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  • Help with a simple script in PERL

    sounds like homework
    Last edited by codecatcher; 01-23-2015, 03:12 PM.

  • #2
    What does your first draft look like?

    Comment


    • #3
      It sounds easy. But I really have no idea about the score! How to calculate the score?
      Which one is the most important, and which one is the second, of your 3 limitations
      Last edited by Phoenix_ICE; 01-22-2015, 12:54 PM.

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      • #4
        Perl is not an acronym and therefore never capitalised. Show some working, or try your luck on stackoverflow.com.

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        • #5
          A quick starting point

          Here's a starting point for you. I copied the 23mer you provided 3 times with a slight modification to the first occurrence.

          === script.pl ======
          Code:
          #!/usr/bin/env perl
          use Data::Dumper;
          
          my $sequence = 'ACGATCTTTGCCCCGACGTGATCGAGGTTTTTTTTTTTTTTCAGAGACCGAGATACGATCCCCCGACGTGATCGAGGACGATCCCCCGACGTGATCGAGG';
          my @sequences = $sequence =~ /.{21}GG/g;
          print Dumper(\@sequences);
          
          __END__
          === output =======
          $ perl script.pl
          $VAR1 = [
          'TCTTTGCCCCGACGTGATCGAGG',
          'ACGATCCCCCGACGTGATCGAGG',
          'ACGATCCCCCGACGTGATCGAGG'
          ];
          Last edited by rdeborja; 01-23-2015, 05:19 AM.

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          • #6
            @rdeborj: Please enclose your code in [CODE_] code here [/_CODE]. Remove the underscores when you use the tags.

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            • #7
              Thanks rdeborja and GenoMax for the comments. I will try it out and see if I can get it working with that.
              Phoenix ICE I assume they are all equal parameters that need to be parsed if possible

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              • #8
                The above
                Code:
                /.{21}GG/g
                won't catch overlapping 23mers. Just keep that in mind. E.g.:
                Code:
                $sequence = 'ACGATCTTTGCCCCGACGTGATCGAGGTTTGGTTGGTTTTTTTTTCAGAGACCGAGATACGATCCCCCGACGTGATCGAGGACGATCCCCCGACGTGATCGAGG';

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