class Bio::PROSITE

Constants

DELIMITER: Delimiter
RS: Delimiter
TAGSIZE: Bio::DB API

Public Class Methods

new(entry) click to toggle source

Calls superclass method Bio::EMBLDB::new

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

pa2re(pattern) click to toggle source

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
467 def self.pa2re(pattern)
468   pattern.gsub!(/\s/, '')     # remove white spaces
469   pattern.sub!(/\.$/, '')     # (1) remove trailing '.'
470   pattern.sub!(/^</, '^')     # (2) restricted to the N-terminal : `<'
471   pattern.sub!(/>$/, '$')     # (2) restricted to the C-terminal : `>'
472   pattern.gsub!(/\{(\w+)\}/) { |m|
473     '[^' + $1 + ']'           # (3) not accepted at a given position : '{}'
474   }
475   pattern.gsub!(/\(([\d,]+)\)/) { |m|
476     '{' + $1 + '}'            # (4) repetition of an element : (n), (n,m)
477   }
478   pattern.tr!('x', '.')       # (5) any amino acid is accepted : 'x'
479   pattern.tr!('-', '')        # (6) each element is separated by a '-'
480   Regexp.new(pattern, Regexp::IGNORECASE)
481 end

Public Instance Methods

ac() click to toggle source

AC Accession number (1 per entry)

AC   PSnnnnn;

Returns

   # File lib/bio/db/prosite.rb
57 def ac
58   unless @data['AC']
59     @data['AC'] = fetch('AC').chomp(';')
60   end
61   @data['AC']
62 end

Also aliased as: entry_id

cc() click to toggle source

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
273 def cc
274   unless @data['CC']
275     hash = {}                 # temporal hash
276     fetch('CC').scan(%r{/(\S+)=([^;]+);}).each do |k, v|
277       hash[k] = v
278     end
279     @data['CC'] = hash
280   end
281   @data['CC']
282 end

Also aliased as: comment

comment()

Alias for: cc

date()

Alias for: dt

de() click to toggle source

DE Short description (1 per entry)

DE   Description.

Returns

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

Also aliased as: definition

definition()

Alias for: de

division() click to toggle source

Returns

   # File lib/bio/db/prosite.rb
44 def division
45   unless @data['TYPE']
46     name
47   end
48   @data['TYPE']
49 end

dr() click to toggle source

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
349 def dr
350   unless @data['DR']
351     hash = {}                 # temporal hash
352     if fetch('DR')
353       fetch('DR').scan(/(\w+)\s*, (\w+)\s*, (.);/).each do |a, e, c|
354         hash[a] = [e, c]      # SWISS-PROT : accession, entry, true/false
355       end
356     end
357     @data['DR'] = hash
358   end
359   @data['DR']
360 end

Also aliased as: sp_xref

dt() click to toggle source

DT Date (1 per entry)

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

Returns

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

Also aliased as: date

entry_id()

Alias for: ac

false_neg() click to toggle source

Returns

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

Also aliased as: false_negative_hits

false_negative_hits()

Alias for: false_neg

false_pos() click to toggle source

Returns

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

false_positive_hits() click to toggle source

Returns

    # File lib/bio/db/prosite.rb
240 def false_positive_hits
241   false_pos.first
242 end

false_positive_sequences() click to toggle source

Returns

    # File lib/bio/db/prosite.rb
245 def false_positive_sequences
246   false_pos.last
247 end

list_falsenegative(by_name = nil) click to toggle source

Returns

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

list_falsepositive(by_name = nil) click to toggle source

Returns

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

list_potentialhit(by_name = nil) click to toggle source

Returns

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

list_truepositive(by_name = nil) click to toggle source

Returns

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

list_unknown(by_name = nil) click to toggle source

Returns

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

list_xref(flag, by_name = nil) click to toggle source

Returns

    # File lib/bio/db/prosite.rb
365 def list_xref(flag, by_name = nil)
366   ary = []
367   sp_xref.each do |sp_acc, value|
368     if value[1] == flag
369       if by_name
370         sp_name = value[0]
371         ary.push(sp_name)
372       else
373         ary.push(sp_acc)
374       end
375     end
376   end
377   return ary
378 end

ma() click to toggle source

MA Matrix/profile (>=0 per entry)

see - ma2re method

Returns

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

Also aliased as: profile

ma2re(matrix) click to toggle source

prosite profile to regular expression

prosite/profile.txt:

