in reply to Re^4: Filter and writing error log file
in thread Filter and writing error log file

See perlre. The carret negates the class, so the regular expression matches non-ACTG characters, but I used !~ to negate that. It's like the difference between

"The sequence doesn't contain invalid characters"

and

"The sequence contains valid characters"

These two are not equivalent, as the second lacks the work "only".
لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ
  • Comment on Re^5: Filter and writing error log file

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Re^6: Filter and writing error log file
by newtoperlprog (Sexton) on Jul 23, 2014 at 19:55 UTC

    Thanks Choroba for the suggestions.

    I am checking a rule against a string of sequence (19 letter longs) in a while loop and formed this filter

    So basically, I want to match A at position 3, T at position 10, [ACT] at position 13, [AT] at position 19 and atleast 3 A's or 3 T's from position 15-19 and the $gcper should be in between 30-52.

    if (($seq =~/\w{2}A\w{6}T\w{2}[ACT]\w[GCA{4}T{4}]{4}[AT]/) 
   && ($gcper >= 30 && $gcper <= 52))
     {
    print "$seq\t$seqpos\t$gcper\n";
     }

    [download]

    I checked the result and it seemed to work, i need help in wheather this code writing is ok or i can improve it better.

    Another thing which I want to check is: no GC stretch more than 9 letters long, but I don't know how I can insert that check in the above code. 

    GCAGGTGGATCTATTTCAT    3201-3220    42.11
TAAGAGGTGTTATTTGGAA    3268-3287    31.58
ATACGATGCTTCAAGAGAA    3346-3365    36.84
CAAGCTCATCATACTGGCT    1201-1220    47.37
GGTACTGACTTTGCTTGCT    2923-2942    47.37
CGTAGTGTTAAGTTATAGT    3003-3022    31.58
GTATGGGTAGGGTAAATCA    3248-3267    42.11
CCTGCTGTGATACGATGCT    3337-3356    52.63
CCTGCGCGCGCGCGATGCT    3300-3318    50.63

    [download]
[reply]
[d/l]
[select]
      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
[reply]
[d/l]
[select]

        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....;}

        [download]

        Thanks again

[reply]
[d/l]

      Dear All, I tried to incorporate the condition: no GC stretch more than 9 letters long, to the below code

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

      [download]

      I was hoping to get some help regarding the regular expression and better writing of this code.

      Thank you
[reply]
[d/l]

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