class Bio::PROSITE
Constants
- DELIMITER
Delimiter
- RS
Delimiter
- TAGSIZE
Bio::DB API
Public Class Methods
# File lib/bio/db/prosite.rb, line 26 def initialize(entry) super(entry, TAGSIZE) end
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-(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
# 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
Public Instance Methods
AC Accession number (1 per entry)
AC PSnnnnn;
Returns
# File lib/bio/db/prosite.rb, line 57 def ac unless @data['AC'] @data['AC'] = fetch('AC').chomp(';') end @data['AC'] end
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
# 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
DE Short description (1 per entry)
DE Description.
Returns
# File lib/bio/db/prosite.rb, line 84 def de field_fetch('DE') end
Returns
# File lib/bio/db/prosite.rb, line 44 def division unless @data['TYPE'] name end @data['TYPE'] end
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
# 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 Date (1 per entry)
DT MMM-YYYY (CREATED); MMM-YYYY (DATA UPDATE); MMM-YYYY (INFO UPDATE).
Returns
# File lib/bio/db/prosite.rb, line 72 def dt field_fetch('DT') end
Returns
# File lib/bio/db/prosite.rb, line 250 def false_neg statistics['FALSE_NEG'] end
Returns
# File lib/bio/db/prosite.rb, line 235 def false_pos statistics['FALSE_POS'] end
Returns
# File lib/bio/db/prosite.rb, line 240 def false_positive_hits false_pos.first end
Returns
# File lib/bio/db/prosite.rb, line 245 def false_positive_sequences false_pos.last end
Returns
# File lib/bio/db/prosite.rb, line 386 def list_falsenegative(by_name = nil) list_xref('F', by_name) end
Returns
# File lib/bio/db/prosite.rb, line 391 def list_falsepositive(by_name = nil) list_xref('P', by_name) end
Returns
# File lib/bio/db/prosite.rb, line 396 def list_potentialhit(by_name = nil) list_xref('P', by_name) end
Returns
# File lib/bio/db/prosite.rb, line 381 def list_truepositive(by_name = nil) list_xref('T', by_name) end
Returns
# File lib/bio/db/prosite.rb, line 401 def list_unknown(by_name = nil) list_xref('?', by_name) end
Returns
# 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 Matrix/profile (>=0 per entry)
see - ma2re method
Returns
# File lib/bio/db/prosite.rb, line 111 def ma field_fetch('MA') end
prosite profile to regular expression
prosite/profile.txt:
Returns
# File lib/bio/db/prosite.rb, line 497 def ma2re(matrix) raise NotImplementedError end
Returns
# File lib/bio/db/prosite.rb, line 306 def max_repeat comment['MAX-REPEAT'].to_i end
ID Identification (Begins each entry; 1 per entry)
ID ENTRY_NAME; ENTRY_TYPE. (ENTRY_TYPE : PATTERN, MATRIX, RULE)
Returns
# 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 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
# 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 Pattern (>=0 per entry)
see - pa2re method
Returns
# 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
# File lib/bio/db/prosite.rb, line 483 def pa2re(pattern) self.class.pa2re(pattern) end
Returns
# File lib/bio/db/prosite.rb, line 256 def partial statistics['PARTIAL'] end
3D Cross-references to PDB (>=0 per entry)
3D name; [name2;...]
Returns
# File lib/bio/db/prosite.rb, line 411 def pdb_xref unless @data['3D'] @data['3D'] = fetch('3D').split(/; */) end @data['3D'] end
DO Pointer to the documentation file (1 per entry)
DO PDOCnnnnn;
Returns
# File lib/bio/db/prosite.rb, line 424 def pdoc_xref @data['DO'] = fetch('DO').chomp(';') end
Returns
# File lib/bio/db/prosite.rb, line 205 def positive statistics['POSITIVE'] end
Returns
# File lib/bio/db/prosite.rb, line 210 def positive_hits positive.first end
Returns
# File lib/bio/db/prosite.rb, line 215 def positive_sequences positive.last end
# File lib/bio/db/prosite.rb, line 487 def re self.class.pa2re(self.pa) end
Returns
# File lib/bio/db/prosite.rb, line 175 def release statistics['RELEASE'] end
RU Rule (>=0 per entry)
RU Rule_Description. The rule is described in ordinary English and is free-format.
Returns
# File lib/bio/db/prosite.rb, line 125 def ru field_fetch('RU') end
Returns
# 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
Returns
# File lib/bio/db/prosite.rb, line 319 def skip_flag if comment['SKIP-FLAG'] == 'TRUE' return true end end
Returns
# File lib/bio/db/prosite.rb, line 180 def swissprot_release_number release.first end
Returns
# File lib/bio/db/prosite.rb, line 185 def swissprot_release_sequences release.last end
Returns
# 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
Returns
# File lib/bio/db/prosite.rb, line 190 def total statistics['TOTAL'] end
Returns
# File lib/bio/db/prosite.rb, line 195 def total_hits total.first end
Returns
# File lib/bio/db/prosite.rb, line 200 def total_sequences total.last end
Returns
# File lib/bio/db/prosite.rb, line 220 def unknown statistics['UNKNOWN'] end
Returns
# File lib/bio/db/prosite.rb, line 225 def unknown_hits unknown.first end
Returns
# File lib/bio/db/prosite.rb, line 230 def unknown_sequences unknown.last end