I can't help but thinking your inner loop is unnecessary. You're scanning through your list of mappings until you find the one for the current line. But you're missing the beauty of hashes - direct access to the value you want..

Consider this:

  while (<INPUT2>) {
    $_ =~ s/[\r\n]+\z//s; # I don't use chomp, sorry

    my ( $bioC, $contig_id, $pip ) = split( "\t", $_ );
    my $origin = $origins{$contig_id};
    print RESULTS "$bioC\t$origin\t$pip\n";
  }

[download]

Update: you could also DIE with an error message in the event that the file contained a code that wasn't in your mapping table:

  my $origin = $origins{$contig_id};
  if ( ! defined( $origin ) ) {
    die( "No mapping for \"$contig_id\" found in origins table" );
  }

[download]

In reply to Re: Make my script faster and more efficient by monarch
in thread Make my script faster and more efficient by sesemin

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!
  • 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, details, 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, summary, 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.