Class: Bio::PROSITE

# File lib/bio/db/prosite.rb, line 26
  def initialize(entry)
    super(entry, TAGSIZE)
  end

pa2re(pattern)

  prosite pattern to regular expression

prosite/prosuser.txt:

The PA (PAttern) lines contains the definition of a PROSITE pattern. The patterns are described using the following conventions:

0) The standard IUPAC one-letter codes for the amino acids are used. 0) Ambiguities are indicated by listing the acceptable amino acids for a

  given position, between square parentheses `[ ]'. For example: [ALT]
  stands for Ala or Leu or Thr.

1) A period ends the pattern. 2) When a pattern is restricted to either the N- or C-terminal of a

  sequence, that pattern either starts with a `<' symbol or respectively
  ends with a `>' symbol.

3) Ambiguities are also indicated by listing between a pair of curly

  brackets `{ }' the amino acids that are not accepted at a given
  position. For example: {AM} stands for any amino acid except Ala and
  Met.

4) Repetition of an element of the pattern can be indicated by following

  that element with a numerical value or a numerical range between
  parenthesis. Examples: x(3) corresponds to x-x-x, x(2,4) corresponds to
  x-x or x-x-x or x-x-x-x.

5) The symbol `x’ is used for a position where any amino acid is accepted. 6) Each element in a pattern is separated from its neighbor by a `-’.

Examples:

PA [AC]-x-V-x(4)-{ED}.

This pattern is translated as: [Ala or Cys]-any-Val-any-any-any-any-{any but Glu or Asp}

PA <A-x-[ST](2)-x(0,1)-V.

This pattern, which must be in the N-terminal of the sequence (`<’), is translated as: Ala-any-[Ser or Thr]-[Ser or Thr]-(any or none)-Val

[Source]

# File lib/bio/db/prosite.rb, line 467
  def self.pa2re(pattern)
    pattern.gsub!(/\s/, '')     # remove white spaces
    pattern.sub!(/\.$/, '')     # (1) remove trailing '.'
    pattern.sub!(/^</, '^')     # (2) restricted to the N-terminal : `<'
    pattern.sub!(/>$/, '$')     # (2) restricted to the C-terminal : `>'
    pattern.gsub!(/\{(\w+)\}/) { |m|
      '[^' + $1 + ']'           # (3) not accepted at a given position : '{}'
    }
    pattern.gsub!(/\(([\d,]+)\)/) { |m|
      '{' + $1 + '}'            # (4) repetition of an element : (n), (n,m)
    }
    pattern.tr!('x', '.')       # (5) any amino acid is accepted : 'x'
    pattern.tr!('-', '')        # (6) each element is separated by a '-'
    Regexp.new(pattern, Regexp::IGNORECASE)
  end

ac()

AC Accession number (1 per entry)

 AC   PSnnnnn;

Returns

[Source]

# File lib/bio/db/prosite.rb, line 57
  def ac
    unless @data['AC']
      @data['AC'] = fetch('AC').chomp(';')
    end
    @data['AC']
  end

cc()

CC Comments (>=0 per entry)

 CC   /QUALIFIER=data; /QUALIFIER=data; .......

/TAXO-RANGE Taxonomic range. /MAX-REPEAT Maximum known number of repetitions of the pattern in a

             single protein.

/SITE Indication of an `interesting’ site in the pattern. /SKIP-FLAG Indication of an entry that can be, in some cases, ignored

             by a program (because it is too unspecific).

Returns

[Source]

# File lib/bio/db/prosite.rb, line 273
  def cc
    unless @data['CC']
      hash = {}                 # temporal hash
      fetch('CC').scan(%r{/(\S+)=([^;]+);}).each do |k, v|
        hash[k] = v
      end
      @data['CC'] = hash
    end
    @data['CC']
  end

comment()

Alias for cc

date()

Alias for dt

de()

DE Short description (1 per entry)

 DE   Description.

Returns

[Source]

# File lib/bio/db/prosite.rb, line 84
  def de
    field_fetch('DE')
  end

definition()

Alias for de

division()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 44
  def division
    unless @data['TYPE']
      name
    end
    @data['TYPE']
  end

dr()

DR Cross-references to SWISS-PROT (>=0 per entry)

 DR   AC_NB, ENTRY_NAME, C; AC_NB, ENTRY_NAME, C; AC_NB, ENTRY_NAME, C;

`AC_NB’ is the SWISS-PROT primary accession number of the entry to which reference is being made.
`ENTRY_NAME’ is the SWISS-PROT entry name.
`C’ is a one character flag that can be one of the following:

T For a true positive. N For a false negative; a sequence which belongs to the set under

  consideration, but which has not been picked up by the pattern or
  profile.

