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Re^7: Filter and writing error log file

by choroba (Bishop)
on Jul 24, 2014 at 13:16 UTC ( #1094911=note: print w/replies, xml ) Need Help??

in reply to Re^6: Filter and writing error log file
in thread Filter and writing error log file

You regexp seems incorrect. [GCA{4}T{4}] is a character class that matches any character of the ones listed, i.e. it's the same as [}4{GCAT]. Also, to make sure you match at a particular position, you should anchor your regex by starting it with ^ to match the beginning of the string.
لսႽ ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ

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Re^8: Filter and writing error log file
by newtoperlprog (Sexton) on Jul 24, 2014 at 14:20 UTC

    Thanks Choroba for your reply.

    So if I understood correctly, I should modify something like this:

    if( ($seq =~/^\w{2}A\w{6}T\w{2}[ACT]\w[^A{4}|^T{4}][GC]{4}[AT]/) && ( $seq !~ /[GC]{9}/) && ( $gcper >= 30 && $gcper <= 52) ) { Do something....;}

    Thanks again

      No. [^A{4}|^T{4}] is equivalent to [^^AT}|{4], i.e. it matches anything except ^, A, T, verbar, curlies and four.
      لսႽ ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ

        Dear Choroba, thank you for your reply.

        I am getting a little bit confused here. As '^' matches the beginning of the character and in my filter criteria position 15-19 should have atleast 3 A's or 3 T's not necessarily starts with A or T but it could be something like like:

        15-AATAG-19 15-ATAAC-19 15-TTTAC-19 15-GCAAA-19 15-GATAA-19

        Sorry for so many posts, but I really want to understand.


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