A short script for function annotation table statistics!

stat_func.pl

#=============================================================================
#     FileName: stat_func.pl
#         Desc:
#       Author: tanhao
#        Email: tanhao2013@gmail.com
#     HomePage: http://buttonwood.github.io
#      Version: 0.0.1
#   LastChange: 2014-05-13 10:06:14
#      History:
#=============================================================================
use Data::Dumper;

#my (%cog, %kegg, %swiss, %nr, %go);

use Getopt::Long;
my ($c,$s,$n,$k,$g,$help);
GetOptions(
    "cog:s"         => \$c,
    "kegg:s"        => \$k,
    "swiss:s"       => \$s,
    "nr:s"          => \$n,
    "go:s"          => \$g,
    "help:s"        => \$help
);

if(defined($help) || (!defined($c) && !defined($k) && !defined($s) && !defined($n) && !defined($g))){
	die("Usage:\n\tperl $0 -cog cog.best -kegg kegg.best -swiss swiss.best ... \n");
}

my %hash;
&hash_id($c, \%hash, 15, "COG") if($c);
&hash_id($k, \%hash, 15, "KEGG") if($k);
&hash_id($s, \%hash, 5, "SWISS") if($s);
&hash_id($n, \%hash, 15,  "NR") if($n);
&hash_id($g, \%hash, 15,  "GO") if($g);
#print Dumper(\%hash);

my @genes =  map { $_->[0] }
             sort{ $a->[1] <=> $b->[1] }
             map { [$_, (split /\_/)[1]] } keys(%hash);

my @func = ("COG","KEGG","SWISS","NR","GO");
foreach my $x (@genes){
	print $x;
    foreach my $y (@func){
        if(exists $hash{$x}{$y}){
            print "\t",$hash{$x}{$y};
        }else{
            print "\t*";
        }
    }
    print "\n";
}

sub hash_id{
    my ($file, $h_r, $clm, $tag) = @_;
    open(IN,"<$file")or die("$file wrong! Plead check\n$!");
    while(<IN>){
        next if (/Query\_id/);
        my @t = split;
        if($clm == 5){
        	my @a = split(/\|/, $t[4]);
        	$h_r->{$t[0]}->{$tag} = $a[1];
        }else{
            $h_r->{$t[0]}->{$tag} = $t[14];
        }
    }
    close IN;
}

########### Float like a butterfly! Stand like a buttonwood! ###########