So I have written a script for perl (I do not have BioPerl) to parse a blast output using filters. Example, I only want to extract hits with alignment lengths, %id,etc greater than a cutoff point. I keep getting uninitialized pattern match and concatenation errors. I have tried using google and other posts on here to fix the error but I am now at my wits end because I've been at it for over 2 days with no success.
Any suggestions?
Any suggestions?