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Re^3: fuzzy match: trim sequences outside of the forward and reverse primer set.

by grizzley (Chaplain)
on Nov 09, 2012 at 07:46 UTC ( #1003076=note: print w/replies, xml ) Need Help??


in reply to Re^2: fuzzy match: trim sequences outside of the forward and reverse primer set.
in thread fuzzy match: trim sequences outside of the forward and reverse primer set.

In that case there are at least two possibilities:
    1. If Bio::Perl can do match with wildcards, you can do fuzzy match 'agct.*'
    2. Do fuzzy match with Bio::Perl and use returned matched string to do perfect match or better substitute: s/.*?(?=$returnedstring)//
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Re^4: fuzzy match: trim sequences outside of the forward and reverse primer set.
by lrl1997 (Novice) on Nov 09, 2012 at 22:43 UTC

    I don't think it returns the fuzzy matched string, but the sequence containing the string. therefore, I have no way to know what was the string found. Any more suggestions?

      Not much. I though perl package will behave in perl-ish way returning matched part of the string as well as storing somewhere "before-string" and "after-string". What remains is to implement the fuzzy-matching yourself.

      If this fuzzy matching would be defined by number of differences between strings then maybe Text::Levenshtein is of use? I mean iterating in simple

      for (0..length($str)-$len_of_match) { if(Text::Levenshtein::distance(substr($str, $_, $len_of_match), matc +hstring) <= $differences_limit) { $found = true; last } }

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