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
StrongConservationGroupsdocument for the origin of the table.
Public Instance Methods
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
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
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
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
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
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