Module Bio::Alignment::GAP
In: lib/bio/alignment.rb

Bio::Alignment::GAP is a set of class methods for gap-related position translation.

Methods

gapped_pos   ungapped_pos  

Public Instance methods

gapped_pos(seq, pos, gap_regexp) 
 position without gaps are translated into the position with gaps.
seq:sequence
pos:position with gaps
gap_regexp:regular expression to specify gaps

[Source]

      # File lib/bio/alignment.rb, line 2168
2168:       def gapped_pos(seq, pos, gap_regexp)
2169:         olen = seq.gsub(gap_regexp, '').length
2170:         pos = olen if pos >= olen
2171:         pos = olen + pos if pos < 0
2172:         
2173:         i = 0
2174:         l = pos + 1
2175:         while l > 0 and i < seq.length
2176:           x = seq[i, l].gsub(gap_regexp, '').length
2177:           i += l
2178:           l -= x
2179:         end
2180:         i -= 1 if i > 0
2181:         i
2182:       end
ungapped_pos(seq, pos, gap_regexp) 
 position with gaps are translated into the position without gaps.
seq:sequence
pos:position with gaps
gap_regexp:regular expression to specify gaps

[Source]

      # File lib/bio/alignment.rb, line 2157
2157:       def ungapped_pos(seq, pos, gap_regexp)
2158:         p = seq[0..pos].gsub(gap_regexp, '').length
2159:         p -= 1 if p > 0
2160:         p
2161:       end

[Validate]