P For a `potential’ hit; a sequence that belongs to the set under

  consideration, but which was not picked up because the region(s) that
  are used as a 'fingerprint' (pattern or profile) is not yet available
  in the data bank (partial sequence).

? For an unknown; a sequence which possibly could belong to the set under

  consideration.

F For a false positive; a sequence which does not belong to the set in

  consideration.

Returns

[Source]

# File lib/bio/db/prosite.rb, line 349
  def dr
    unless @data['DR']
      hash = {}                 # temporal hash
      if fetch('DR')
        fetch('DR').scan(/(\w+)\s*, (\w+)\s*, (.);/).each do |a, e, c|
          hash[a] = [e, c]      # SWISS-PROT : accession, entry, true/false
        end
      end
      @data['DR'] = hash
    end
    @data['DR']
  end

dt()

DT Date (1 per entry)

 DT   MMM-YYYY (CREATED); MMM-YYYY (DATA UPDATE); MMM-YYYY (INFO UPDATE).

Returns

[Source]

# File lib/bio/db/prosite.rb, line 72
  def dt
    field_fetch('DT')
  end

entry_id()

Alias for ac

false_neg()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 250
  def false_neg
    statistics['FALSE_NEG']
  end

false_negative_hits()

Alias for false_neg

false_pos()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 235
  def false_pos
    statistics['FALSE_POS']
  end

false_positive_hits()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 240
  def false_positive_hits
    false_pos.first
  end

false_positive_sequences()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 245
  def false_positive_sequences
    false_pos.last
  end

list_falsenegative(by_name = nil)

Returns

[Source]

# File lib/bio/db/prosite.rb, line 386
  def list_falsenegative(by_name = nil)
    list_xref('F', by_name)
  end

list_falsepositive(by_name = nil)

Returns

[Source]

# File lib/bio/db/prosite.rb, line 391
  def list_falsepositive(by_name = nil)
    list_xref('P', by_name)
  end

list_potentialhit(by_name = nil)

Returns

[Source]

# File lib/bio/db/prosite.rb, line 396
  def list_potentialhit(by_name = nil)
    list_xref('P', by_name)
  end

list_truepositive(by_name = nil)

Returns

[Source]

# File lib/bio/db/prosite.rb, line 381
  def list_truepositive(by_name = nil)
    list_xref('T', by_name)
  end

list_unknown(by_name = nil)

Returns

[Source]

# File lib/bio/db/prosite.rb, line 401
  def list_unknown(by_name = nil)
    list_xref('?', by_name)
  end

list_xref(flag, by_name = nil)

Returns

[Source]

# File lib/bio/db/prosite.rb, line 365
  def list_xref(flag, by_name = nil)
    ary = []
    sp_xref.each do |sp_acc, value|
      if value[1] == flag
        if by_name
          sp_name = value[0]
          ary.push(sp_name)
        else
          ary.push(sp_acc)
        end
      end
    end
    return ary
  end

ma()

MA Matrix/profile (>=0 per entry)

 see - ma2re method

Returns

[Source]

# File lib/bio/db/prosite.rb, line 111
  def ma
    field_fetch('MA')
  end

ma2re(matrix)

  prosite profile to regular expression

prosite/profile.txt:

Returns

[Source]

# File lib/bio/db/prosite.rb, line 497
  def ma2re(matrix)
    raise NotImplementedError
  end

max_repeat()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 306
  def max_repeat
    comment['MAX-REPEAT'].to_i
  end

name()

ID Identification (Begins each entry; 1 per entry)

 ID   ENTRY_NAME; ENTRY_TYPE.  (ENTRY_TYPE : PATTERN, MATRIX, RULE)

Returns

[Source]

# File lib/bio/db/prosite.rb, line 36
  def name
    unless @data['ID']
      @data['ID'], @data['TYPE'] = fetch('ID').chomp('.').split('; ')
    end
    @data['ID']
  end

nr()

NR Numerical results (>=0 per entry)

  - SWISS-PROT scan statistics of true and false positives/negatives

/RELEASE SWISS-PROT release number and total number of sequence

             entries in that release.

/TOTAL Total number of hits in SWISS-PROT. /POSITIVE Number of hits on proteins that are known to belong to the

             set in consideration.

/UNKNOWN Number of hits on proteins that could possibly belong to

             the set in consideration.

/FALSE_POS Number of false hits (on unrelated proteins). /FALSE_NEG Number of known missed hits. /PARTIAL Number of partial sequences which belong to the set in

             consideration, but  which  are  not  hit  by the pattern or
             profile because they are partial (fragment) sequences.

