9 use base qw(Root Common);
14 my ($self, $path) = @_;
15 if (defined $path) { $self->{path}= $path }
17 if (defined $self->{path}) { return $self->{path} }
18 else { croak "Path not defined" }
23 my ($self, $fasta) = @_;
25 croak "Non FASTA::File object passed to Pairwise::run" unless isa $fasta, 'FASTA::File';
27 local ($/, $?) = (undef, 0);
29 my $f = File::Temp->new->filename;
30 $fasta->write_file($f);
32 my $pid = open my $fh, $self->path." $f |" or die $!;
34 my @output = join "\n", split "\n", <$fh>;
37 check($self->path, $?) or die "Pairwise was naughty\n";