Bio::EnsEMBL::Pipeline::SeqFetcher::Pfetch

    my $obj = Bio::EnsEMBL::Pipeline::SeqFetcher::Pfetch->new(
							      -executable => $exe
							     );
    my $seq = $obj->get_Seq_by_acc($acc);

  Object to retrieve sequences as Bio::Seq, using pfetch.

  my $self = shift @_;

  my @sequence_list;
  
  unless (scalar @_) {
    $self->throw("No accession input");
  }  

  my $accession_concatenation;
  my @accession_list;

  while (my $acc = shift @_) {
    push (@accession_list, $acc);
    $accession_concatenation .= $acc . ' ';
  }
  
  my $pfetch = $self->executable;
  my $options = $self->options;
  if (defined($options)) { $options = '-' . $options  unless $options =~ /^-/; }

  my $command = "$pfetch -q ";
  if (defined $options){
    $command .= "$options ";
  }

  $command .= $accession_concatenation;

  #print STDERR "$command\n";

  open(IN,"$command |") or $self->throw("Error opening pipe to pfetch : $pfetch");

  my $seq_placemarker = -1;

 SEQ:
  while (my $seqstr = <IN>) {
    
    $seq_placemarker++;

    chomp($seqstr);
    
    my $seq;
    
    unless (defined $seqstr && $seqstr eq 'no match') {

      eval{
	if(defined $seqstr && $seqstr ne "no match") {
	  $seq = new Bio::Seq('-seq'               => $seqstr,
			      '-accession_number'  => $accession_list[$seq_placemarker],
			      '-display_id'        => $accession_list[$seq_placemarker]);
	}
      };
      
      if($@){
	print STDERR "$@\n";
      }
    }

    unless (defined $seq){
      $self->warn("PFetch Error : Could not pfetch sequence for " . 
		  $accession_list[$seq_placemarker] . "\n");
      next SEQ;
    }

    push (@sequence_list, $seq);
  }
  
  close IN or $self->throw("Error running pfetch : $pfetch");
  
  return\@ sequence_list;
}



1;

  my ($self, $exe) = @_;
  if ($exe)
    {
      $self->{'_exe'} = $exe;
    }
  return $self->{'_exe'};

  my ($self, $acc) = @_;
  
  if (!defined($acc)) {
    $self->throw("No accession input");
  }  
 
  if ( defined ( $self->{_seq_cache}{$acc})) {  
     return $self->{_seq_cache}{$acc};
  } 
  # seqence not cached, needs to be fetched 
  my $seqstr;
  my $seq;
  my $pfetch = $self->executable;
  my $options = $self->options;
  if (defined($options)) { $options = '-' . $options  unless $options =~ /^-/; }

  my $command = "$pfetch -q ";
  if (defined $options){
    $command .= "$options ";
  }

  $command .= $acc;

  #print STDERR "$command\n";

  open(IN,"$command |") or $self->throw("Error opening pipe to pfetch for accession [$acc]: $pfetch");
  $seqstr = <IN>;
  close IN or $self->throw("Error running pfetch for accession [$acc]: $pfetch");
  
  chomp($seqstr);
  eval{
    if(defined $seqstr && $seqstr ne "no match") {
      $seq = new Bio::Seq('-seq'               => $seqstr,
			  '-accession_number'  => $acc,
			  '-display_id'        => $acc);
    }
  };

  if($@){
    print STDERR "$@\n";
  }
  
  $self->throw("Could not pfetch sequence for [$acc]\n") unless defined $seq;

  $self->{_seq_cache}{$acc}=$seq;
  return $seq;

  my ($class, @args) = @_;
  my $self = bless {}, $class;

  my ($exe, $options) = rearrange(['EXECUTABLE', 'OPTIONS'], @args);
  
  if (!defined $exe) {
    $exe = 'pfetch';
  }
  $self->executable($exe);

  if (defined $options) {
    $self->options($options);
  } 
  # caching of sequences 
  $self->{_seq_cache}={};    

  return $self; # success - we hope!

  my ($self, $options) = @_;
  if ($options)
    {
      $self->{'_options'} = $options;
    }
  return $self->{'_options'};