gc.pl

来自「ncbi源码」· PL 代码 · 共 95 行

#!/usr/local/bin/perl

# $Id: gc.pl,v 1000.0 2003/10/31 21:38:25 gouriano Exp $
#
# Author:  Josh Cherry
#
# calculate G+C+S content
# (from gbench)

use CGI;

$qs = <STDIN>;
$query = new CGI($qs);

#if a get info call...
if ($query->param('action') eq "info") {
    print '
   PluginInfo ::= {
      ver-major 0,
      ver-minor 0,
      ver-revision 0,
      ver-build-date "",
      class-name "gc.pl",
      menu-item "Test scripts/GC content in perl",
      tooltip "G+C+S content by a perl script ",
      commands algo {
        {
          command 3,
          args {
            {
              name "locs",
              desc "Locations to evaluate",
              data array {
                object {
                  docaddr "(nil)",
                  objaddr "(nil)",
                  subtype "Seq-loc"
                }
              }
            }
          }
        }
      }
    }
   '
} else {  # otherwise, run
    @locs = $query->param('locs');
    foreach $loc (@locs) {
        $seq = new CGI($loc);
        print($seq->param("short_title"), "\t",
              &gc_content($seq->param("seq")), "\n");
    }
}


sub gc_content {
    my $s = $_[0];
    my $count = 0;
    for ($i=0;  $i < length($s); $i++) {
        $c = substr($s, $i, 1);
        if ($c eq "G" || $c eq "C" || $c eq "S") {
            $count++;
        }
    }
    return $count / length($s);
}


# ===========================================================================
# $Log: gc.pl,v $
# Revision 1000.0  2003/10/31 21:38:25  gouriano
# PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.3
#
# Revision 1.3  2003/10/29 20:12:05  jcherry
# Reflect new spec for plugin args
#
# Revision 1.2  2003/10/07 13:47:03  dicuccio
# Renamed CPluginURL* to CPluginValue*
#
# Revision 1.1  2003/07/28 19:59:10  jcherry
# Initial version
#
# ===========================================================================


# 
#  ===========================================================================
#  PRODUCTION $Log: gc.pl,v $
#  PRODUCTION Revision 1000.0  2003/10/31 21:38:25  gouriano
#  PRODUCTION PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.3
#  PRODUCTION
#  ===========================================================================
#