### Home Classes Methods

### In Files

- lib/bio/db/fasta/defline.rb

### Parent

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### Methods

- ::new
- #acc_version
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- #description
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### Files

- ChangeLog
- KNOWN_ISSUES.rdoc
- LEGAL
- README.rdoc
- README_DEV.rdoc
- RELEASE_NOTES.rdoc
- Changes-1.3.rdoc
- RELEASE_NOTES-1.4.0.rdoc
- RELEASE_NOTES-1.4.1.rdoc
- RELEASE_NOTES-1.4.2.rdoc

### Class/Module Index

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- Bio
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- Bio::FANTOM
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- Bio::Fasta
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- Bio::Fasta::Report::FLATFILE_SPLITTER
- Bio::Fasta::Report::FastaFormat10Splitter
- Bio::Fasta::Report::Hit
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- Bio::Fasta::Report::Hit::Target
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- Bio::FastaDefline
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- Bio::Fastq
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- Bio::Fastq::Error::Skipped_unformatted_lines
- Bio::Fastq::FormatData
- Bio::Fastq::FormatData::FASTQ_ILLUMINA
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- Bio::Fastq::FormatData::FASTQ_SOLEXA
- Bio::Feature
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- Bio::Fetch
- Bio::FlatFile
- Bio::FlatFile::AutoDetect
- Bio::FlatFile::AutoDetect::RuleDebug
- Bio::FlatFile::AutoDetect::RuleProc
- Bio::FlatFile::AutoDetect::RuleRegexp
- Bio::FlatFile::AutoDetect::RuleRegexp2
- Bio::FlatFile::AutoDetect::RuleSpecial
- Bio::FlatFile::AutoDetect::RuleTemplate
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- Bio::FlatFile::BufferedInputStream
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- Bio::FlatFile::Splitter::Default
- Bio::FlatFile::Splitter::LineOriented
- Bio::FlatFile::Splitter::Template
- Bio::FlatFile::UnknownDataFormatError
- Bio::FlatFileIndex
- Bio::FlatFileIndex::BDB_1
- Bio::FlatFileIndex::BDB_1::BDBMappingFile
- Bio::FlatFileIndex::BDB_1::PrimaryNameSpace
- Bio::FlatFileIndex::BDB_1::SecondaryNameSpace
- Bio::FlatFileIndex::BDBdefault
- Bio::FlatFileIndex::BDBwrapper
- Bio::FlatFileIndex::DEBUG
- Bio::FlatFileIndex::DataBank
- Bio::FlatFileIndex::FileID
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- Bio::FlatFileIndex::Flat_1
- Bio::FlatFileIndex::Flat_1::FlatMappingFile
- Bio::FlatFileIndex::Flat_1::PrimaryNameSpace
- Bio::FlatFileIndex::Flat_1::Record
- Bio::FlatFileIndex::Flat_1::SecondaryNameSpace
- Bio::FlatFileIndex::Indexer
- Bio::FlatFileIndex::Indexer::NameSpace
- Bio::FlatFileIndex::Indexer::NameSpaces
- Bio::FlatFileIndex::Indexer::Parser
- Bio::FlatFileIndex::Indexer::Parser::BlastDefaultParser
- Bio::FlatFileIndex::Indexer::Parser::EMBLParser
- Bio::FlatFileIndex::Indexer::Parser::FastaFormatParser
- Bio::FlatFileIndex::Indexer::Parser::GenBankParser
- Bio::FlatFileIndex::Indexer::Parser::GenPeptParser
- Bio::FlatFileIndex::Indexer::Parser::MaXMLClusterParser
- Bio::FlatFileIndex::Indexer::Parser::MaXMLSequenceParser
- Bio::FlatFileIndex::Indexer::Parser::PDBChemicalComponentParser
- Bio::FlatFileIndex::Indexer::Parser::SPTRParser
- Bio::FlatFileIndex::Indexer::Parser::TemplateParser
- Bio::FlatFileIndex::NameSpaces
- Bio::FlatFileIndex::Results
- Bio::FlatFileIndex::Template
- Bio::FlatFileIndex::Template::NameSpace
- Bio::GCG
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- Bio::GFF
- Bio::GFF::GFF2
- Bio::GFF::GFF2::Escape
- Bio::GFF::GFF2::MetaData
- Bio::GFF::GFF2::Record
- Bio::GFF::GFF2::Record::Value
- Bio::GFF::GFF3
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- Bio::GFF::GFF3::Record
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- Bio::GFF::GFF3::RecordBoundary
- Bio::GFF::GFF3::SequenceRegion
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- Bio::GO
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- Bio::GenBank
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- Bio::GenPept
- Bio::GenPept::Locus
- Bio::Genscan
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- Bio::Genscan::Report::Exon
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- Bio::HGC
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- Bio::HMMER
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- Bio::Hinv
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- Object
- String

No matching classes.

