Beefy Boxes and Bandwidth Generously Provided by pair Networks
Perl-Sensitive Sunglasses
 
PerlMonks  

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 ( #1003400=note: print w/ replies, xml ) Need Help??


in reply to Re^4: 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.

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 } }


Comment on Re^5: fuzzy match: trim sequences outside of the forward and reverse primer set.
Download Code

Log In?
Username:
Password:

What's my password?
Create A New User
Node Status?
node history
Node Type: note [id://1003400]
help
Chatterbox?
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others wandering the Monastery: (19)
As of 2014-07-31 14:25 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?

    My favorite superfluous repetitious redundant duplicative phrase is:









    Results (249 votes), past polls