#!/usr/bin/env /home/mkubal/public_html/FIGdisk/env/cee/bin/perl

BEGIN {
    @INC = qw(
              /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib
              /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib/PPO
              /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib/FigKernelPackages
              /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib/WebApplication
              /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib/FortyEight
              /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib/SeedViewer
              /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib/Flower
              /home/mkubal/public_html/FIGdisk/dist/dev/cee/lib
              /home/mkubal/public_html/FIGdisk/dist/dev/cee/lib/FigKernelPackages
              /home/mkubal/public_html/FIGdisk/env/cee/lib/perl5/5.8.7/i686-linux
              /home/mkubal/public_html/FIGdisk/env/cee/lib/perl5/5.8.7
              /home/mkubal/public_html/FIGdisk/env/cee/lib/perl5/site_perl/5.8.7/i686-linux
              /home/mkubal/public_html/FIGdisk/env/cee/lib/perl5/site_perl/5.8.7
              /home/mkubal/public_html/FIGdisk/env/cee/lib/perl5/site_perl
	      /home/mkubal/public_html/FIGdisk/env/cee/lib/perl5/site_perl/5.8.7/Bio/Tools
              .
              /home/mkubal/public_html/FIGdisk/config

	      );
}

use Data::Dumper;
use Carp;
use FIG_Config;
$ENV{'BLASTMAT'} = "/home/mkubal/public_html/FIGdisk/BLASTMAT";
$ENV{'FIG_HOME'} = "/home/mkubal/public_html/FIGdisk";

use SeqStats;
use pICalculator;
use FIG;

open(MW,">/vol/seed-attributes/molecular_weight/molecular_weight.txt");
open(ISO,">/vol/seed-attributes/isoelectric_point/isoelectric_point.txt");

$fig = new FIG;

my @genomes = $fig->genomes('complete');
foreach my $genome (@genomes){
    my @pegs = $fig->pegs_of($genome);
    foreach $peg (@pegs){
	my $seq = $fig->get_translation($peg);
	$mw_seqobj = Bio::PrimarySeq->new(-seq=>$seq,
					  -alphabet=>'protein',
					  -id=>'test');
	
	$weight = Bio::Tools::SeqStats->get_mol_wt($mw_seqobj);
	print MW "$peg\tmolecular_weight\t$$weight[0]\n";
	#print "$peg\tmolecular_weight\t$$weight[0]\n";
	
	$pi_seqobj = Bio::Seq->new(-seq=>$seq,
				   -alphabet=>'protein',
				   -id=>'test');
	
	$calc = Bio::Tools::pICalculator->new(-places => 2);
	$calc->seq($pi_seqobj);
	$iep = $calc->iep;
	print ISO "$peg\tisoelectric_point\t$iep\n";
	#print "$peg\tisoelectric_point\t$iep\n";
    }
}