module Bio::Alignment::GAP
Bio::Alignment::GAP is a set of class methods for gap-related position translation.
Public Class Methods
Source
# File lib/bio/alignment.rb 2162 def gapped_pos(seq, pos, gap_regexp) 2163 olen = seq.gsub(gap_regexp, '').length 2164 pos = olen if pos >= olen 2165 pos = olen + pos if pos < 0 2166 2167 i = 0 2168 l = pos + 1 2169 while l > 0 and i < seq.length 2170 x = seq[i, l].gsub(gap_regexp, '').length 2171 i += l 2172 l -= x 2173 end 2174 i -= 1 if i > 0 2175 i 2176 end
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 2151 def ungapped_pos(seq, pos, gap_regexp) 2152 p = seq[0..pos].gsub(gap_regexp, '').length 2153 p -= 1 if p > 0 2154 p 2155 end
position with gaps are translated into the position without gaps.
- seq
-
sequence
- pos
-
position with gaps
- gap_regexp
-
regular expression to specify gaps