gistfile1.pl

use 5.12.2;
use warnings;
use Data::Dump qw/dump/;
use Data::Dumper;
use G;
use Storable;

my $hoge;
my $gb = load ("ecoli","no msg");

my $comp = complement($gb->{SEQ});

for my $i (0 .. length $gb->{SEQ}){
        my $hex = substr $gb->{SEQ},$i, 6;
        my @hoge = `echo "CACCUCCU&$hex" |RNAsubopt -s`;
        chomp $hoge[1];
        my @detail = split /\s+/, $hoge[1];
        my $energy = $detail[1];
        $hoge->{direct}->[$i] = $energy;
}

for my $i (0 .. length $comp){
        my $hex = substr $comp,$i, 6;
        my @hoge = `echo "CACCUCCU&$hex" |RNAsubopt -s`;
        chomp $hoge[1];
        my @detail = split /\s+/, $hoge[1];
        my $energy = $detail[1];
        $hoge->{complement}->[$i] = $energy;
}

store $hoge, 'energy.store';