module Bio::Alignment::SiteMethods

Bio::Alignment::SiteMethods is a set of methods for Bio::Alignment::Site. It can also be used for extending an array of single-letter strings.

Constants

IUPAC_NUC

IUPAC nucleotide groups. Internal use only.

StrongConservationGroups

Table of strongly conserved amino-acid groups.

The value of the tables are taken from BioPerl (Bio/SimpleAlign.pm in BioPerl 1.0), and the BioPerl's document says that it is taken from Clustalw documentation and

These are all the positively scoring groups that occur in the 
Gonnet Pam250 matrix. The strong and weak groups are 
defined as strong score >0.5 and weak score =<0.5 respectively.
WeakConservationGroups

Table of weakly conserved amino-acid groups.

Please refer StrongConservationGroups document for the origin of the table.

Public Instance Methods

consensus_iupac() click to toggle source

Returns an IUPAC consensus base for the site. If consensus is found, eturns a single-letter string. If not, returns nil.

    # File lib/bio/alignment.rb
218 def consensus_iupac
219   a = self.collect { |x| x.downcase }.sort.uniq
220   if a.size == 1 then
221     case a[0]
222     when 'a', 'c', 'g', 't'
223       a[0]
224     when 'u'
225       't'
226     else
227       IUPAC_NUC.find { |x| a[0] == x[0] } ? a[0] : nil
228     end
229   elsif r = IUPAC_NUC.find { |x| (a - x).size <= 0 } then
230     r[0]
231   else
232     nil
233   end
234 end
consensus_string(threshold = 1.0) click to toggle source

Returns consensus character of the site. If consensus is found, eturns a single-letter string. If not, returns nil.

    # File lib/bio/alignment.rb
181 def consensus_string(threshold = 1.0)
182   return nil if self.size <= 0
183   return self[0] if self.sort.uniq.size == 1
184   h = Hash.new(0)
185   self.each { |x| h[x] += 1 }
186   total = self.size
187   b = h.to_a.sort do |x,y|
188     z = (y[1] <=> x[1])
189     z = (self.index(x[0]) <=> self.index(y[0])) if z == 0
190     z
191   end
192   if total * threshold <= b[0][1] then
193     b[0][0]
194   else
195     nil
196   end
197 end
has_gap?() click to toggle source

If there are gaps, returns true. Otherwise, returns false.

    # File lib/bio/alignment.rb
164 def has_gap?
165   (find { |x| is_gap?(x) }) ? true : false
166 end
match_line_amino(opt = {}) click to toggle source

Returns the match-line character for the site. This is amino-acid version.

    # File lib/bio/alignment.rb
258 def match_line_amino(opt = {})
259   # opt[:match_line_char]   ==> 100% equal    default: '*'
260   # opt[:strong_match_char] ==> strong match  default: ':'
261   # opt[:weak_match_char]   ==> weak match    default: '.'
262   # opt[:mismatch_char]     ==> mismatch      default: ' '
263   mlc = (opt[:match_line_char]   or '*')
264   smc = (opt[:strong_match_char] or ':')
265   wmc = (opt[:weak_match_char]   or '.')
266   mmc = (opt[:mismatch_char]     or ' ')
267   a = self.collect { |c| c.upcase }.sort.uniq
268   a.extend(SiteMethods)
269   if a.has_gap? then
270     mmc
271   elsif a.size == 1 then
272     mlc
273   elsif StrongConservationGroups.find { |x| (a - x).empty? } then
274     smc
275   elsif WeakConservationGroups.find { |x| (a - x).empty? } then
276     wmc
277   else
278     mmc
279   end
280 end
match_line_nuc(opt = {}) click to toggle source

Returns the match-line character for the site. This is nucleic-acid version.

    # File lib/bio/alignment.rb
284 def match_line_nuc(opt = {})
285   # opt[:match_line_char]   ==> 100% equal    default: '*'
286   # opt[:mismatch_char]     ==> mismatch      default: ' '
287   mlc = (opt[:match_line_char]   or '*')
288   mmc = (opt[:mismatch_char]     or ' ')
289   a = self.collect { |c| c.upcase }.sort.uniq
290   a.extend(SiteMethods)
291   if a.has_gap? then
292     mmc
293   elsif a.size == 1 then
294     mlc
295   else
296     mmc
297   end
298 end
remove_gaps!() click to toggle source

Removes gaps in the site. (destructive method)

    # File lib/bio/alignment.rb
169 def remove_gaps!
170   flag = nil
171   self.collect! do |x|
172     if is_gap?(x) then flag = self; nil; else x; end
173   end
174   self.compact!
175   flag
176 end