Returns

[Source]

# File lib/bio/db/prosite.rb, line 150
  def nr
    unless @data['NR']
      hash = {}                 # temporal hash
      fetch('NR').scan(%r{/(\S+)=([^;]+);}).each do |k, v|
        if v =~ /^(\d+)\((\d+)\)$/
          hits = $1.to_i                # the number of hits
          seqs = $2.to_i                # the number of sequences
          v = [hits, seqs]
        elsif v =~ /([\d\.]+),(\d+)/
          sprel = $1                    # the number of SWISS-PROT release
          spseq = $2.to_i               # the number of SWISS-PROT sequences
          v = [sprel, spseq]
        else
          v = v.to_i
        end
        hash[k] = v
      end
      @data['NR'] = hash
    end
    @data['NR']
  end

pa()

PA Pattern (>=0 per entry)

 see - pa2re method

Returns

[Source]

# File lib/bio/db/prosite.rb, line 96
  def pa
    field_fetch('PA')
    @data['PA'] = fetch('PA') unless @data['PA']
    @data['PA'].gsub!(/\s+/, '') if @data['PA']
    @data['PA']
  end

pa2re(pattern)

[Source]

# File lib/bio/db/prosite.rb, line 483
  def pa2re(pattern)
    self.class.pa2re(pattern)
  end

partial()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 256
  def partial
    statistics['PARTIAL']
  end

pattern()

Alias for pa

pdb_xref()

3D Cross-references to PDB (>=0 per entry)

 3D   name; [name2;...]

Returns

[Source]

# File lib/bio/db/prosite.rb, line 411
  def pdb_xref
    unless @data['3D']
      @data['3D'] = fetch('3D').split(/; */)
    end
    @data['3D']
  end

pdoc_xref()

DO Pointer to the documentation file (1 per entry)

 DO   PDOCnnnnn;

Returns

[Source]

# File lib/bio/db/prosite.rb, line 424
  def pdoc_xref
    @data['DO'] = fetch('DO').chomp(';')
  end

positive()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 205
  def positive
    statistics['POSITIVE']
  end

positive_hits()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 210
  def positive_hits
    positive.first
  end

positive_sequences()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 215
  def positive_sequences
    positive.last
  end

profile()

Alias for ma

re()

[Source]

# File lib/bio/db/prosite.rb, line 487
  def re
    self.class.pa2re(self.pa)
  end

release()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 175
  def release
    statistics['RELEASE']
  end

ru()

RU Rule (>=0 per entry)

 RU   Rule_Description.

 The rule is described in ordinary English and is free-format.

Returns

[Source]

# File lib/bio/db/prosite.rb, line 125
  def ru
    field_fetch('RU')
  end

rule()

Alias for ru

site()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 311
  def site
    if comment['SITE']
      num, desc = comment['SITE'].split(',')
    end
    return [num.to_i, desc]
  end

skip_flag()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 319
  def skip_flag
    if comment['SKIP-FLAG'] == 'TRUE'
      return true
    end
  end

sp_xref()

Alias for dr

statistics()

Alias for nr

swissprot_release_number()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 180
  def swissprot_release_number
    release.first
  end

swissprot_release_sequences()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 185
  def swissprot_release_sequences
    release.last
  end

taxon_range(expand = nil)

Returns

[Source]

# File lib/bio/db/prosite.rb, line 287
  def taxon_range(expand = nil)
    range = comment['TAXO-RANGE']
    if range and expand
      expand = []
      range.scan(/./) do |x|
        case x
        when 'A'; expand.push('archaebacteria')
        when 'B'; expand.push('bacteriophages')
        when 'E'; expand.push('eukaryotes')
        when 'P'; expand.push('prokaryotes')
        when 'V'; expand.push('eukaryotic viruses')
        end
      end
      range = expand
    end
    return range
  end

total()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 190
  def total
    statistics['TOTAL']
  end

total_hits()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 195
  def total_hits
    total.first
  end

total_sequences()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 200
  def total_sequences
    total.last
  end

unknown()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 220
  def unknown
    statistics['UNKNOWN']
  end

unknown_hits()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 225
  def unknown_hits
    unknown.first
  end

unknown_sequences()

Returns

[Source]

# File lib/bio/db/prosite.rb, line 230
  def unknown_sequences
    unknown.last
  end

DELIMITER	=	"\n//\n"	Delimiter
RS	=	DELIMITER	Delimiter
TAGSIZE	=	5	Bio::DB API

Methods

Constants

Public Class methods

Public Instance methods