class::KillRegexpArray, kwhash = self.class::KillWordsHash) ⇒ Object
Shows words used in the defline.
Constructor Details
#initialize(str) ⇒ FastaDefline
Parses given string.
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# File 'lib/bio/db/fasta/defline.rb', line 180 def initialize(str) @deflines = [] @info = {} @list_ids = [] @entry_id = nil lines = str.split("\x01") lines.each do |line| add_defline(line) end end |
Dynamic Method Handling
This class handles dynamic methods through the method_missing method
#method_missing(name, *args) ⇒ Object
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# File 'lib/bio/db/fasta/defline.rb', line 521 def method_missing(name, *args) # raise ArgumentError, # "wrong # of arguments(#{args.size} for 1)" if args.size >= 2 r = get(name, *args) if !r and !(self.class::NSIDs[name.to_s]) then raise "NameError: undefined method `#{name.inspect}'" end r end |
Instance Attribute Details
#entry_id ⇒ Object (readonly)
Shows a possibly unique identifier. Returns a string.
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# File 'lib/bio/db/fasta/defline.rb', line 177 def entry_id @entry_id end |
#list_ids ⇒ Object (readonly)
Shows array that contains IDs (or ID-like strings). Returns an array of arrays of strings.
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# File 'lib/bio/db/fasta/defline.rb', line 173 def list_ids @list_ids end |
Instance Method Details
#acc_version ⇒ Object
Shows accession with version number. If the entry has more than two of such IDs, only the first ID are shown. Returns a string or nil.
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# File 'lib/bio/db/fasta/defline.rb', line 492 def acc_version unless defined?(@acc_version) then @acc_version = get_by_type('acc_version') end @acc_version end |
#accession ⇒ Object
Shows an accession number.
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# File 'lib/bio/db/fasta/defline.rb', line 510 def accession unless defined?(@accession) then if acc_version then @accession = acc_version.split('.')[0] else @accession = accessions[0] end end @accession end |
#accessions ⇒ Object
Shows accession numbers. Returns an array of strings.
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# File 'lib/bio/db/fasta/defline.rb', line 501 def accessions unless defined?(@accessions) then @accessions = get_all_by_type('accession', 'acc_version') @accessions.collect! { |x| x.sub(/\..*\z/, '') } end @accessions end |
#add_defline(str) ⇒ Object
Parses given string and adds parsed data.
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# File 'lib/bio/db/fasta/defline.rb', line 194 def add_defline(str) case str when /^\>?\s*((?:[^\|\s]*\|)+[^\s]+)\s*(.*)$/ # NSIDs # examples: # >gi|9910844|sp|Q9UWG2|RL3_METVA 50S ribosomal protein L3P # # note: regexp (:?) means grouping without backreferences i = $1 d = $2 tks = i.split('|') tks << '' if i[-1,1] == '|' a = parse_NSIDs(tks) i = a[0].join('|') a.unshift('|') d = tks.join('|') + ' ' + d unless tks.empty? a << d this_line = a match_EC(d) parse_square_brackets(d).each do |x| if !match_EC(x, false) and x =~ /\A[A-Z]/ then di = [ x ] @list_ids << di @info['organism'] = x unless @info['organism'] end end when /^\>?\s*([a-zA-Z0-9]+\:[^\s]+)\s*(.*)$/ # examples: # >sce:YBR160W CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST] # >emb:CACDC28 [X80034] C.albicans CDC28 gene i = $1 d = $2 a = parse_ColonSepID(i) i = a.join(':') this_line = [ ':', a , d ] match_EC(d) parse_square_brackets(d).each do |x| if !match_EC(x, false) and x =~ /:/ then parse_ColonSepID(x) elsif x =~ /\A\s*([A-Z][A-Z0-9_\.]+)\s*\z/ then @list_ids << [ $1 ] end end when /^\>?\s*(\S+)(?:\s+(.+))?$/ # examples: # >ABC12345 this is test i = $1 d = $2.to_s @list_ids << [ i.chomp('.') ] this_line = [ '', [ i ], d ] match_EC(d) else i = str d = '' match_EC(i) this_line = [ '', [ i ], d ] end @deflines << this_line @entry_id = i unless @entry_id end |
#description ⇒ Object
Shows description.
