Re^3: 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)//

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

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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?	[reply]
Re^5: fuzzy match: trim sequences outside of the forward and reverse primer set. by grizzley (Chaplain) on Nov 12, 2012 at 10:03 UTC
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 } }` [download]	[reply] [d/l]