# Bio::FastaDefline

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

- Fasta format description (NCBI) www.ncbi.nlm.nih.gov/BLAST/fasta.shtml

- 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

### Constants

KillRegexpArray
KillWords
KillWordsHash
NSIDs

### Attributes

entry_id[R]

Shows a possibly unique identifier. Returns a string.

list_ids[R]

Shows array that contains IDs (or ID-like strings). Returns an array of arrays of strings.

### Public Class Methods

new(str) click to toggle source

Parses given string.

    # File lib/bio/db/fasta/defline.rb, line 181
    def initialize(str)
      @deflines = []
      @info = {}
      @list_ids = []

      @entry_id = nil

      lines = str.split("\x01")
      lines.each do |line|
        add_defline(line)
      end
    end

### Public Instance Methods

acc_version() click to toggle source

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.

    # File lib/bio/db/fasta/defline.rb, line 494
    def acc_version
      unless defined?(@acc_version) then
        @acc_version = get_by_type('acc_version')
      end
      @acc_version
    end

accession() click to toggle source

Shows an accession number.

    # File lib/bio/db/fasta/defline.rb, line 512
    def accession
      unless defined?(@accession) then
        if acc_version then
          @accession = acc_version.split('.')[0]
        else
          @accession = accessions[0]
        end
      end
      @accession
    end

accessions() click to toggle source

Shows accession numbers. Returns an array of strings.

    # File lib/bio/db/fasta/defline.rb, line 503
    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) click to toggle source

Parses given string and adds parsed data.

    # File lib/bio/db/fasta/defline.rb, line 195
    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() click to toggle source

Shows description.

    # File lib/bio/db/fasta/defline.rb, line 337
    def description
      @deflines[0].to_a[-1]
    end

descriptions() click to toggle source

Returns descriptions.

    # File lib/bio/db/fasta/defline.rb, line 342
    def descriptions
      @deflines.collect do |a|
        a[-1]
      end
    end

get(dbname) click to toggle source

Returns identifires by a database name.

    # File lib/bio/db/fasta/defline.rb, line 418
    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) click to toggle source

Returns identifiers by given type.

    # File lib/bio/db/fasta/defline.rb, line 454
    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) click to toggle source

Returns an identifier by given type.

    # File lib/bio/db/fasta/defline.rb, line 442
    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() click to toggle source

Shows GI. If the entry has more than two of such IDs, only the first ID are shown. Returns a string or nil.

    # File lib/bio/db/fasta/defline.rb, line 483
    def gi
      unless defined?(@gi) then
        @gi = get_by_type('gi')
      end
      @gi
    end

id_strings() click to toggle source

Shows ID-like strings. Returns an array of strings.

    # File lib/bio/db/fasta/defline.rb, line 350
    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() click to toggle source

Shows locus. If the entry has more than two of such IDs, only the first ID are shown. Returns a string or nil.

    # File lib/bio/db/fasta/defline.rb, line 472
    def locus
      unless defined?(@locus)
        @locus = get_by_type('locus')
      end
      @locus
    end

method_missing(name, *args) click to toggle source

    # File lib/bio/db/fasta/defline.rb, line 523
    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

to_s() click to toggle source

Shows original string. Note that the result of this method may be different from original string which is given in FastaDefline.new method.

    # File lib/bio/db/fasta/defline.rb, line 329
    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) click to toggle source

Shows words used in the defline. Returns an Array.

    # File lib/bio/db/fasta/defline.rb, line 392
    def words(case_sensitive = nil, kill_regexp = self.class::KillRegexpArray,
              kwhash = self.class::KillWordsHash)
      a = descriptions.join(' ').split(/[\.\,\;\:\(\)\[\]\{\}\<\>\"\'\`\~\/\|\?\!\&\@\#\s\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

[Validate]

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