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Re: [PBML] Up and learning

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  • merlyn@stonehenge.com
    ... fres4 ALSO, which of the various Perl IDE s do people like the most? GNU Emacs. -- Randal L. Schwartz - Stonehenge Consulting Services, Inc. - +1 503 777
    Message 1 of 7 , Feb 28, 2005
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      >>>>> "fres4" == fres4 <fres4@...> writes:

      fres4> ALSO, which of the various Perl IDE's do people like the most?

      GNU Emacs.

      --
      Randal L. Schwartz - Stonehenge Consulting Services, Inc. - +1 503 777 0095
      <merlyn@...> <URL:http://www.stonehenge.com/merlyn/>
      Perl/Unix/security consulting, Technical writing, Comedy, etc. etc.
      See PerlTraining.Stonehenge.com for onsite and open-enrollment Perl training!
    • Scot Robnett
      TextPad here... ... From: merlyn@stonehenge.com [mailto:merlyn@stonehenge.com] Sent: Monday, February 28, 2005 7:51 PM To: fres4@yahoo.com Cc:
      Message 2 of 7 , Mar 1, 2005
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        TextPad here...



        -----Original Message-----
        From: merlyn@... [mailto:merlyn@...]
        Sent: Monday, February 28, 2005 7:51 PM
        To: fres4@...
        Cc: perl-beginner@yahoogroups.com
        Subject: Re: [PBML] Up and learning



        >>>>> "fres4" == fres4 <fres4@...> writes:

        fres4> ALSO, which of the various Perl IDE's do people like the most?

        GNU Emacs.

        --
        Randal L. Schwartz - Stonehenge Consulting Services, Inc. - +1 503 777 0095
        <merlyn@...> <URL:http://www.stonehenge.com/merlyn/>
        Perl/Unix/security consulting, Technical writing, Comedy, etc. etc.
        See PerlTraining.Stonehenge.com for onsite and open-enrollment Perl
        training!


        Unsubscribing info is here:
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      • Dave Gray
        ... /s[0h].*?ll.*?v/i should get you started. Check out while loops, global regexes and backreferences (like $1). ... Whatever text editor you re used to is
        Message 3 of 7 , Mar 1, 2005
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          > I guess I will try looking at loops now to see how I can search for
          > motif sequences in a string? I have to somehow program something
          > that will look for the following variations; "S folowed by a zero or
          > an H, followed by anything, followed by two L's, and ends in V" I
          > guess that leaves these combos?
          >
          > s*ll**v
          > sh*ll****V

          /s[0h].*?ll.*?v/i should get you started. Check out while loops,
          global regexes and backreferences (like $1).

          > ALSO, which of the various Perl IDE's do people like the most?

          Whatever text editor you're used to is fine.

          > #!/usr/bin/perl -w
          > use strict;

          Always a good start.

          > # Read a DNA sequence from ecoli.1 and manipulate it to find
          > # it's revers compliment.
          >
          > #First breakdown data and put into an array.
          > #Put ecoli.1 into this scalar
          > $dnafile = "ecoli.1";
          >
          > # Remove the line breaks from the ecoli.1 file
          > chomp $dnafile;

          This is not what you want... It's chomping the filename you just set
          the variable to, which does nothing. See chomp use below.

          > #open the file, or exit
          > unless ( open(DNAFILE, $dnafile) )
          > {
          > print "Cannot open file \"$dnafile\"\n\n";
          > exit;
          > }

          open(DNAFILE, $dnafile) or die "cannot open file [$dnafile]: $!\n";

          > # Read the DNA letters from the file, and store it
          > # into the array variable @DNA
          > @DNA = <DNAFILE>;

          # chomp each array element
          chomp(@DNA = <DNAFILE>);

          > # Close the file
          > close DNAFILE;
          >
          > # Put the whole thing into one line
          > $DNA = join( '', @DNA);
          >
          > # Remove whitespace
          > $DNA =~ s/\s//g;
          > print "The DNA strand:\n";
          > print "$DNA\n";
          > print "Now the reverse compliment:\n";
          >
          > #Now I need to find the reverse compliment.
          > $revcom = reverse $DNA;
          >
          > # now I need to substitute
          > $revcom =~ tr/ACGTacgt/TGCAtgca/;
          >
          > #store in an array named @REV
          > #@REV = $revcom;

          # split on nothing to get each letter in its own element
          @REV = split //, $revcom;
        • Rick Apichairuk
          vim + syntax coloring
          Message 4 of 7 , Mar 1, 2005
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            vim + syntax coloring


            On Tue, 1 Mar 2005 10:28:24 -0600, Scot Robnett <scot@...> wrote:
            >
            > TextPad here...
            >
            >
            > -----Original Message-----
            > From: merlyn@... [mailto:merlyn@...]
            > Sent: Monday, February 28, 2005 7:51 PM
            > To: fres4@...
            > Cc: perl-beginner@yahoogroups.com
            > Subject: Re: [PBML] Up and learning
            >
            > >>>>> "fres4" == fres4 <fres4@...> writes:
            >
            > fres4> ALSO, which of the various Perl IDE's do people like the most?
            >
            > GNU Emacs.
            >
            > --
            > Randal L. Schwartz - Stonehenge Consulting Services, Inc. - +1 503 777 0095
            > <merlyn@...> <URL:http://www.stonehenge.com/merlyn/>
            > Perl/Unix/security consulting, Technical writing, Comedy, etc. etc.
            > See PerlTraining.Stonehenge.com for onsite and open-enrollment Perl
            > training!
            >
            > Unsubscribing info is here:
            > http://help.yahoo.com/help/us/groups/groups-32.html
            > Yahoo! Groups Links
            >
            > --
            > No virus found in this incoming message.
            > Checked by AVG Anti-Virus.
            > Version: 7.0.300 / Virus Database: 266.5.1 - Release Date: 2/27/2005
            >
            > --
            > No virus found in this outgoing message.
            > Checked by AVG Anti-Virus.
            > Version: 7.0.300 / Virus Database: 266.5.1 - Release Date: 2/27/2005
            >
            >
            > Unsubscribing info is here: http://help.yahoo.com/help/us/groups/groups-32.html
            > Yahoo! Groups Links
            >
            >
            >
            >
            >
          • J.E. Cripps
            ... glad to see you again! ... any Linux/FreeBSD command line account, GNU emacs (struggling with this a bit myself) I do know there s vs emacs available for
            Message 5 of 7 , Mar 1, 2005
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              > Thanks to everyone that suggested the Perl resources that are out
              > there.

              glad to see you again!

              > ALSO, which of the various Perl IDE's do people like the most?

              any Linux/FreeBSD command line account, GNU emacs (struggling
              with this a bit myself) I do know there's vs emacs available
              for other OSes, and in fact have installed in several times
              from the CD that came with one of the SAMS books.
            • J.E. Cripps
              ... which proves again, THTOWTDI.
              Message 6 of 7 , Mar 1, 2005
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                > vim + syntax coloring

                which proves again, THTOWTDI.
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