Returns

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

max_repeat() click to toggle source

Returns

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

name() click to toggle source

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
36 def name
37   unless @data['ID']
38     @data['ID'], @data['TYPE'] = fetch('ID').chomp('.').split('; ')
39   end
40   @data['ID']
41 end

nr() click to toggle source

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
150 def nr
151   unless @data['NR']
152     hash = {}                 # temporal hash
153     fetch('NR').scan(%r{/(\S+)=([^;]+);}).each do |k, v|
154       if v =~ /^(\d+)\((\d+)\)$/
155         hits = $1.to_i                # the number of hits
156         seqs = $2.to_i                # the number of sequences
157         v = [hits, seqs]
158       elsif v =~ /([\d\.]+),(\d+)/
159         sprel = $1                    # the number of SWISS-PROT release
160         spseq = $2.to_i               # the number of SWISS-PROT sequences
161         v = [sprel, spseq]
162       else
163         v = v.to_i
164       end
165       hash[k] = v
166     end
167     @data['NR'] = hash
168   end
169   @data['NR']
170 end

Also aliased as: statistics

pa() click to toggle source

PA Pattern (>=0 per entry)

see - pa2re method

Returns

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

Also aliased as: pattern

pa2re(pattern) click to toggle source

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

partial() click to toggle source

Returns

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

pattern()

Alias for: pa

pdb_xref() click to toggle source

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

3D   name; [name2;...]

Returns

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

pdoc_xref() click to toggle source

DO Pointer to the documentation file (1 per entry)

DO   PDOCnnnnn;

Returns

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

positive() click to toggle source

Returns

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

positive_hits() click to toggle source

Returns

    # File lib/bio/db/prosite.rb
210 def positive_hits
211   positive.first
212 end

positive_sequences() click to toggle source

Returns

    # File lib/bio/db/prosite.rb
215 def positive_sequences
216   positive.last
217 end

profile()

Alias for: ma

re() click to toggle source

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

release() click to toggle source

Returns

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

ru() click to toggle source

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
125 def ru
126   field_fetch('RU')
127 end

Also aliased as: rule

rule()

Alias for: ru

site() click to toggle source

Returns

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

skip_flag() click to toggle source

Returns

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

sp_xref()

Alias for: dr

statistics()

Alias for: nr

swissprot_release_number() click to toggle source

Returns

    # File lib/bio/db/prosite.rb
180 def swissprot_release_number
181   release.first
182 end

swissprot_release_sequences() click to toggle source

Returns

    # File lib/bio/db/prosite.rb
185 def swissprot_release_sequences
186   release.last
187 end

taxon_range(expand = nil) click to toggle source

Returns

    # File lib/bio/db/prosite.rb
287 def taxon_range(expand = nil)
288   range = comment['TAXO-RANGE']
289   if range and expand
290     expand = []
291     range.scan(/./) do |x|
292       case x
293       when 'A'; expand.push('archaebacteria')
294       when 'B'; expand.push('bacteriophages')
295       when 'E'; expand.push('eukaryotes')
296       when 'P'; expand.push('prokaryotes')
297       when 'V'; expand.push('eukaryotic viruses')
298       end
299     end
300     range = expand
301   end
302   return range
303 end

total() click to toggle source

Returns

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

total_hits() click to toggle source

Returns

    # File lib/bio/db/prosite.rb
195 def total_hits
196   total.first
197 end

total_sequences() click to toggle source

Returns

    # File lib/bio/db/prosite.rb
200 def total_sequences
201   total.last
202 end

unknown() click to toggle source

Returns

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

unknown_hits() click to toggle source

Returns

    # File lib/bio/db/prosite.rb
225 def unknown_hits
226   unknown.first
227 end

unknown_sequences() click to toggle source

Returns

    # File lib/bio/db/prosite.rb
230 def unknown_sequences
231   unknown.last
232 end