JPRED-2 Current state of the SVN trank

[jpred.git] / jpred / lib / PSIBLAST / Run.pm

diff --git a/jpred/lib/PSIBLAST/Run.pm b/jpred/lib/PSIBLAST/Run.pm
index 99188e1..bf74c71 100644 (file)
--- a/jpred/lib/PSIBLAST/Run.pm
+++ b/jpred/lib/PSIBLAST/Run.pm
@@ -5,68 +5,71 @@ use base qw(Root);
 use Run qw(check);
 
 sub new {
-       my ($class, %args) = @_;
-       my $self = {};
-       bless $self, ref($class) || $class;
-
-       # -a number of CPUs used (default 1)
-       # -e e-value threshold for reporting sequences (default 10)
-       # -h e-value threshold for including sequences in PSSM (default 0.002)
-       # -m type of output
-       # -b max number of alignments reported (default 250)
-       # -v max number of sequences described (default 500)
-       # -j max number of itterations (default 1)
-       $self->args("-e0.05 -h0.01 -m6 -b10000 -v10000 -j3");
-       #$self->args("-a2 -e0.05 -h0.01 -m6 -b20000 -v20000 -j15");
-#      $self->BLASTMAT("/software/jpred_bin/blast");
-#      $self->BLASTDB("/software/jpred_uniprot_all_filt");
-
-       # Automatically run any arguments passed to the constructor
-       for (keys %args) {
-               croak "No such method '$_' of object $class" unless $self->can($_);
-               $self->$_($args{$_});
-       }
-
-       return $self;
+  my ( $class, %args ) = @_;
+  my $self = {};
+  bless $self, ref($class) || $class;
+
+  # -a number of CPUs used (default 1)
+  # -e e-value threshold for reporting sequences (default 10)
+  # -h e-value threshold for including sequences in PSSM (default 0.002)
+  # -m type of output
+  # -b max number of alignments reported (default 250)
+  # -v max number of sequences described (default 500)
+  # -j max number of itterations (default 1)
+  $self->args("-e0.05 -h0.01 -m6 -b10000 -v10000 -j3");
+
+  #$self->args("-a2 -e0.05 -h0.01 -m6 -b20000 -v20000 -j15");
+  #    $self->BLASTMAT("/software/jpred_bin/blast");
+  #    $self->BLASTDB("/software/jpred_uniprot_all_filt");
+
+  # Automatically run any arguments passed to the constructor
+  for ( keys %args ) {
+    croak "No such method '$_' of object $class" unless $self->can($_);
+    $self->$_( $args{$_} );
+  }
+
+  return $self;
 }
 
-sub path { defined $_[1] ? $_[0]->{path} = $_[1] : $_[0]->{path} }
-sub args { defined $_[1] ? $_[0]->{args} = $_[1] : $_[0]->{args} }
-sub database { defined $_[1] ? $_[0]->{data} = "-d $_[1]" : $_[0]->{data} }
-sub input { defined $_[1] ? $_[0]->{input} = "-i $_[1]" : $_[0]->{input} }
-sub output { defined $_[1] ? $_[0]->{output} = "-o $_[1]" : $_[0]->{output} }
-sub matrix { defined $_[1] ? $_[0]->{matrix} = "-Q $_[1]" : $_[0]->{matrix} }
-sub debug { defined $_[1] ? $_[0]->{debug} = $_[1] : $_[0]->{debug} }      # CC corrected - now works as expected. Before, debug was always on.
+sub path     { defined $_[1] ? $_[0]->{path}   = $_[1]      : $_[0]->{path} }
+sub args     { defined $_[1] ? $_[0]->{args}   = $_[1]      : $_[0]->{args} }
+sub database { defined $_[1] ? $_[0]->{data}   = "-d $_[1]" : $_[0]->{data} }
+sub input    { defined $_[1] ? $_[0]->{input}  = "-i $_[1]" : $_[0]->{input} }
+sub output   { defined $_[1] ? $_[0]->{output} = "-o $_[1]" : $_[0]->{output} }
+sub matrix   { defined $_[1] ? $_[0]->{matrix} = "-Q $_[1]" : $_[0]->{matrix} }
+sub debug    { defined $_[1] ? $_[0]->{debug}  = $_[1]      : $_[0]->{debug} }    # CC corrected - now works as expected. Before, debug was always on.
 sub BLASTMAT { $ENV{BLASTMAT} = $_[1] }
-sub BLASTDB { $ENV{BLASTDB} = $_[1] }
+sub BLASTDB  { $ENV{BLASTDB}  = $_[1] }
 
 sub run {
-       my ($self) = @_;
-
-       # Required arguments
-       for (qw(path output database input)) {
-               croak "Method '$_' needs to be set" unless defined $self->$_;
-       }
-
-       # Construct the command line
-       my @cmd;
-       for (qw(path args database input matrix output)) {
-               next unless $self->$_;
-               push @cmd, $self->$_;
-       }
-
-       my $cmd = join " ", @cmd;
-       # Execute PSIBLAST and check it ran okay
-       if ($self->debug) {
-               #for (keys %ENV) { warn "$_=$ENV{$_}\n" }
-               warn "$cmd\n"
-       }
-
-       system($cmd) == 0 or check("blastpgp", $?) and die "blastpgp was naughty";
-
-       # Clean up the error.log file it produces
-       if (-z "error.log") { unlink "error.log" }
-       else { warn "blastpgp error.log file was not empty\n" }
+  my ($self) = @_;
+
+  # Required arguments
+  for (qw(path output database input)) {
+    croak "Method '$_' needs to be set" unless defined $self->$_;
+  }
+
+  # Construct the command line
+  my @cmd;
+  for (qw(path args database input matrix output)) {
+    next unless $self->$_;
+    push @cmd, $self->$_;
+  }
+
+  my $cmd = join " ", @cmd;
+
+  # Execute PSIBLAST and check it ran okay
+  if ( $self->debug ) {
+
+    #for (keys %ENV) { warn "$_=$ENV{$_}\n" }
+    warn "$cmd\n";
+  }
+
+  system($cmd) == 0 or check( "blastpgp", $? ) and die "blastpgp was naughty";
+
+  # Clean up the error.log file it produces
+  if   ( -z "error.log" ) { unlink "error.log" }
+  else                    { warn "blastpgp error.log file was not empty\n" }
 }
 
 1;