Beefy Boxes and Bandwidth Generously Provided by pair Networks
"be consistent"

Comment on

( #3333=superdoc: print w/replies, xml ) Need Help??
Dear monks, My question is related to file parsing within while loops. I have a large file containing many individual files all in the same format.
I don't think so. I suppose you have a large file containing info related to many individual files.
This is how the file looks: How can I extract all the info between ORIGIN and // for each record??
# extract of file:  

FEATURES             Location/Qualifiers    
                     /note="blah blah"   
COUNT                200
        1 lots of nice info
       61 lots of nice info
      121 lots of nice info
If you can rely on this format, here's how I'd do it:
#!/usr/bin/perl -ln use strict; use warnings; if ($_ eq 'ORIGIN') { local $/='//'; print <>; }
#!/usr/bin/perl -ln use strict; use warnings; print if $_ eq 'ORIGIN' .. $_ eq '//' __END__
Of course these are intended to be as minimal examples: adapt the techniques shown here to your needs.
This is my code so far:
open (FILE, $ARGV[0]) or die "unable to open FILE\n";
Why not using <> in the first place? Also, you'd better:
  • use lexical FHs,
  • use the three args form of open(),
  • put relevant info in the error message (i.e. at least include $!).
Note: I skipped the rest

In reply to Re: Genbank file parsing by blazar
in thread Genbank file parsing by Anonymous Monk

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 all is quiet...

    How do I use this? | Other CB clients
    Other Users?
    Others chanting in the Monastery: (7)
    As of 2017-10-18 19:13 GMT
    Find Nodes?
      Voting Booth?
      My fridge is mostly full of:

      Results (250 votes). Check out past polls.