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revision 1.10, Mon Mar 21 18:08:40 2011 UTC revision 1.11, Tue Apr 19 19:55:47 2011 UTC
# Line 142  Line 142 
142          copy("$ofdir/fasta", "$nfdir/fasta");          copy("$ofdir/fasta", "$nfdir/fasta");
143      }      }
144    
145        my $genome_ss_dir = catfile($gdir, "Subsystems");
146        if (-d $genome_ss_dir && -s "$genome_ss_dir/bindings" && -s "$genome_ss_dir/subsystems")
147        {
148            my $my_ss_dir = $self->genome_dir . "/Subsystems";
149            mkdir($my_ss_dir) or die "Cannot mkdir $my_ss_dir: $!";
150            for my $f (qw(bindings subsystems))
151            {
152                copy("$genome_ss_dir/$f", "$my_ss_dir/$f") or die "Cannot copy $genome_ss_dir/$f to $my_ss_dir/$f: $!";
153            }
154        }
155    
156      open(SS, ">", catfile($self->genome_dir, "subsystem.data"));      open(SS, ">", catfile($self->genome_dir, "subsystem.data"));
157      my %phash = $fig->subsystems_for_pegs_complete(\@pegs);      my %phash = $fig->subsystems_for_pegs_complete(\@pegs);
158      for my $peg (keys %phash)      for my $peg (keys %phash)
# Line 778  Line 789 
789      my $probes_always_on = catfile($self->expr_dir, "probes.always.on");      my $probes_always_on = catfile($self->expr_dir, "probes.always.on");
790      my $pegs_always_on = catfile($self->expr_dir, "pegs.always.on");      my $pegs_always_on = catfile($self->expr_dir, "pegs.always.on");
791    
792    
793      $self->run([executable_for("call_coregulated_clusters_on_chromosome"), $self->expr_dir],      $self->run([executable_for("call_coregulated_clusters_on_chromosome"), $self->expr_dir],
794             { stdout => $coreg_clusters });             { stdout => $coreg_clusters });
795      $self->run([executable_for("make_coreg_conjectures_based_on_subsys"), $self->expr_dir],  
796        my $genome_ss_dir = $self->genome_dir . "/Subsystems";
797        $self->run([executable_for("make_coreg_conjectures_based_on_subsys"),
798                    $self->expr_dir,
799                    (-d $genome_ss_dir ? $genome_ss_dir : ()),
800                    ],
801             { stdout => $coreg_subsys });             { stdout => $coreg_subsys });
802    
803      $self->run([executable_for("filter_and_merge_gene_sets"), $self->expr_dir, $coreg_clusters, $coreg_subsys],      $self->run([executable_for("filter_and_merge_gene_sets"), $self->expr_dir, $coreg_clusters, $coreg_subsys],

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