view toolExample.pl @ 3:079f44f300da draft

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#!/usr/bin/perl -w

# usage : perl toolExample.pl <FASTA file> <output file>

open (IN, "<$ARGV[0]");
open (OUT, ">$ARGV[1]");
while (<IN>) {
    chop;
    if (m/^>/) {
        s/^>//;
        if ($. > 1) {
            print OUT sprintf("%.3f", $gc/$length) . "\n";
        }
        $gc = 0;
        $length = 0;
    } else {
        ++$gc while m/[gc]/ig;
        $length += length $_;
    }
}
print OUT sprintf("%.3f", $gc/$length) . "\n";
close( IN );
close( OUT );