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# File 'lib/bio/db/fasta/defline.rb', line 335 def description @deflines[0].to_a[-1] end |
#descriptions ⇒ Object
Returns descriptions.
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# File 'lib/bio/db/fasta/defline.rb', line 340 def descriptions @deflines.collect do |a| a[-1] end end |
#get(dbname) ⇒ Object
Returns identifires by a database name.
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# File 'lib/bio/db/fasta/defline.rb', line 416 def get(dbname) db = dbname.to_s r = nil unless r = @info[db] then di = @list_ids.find { |x| x[0] == db.to_s } if di and di.size <= 2 then r = di[-1] elsif di then labels = self.class::NSIDs[db] [ 'acc_version', 'entry_id', 'locus', 'accession', 'number'].each do |x| if i = labels.index(x) then r = di[i+1] break if r end end r = di[1..-1].find { |x| x } unless r end @info[db] = r if r end r end |
#get_all_by_type(*type_strarg) ⇒ Object
Returns identifiers by given type.
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# File 'lib/bio/db/fasta/defline.rb', line 452 def get_all_by_type(*type_strarg) d = [] @list_ids.each do |x| if labels = self.class::NSIDs[x[0]] then type_strarg.each do |y| if i = labels.index(y) then d << x[i+1] if x[i+1] end end end end d end |
#get_by_type(type_str) ⇒ Object
Returns an identifier by given type.
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# File 'lib/bio/db/fasta/defline.rb', line 440 def get_by_type(type_str) @list_ids.each do |x| if labels = self.class::NSIDs[x[0]] then if i = labels.index(type_str) then return x[i+1] end end end nil end |
#gi ⇒ Object
Shows GI. If the entry has more than two of such IDs, only the first ID are shown. Returns a string or nil.
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# File 'lib/bio/db/fasta/defline.rb', line 481 def gi unless defined?(@gi) then @gi = get_by_type('gi') end @gi end |
#id_strings ⇒ Object
Shows ID-like strings. Returns an array of strings.
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# File 'lib/bio/db/fasta/defline.rb', line 348 def id_strings r = [] @list_ids.each do |a| if a.size >= 2 then r.concat a[1..-1].find_all { |x| x } else if a[0].to_s.size > 0 and a[0] =~ /\A[A-Za-z0-9\.\-\_]+\z/ r << a[0] end end end r.concat( words(true, []).find_all do |x| x =~ /\A[A-Z][A-Za-z0-9\_]*[0-9]+[A-Za-z0-9\_]+\z/ or x =~ /\A[A-Z][A-Z0-9]*\_[A-Z0-9\_]+\z/ end) r end |
#locus ⇒ Object
Shows locus. If the entry has more than two of such IDs, only the first ID are shown. Returns a string or nil.
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# File 'lib/bio/db/fasta/defline.rb', line 470 def locus unless defined?(@locus) @locus = get_by_type('locus') end @locus end |
#to_s ⇒ Object
Shows original string. Note that the result of this method may be different from original string which is given in FastaDefline.new method.
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# File 'lib/bio/db/fasta/defline.rb', line 327 def to_s @deflines.collect { |a| s = a[0] (a[1..-2].collect { |x| x.join(s) }.join(s) + ' ' + a[-1]).strip }.join("\x01") end |
#words(case_sensitive = nil, kill_regexp = self.class::KillRegexpArray, kwhash = self.class::KillWordsHash) ⇒ Object
Shows words used in the defline. Returns an Array.
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# File 'lib/bio/db/fasta/defline.rb', line 390 def words(case_sensitive = nil, kill_regexp = self.class::KillRegexpArray, kwhash = self.class::KillWordsHash) a = descriptions.join(' ').split(/[\.\,\;\:\(\)\[\]\{\}\<\>\"\'\`\~\/\|\?\!\&\@\# \x00-\x1f\x7f]+/) a.collect! do |x| x.sub!(/\A[\$\*\-\+]+/, '') x.sub!(/[\$\*\-\=]+\z/, '') if x.size <= 1 then nil elsif kwhash[x.downcase] then nil else if kill_regexp.find { |expr| expr =~ x } then nil else x end end end a.compact! a.collect! { |x| x.downcase } unless case_sensitive a.sort! a.uniq! a end |