Beefy Boxes and Bandwidth Generously Provided by pair Networks
Perl Monk, Perl Meditation

Comment on

( #3333=superdoc: print w/replies, xml ) Need Help??

In the code I posted above, everything between the text "Here's exactly what I used to test your code and data:" and the [download] link is part of the one script. I suspect you tried to separate that into two files (script and data). Also, on this site, when code lines don't fit on one line they wrap to the next line - this is indicated by the addition of a plus (+) sign (which is coloured red by default). You don't want these additional plusses in your code; so, use the [download] link to get a plain text version. Save this plain text to a file - the usual filename extension for Perl scripts is ".pl" - the filename I used was (the following assumes you've used the same name). You can now run


and, hopefully, you'll now get the expected output (displayed on the screen - not in a file).

Lines in Perl code that start with a hash (#) sign are comments: they are ignored by Perl when the script is run. [Exception: if the first line begins with #! it's not actually a comment - I think you can safely ignore that for now - see perlrun - #! and quoting on non-Unix systems for more information.] Adding a # to the start of a line of code is referred to as commenting out that line of code. Where I earlier referred to "removing the debug print statements", I actually commented them out, e.g.

#say qq(DEBUG: Line = "$line");

I also commented out all the lines relating to external files:

#my $file = ""; ... #open my $in, "<", "$file"; #open my $out, ">", "output.txt";

and also changed these three lines:

say $out "Coordinate No of Strains AA Change"; ... while ( my $line = <$in> ) { ... printf $out "%-12.12s %-15.15s %s\n", $SNP, $count, $change;


say "Coordinate No of Strains AA Change"; ... while ( my $line = <DATA> ) { ... printf "%-12.12s %-15.15s %s\n", $SNP, $count, $change;

Removing $out from the say and printf statements means output now goes to the screen instead of a file (that's an oversimplification but will suffice for this discussion). Changing $in to DATA means the input is now everything following __DATA__ - see perldata (under Special Literals) for more details about this. Assuming that you did put everything after __DATA__ in a separate file, all of this explains "I get "Coordinates No of Strains AA Change" printed in my command line, and no output file created.".

That should get us back to: "Try running this. Assuming it works, try changing the data to something you know will generate the warnings - keeping the data to an absolute minimum.".

Going all the way back to your original posting, you have an input file called and a script called Script.txt. I don't have a Perl running under MSWin to test this; however, I expect MSWin will interpret your input file as a Perl script and your actual Perl script as a plain text file. It's possible one (or both) of these may be related to your original problem. Try renaming your input file to BSAC.txt and your Perl script to and see if you get better results.

I'd also recommend you read perlintro (a brief introduction and overview of Perl) and bookmark perl (which has links to all the Perl documentation).

-- Ken

In reply to Re^7: Parsing problem by kcott
in thread Parsing problem by MB123

Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post; it's "PerlMonks-approved HTML":

  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.
  • Log In?

    What's my password?
    Create A New User
    and the fog begins to lift...

    How do I use this? | Other CB clients
    Other Users?
    Others musing on the Monastery: (10)
    As of 2018-03-17 11:19 GMT
    Find Nodes?
      Voting Booth?
      When I think of a mole I think of:

      Results (223 votes). Check out past polls.