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RE: [PBML] Up and learning

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  • 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 1 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
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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 2 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 3 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 4 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 5 of 7 , Mar 1, 2005
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              > vim + syntax coloring

              which proves again, THTOWTDI.
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