Fasta.stat.gc.ratio.pl

#! perl

use warnings;
use strict;
use Getopt::Long;
use Bio::SeqIO;
use List::Util qw(sum);

my ($e);

GetOptions(
           'e' => \$e
          );
my $f = shift or die "perl $0 fa\n";
my @b = (0,0,0,0,0);
my $oa = 0;
print STDERR "id\tA\tT\tC\tG\tN\tGC\tother\n";
my $s_obj = Bio::SeqIO -> new(-file => $f,-format => "fasta" );
while(my $s_io = $s_obj->next_seq){
    my $id = $s_io -> display_id;
    my $len = $s_io -> length;
    my $seq = $s_io -> seq;
    my @a = (0,0,0,0,0);
    $a[0] += ($seq =~tr/Aa//);
    $a[1] += ($seq =~tr/Tt//);
    $a[2] += ($seq =~tr/Gg//);
    $a[3] += ($seq =~tr/Cc//);
    $a[4] += ($seq =~tr/Nn//);
    my $total = sum (@a);
    for(my$i = 0; $i < @a;$i += 1){
        $b[$i] += $a[$i];
        $a[$i] = ($a[$i]/$total) * 100;
        $a[$i] = sprintf('%.04f',$a[$i]);
    }
    my $ot = $len - $total;
    $oa += $ot;
    if ($e) {
        my $gc = $a[2]+$a[3];
        print "$id\t$a[0]\t$a[1]\t$a[2]\t$a[3]\t$a[4]\t$gc\t$ot\n";
    }
}
if(!$e){
    my $t = sum(@b);
    for(my$i = 0; $i < @b;$i += 1){
        $b[$i] = ($b[$i]/$t)*100;
        $b[$i] = sprintf('%.04f',$b[$i]);
    }
    my $gc = $b[2]+$b[3];
    print "All\t$b[0]\t$b[1]\t$b[2]\t$b[3]\t$b[4]\t".$gc."\t$oa\n";
}