Merge branch 'JABAWS_Release_2_5' into develop

[jabaws.git] / binaries / src / jpred / lib / PSIBLAST / Run.pm

diff --git a/binaries/src/jpred/lib/PSIBLAST/Run.pm b/binaries/src/jpred/lib/PSIBLAST/Run.pm
new file mode 100644 (file)
index 0000000..56cb471
--- /dev/null
+++ b/binaries/src/jpred/lib/PSIBLAST/Run.pm
@@ -0,0 +1,68 @@
+package PSIBLAST::Run;
+
+use Carp;
+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");
+  # $self->args("-a2 -e0.05 -h0.01 -m6 -b20000 -v20000 -j15");
+
+  # Automatically run any arguments passed to the constructor
+  for ( keys %args ) {
+    croak "No such method '$_' 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} }
+sub BLASTMAT { $ENV{BLASTMAT} = $_[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 $cmd = join " ", @cmd;
+
+  # Execute PSIBLAST and check it ran okay
+  warn "$cmd\n" if ( $self->debug );
+
+  system($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;