Beefy Boxes and Bandwidth Generously Provided by pair Networks
Keep It Simple, Stupid
 
PerlMonks  

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 want to extract certain features from each file which mainly is easy. My problem is when I need to extract everything between two markers in the file. I am struggling to get all the nice info between ORIGIN and // in each file.

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 ORIGIN 1 lots of nice info 61 lots of nice info 121 lots of nice info //
This is my code so far:
open (FILE, $ARGV[0]) or die "unable to open FILE\n"; + my ($note, $info, $features,$count); my ($c,$d); my @seq; my $in_seq = 0; my $seq = ''; + while (<FILE>) { my $line = $_; if ($line =~ /(FEATURES)\s+(\w+)/) { $features = $2; } if ($line =~ /(COUNT)\s+(\d+)/) { $count = $2; } if ($line =~ /^ORIGIN/) { # print "$line\n"; push @seq, "$line\n"; } until ($line =~ /\/\/) {}; } + print "@seq\n";

Retitled by davido.


In reply to Genbank file parsing by Anonymous Monk

Title:
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!
  • 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
  • Outside of code tags, you may need to use entities for some characters:
            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?
    Username:
    Password:

    What's my password?
    Create A New User
    Chatterbox?
    and the web crawler heard nothing...

    How do I use this? | Other CB clients
    Other Users?
    Others cooling their heels in the Monastery: (8)
    As of 2014-12-25 04:57 GMT
    Sections?
    Information?
    Find Nodes?
    Leftovers?
      Voting Booth?

      Is guessing a good strategy for surviving in the IT business?





      Results (159 votes), past polls