in reply to Re^2: Filter and writing error log file
in thread Filter and writing error log file

To check that a string contains something other than A, C, T, or G, search for the offending character, so in your condition, use 
$seq !~ /[^ACTG]/

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Note that | is not needed in a character class (in fact, it matches literally, so avoid it if you don't want to match it).

لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ

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Re^4: Filter and writing error log file
by newtoperlprog (Sexton) on Jul 23, 2014 at 13:44 UTC

    Thanks for the suggestions. One question, why we have to use '^' to match rather than

    [ATGC]
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[d/l]
      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
[reply]

        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]
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Re^4: Filter and writing error log file
by newtoperlprog (Sexton) on Jul 23, 2014 at 15:20 UTC

    I have one loop related question. I have defined an array of alphabet from ("A" .. "Z") but after reading a long file the alphabets end and the program shows error of uninitialized values.

    My questions is how can I define an array of alphabets which can go to AA, BB, CC and ...so on when the "A" .. "Z" ends.

[reply]
      Alphabet stands for the whole series of letters. Use the word "letter" for a single character like "A" or "Z", please, not alphabet.

      Don't create an array. Just start with 

      my $letter = 'A';

      [download]

      In every iteration, do 

      $letter++;

      [download]

      and let the magic do all the work.

      لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ
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[d/l]
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      Thanks for explaining the '^' behaviour and loop through the letters.

      I have some more doubts and questions regarding one of my another programs which I have written but its very crude and i want some help in making in more robust.

      Is it ok to post it here and get some help.

      Thanks
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