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Summary

Bio::Tools::Run::Alignment::Gmap - Wrapper for running gmap.

Package variables

Included modules

Inherit

Bio::Factory::ApplicationFactoryI Bio::Root::Root Bio::Tools::Run::WrapperBase

Synopsis

  use Bio::Tools::Run::Alignment::Gmap;
  use Bio::SeqIO;

  my $sio = Bio::SeqIO->new(-file=>$filename ,-format=>'fasta');
  my @seq;
  while(my $seq = $sio->next_seq()){
    push @seq,$seq;
  }
  my $mapper =Bio::Tools::Run::Gmap->new();
  my $result = $mapper->run(\@seq);

Description

Bioperl-run wrapper around gmap. See
http://www.gene.com/share/gmap/ for information about gmap.
It requires a reference to an array of bioperl SeqI objects and
returns a reference to a filehandle from which the gmap output can be
read.
One can explicitly set the name of the genome database (defaults to
NHGD_R36) using the 'genome_db()' method. One can also explicitly set
the flags that are passed to gmap (defaults to '-f 9 -5 -e') using the
'flags()' method.
The name of the gmap executable can be overridden using the
program_name() method and the directory in which to find that
executable can be overridden using the program_dir() method.

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::Tools::Run::Alignment::Gmap();
 Function: Builds a new Bio::Tools::Run::Alignment::Gmap object
 Returns : an instance of Bio::Tools::Run::Alignment::Gmap
 Args    :

 Title   : version
 Usage   : print "gmap version: " . $mapper->version() . "\n";
 Function: retrieves and returns the version of the gmap package.
 Example :
 Returns : scalar string containing the version number.  Probably looks
           like YYYY-MM-DD.
 Args    : none.

 Title   : program_name
 Usage   : $mapper->program_name('gmap-dev');
           my $pname = $mapper->program_name();
 Function: sets/gets the name of the program to run.
 Returns : string representing the name of the executable.
 Args    : [optional] string representing the name of the executable
           to set.

 Title   : program_dir
 Usage   : $mapper->program_dir('/usr/local/sandbox/gmap/bin');
           my $pdir = $mapper->program_dir();
 Function: sets/gets the directory path in which
           to find the gmap executable.
 Returns : string representing the path to the directory.
 Args    : [optional] string representing the directory path to set.

 Title   : input_file
 Usage   : $mapper->input_file('/tmp/moose.fasta');
           my $filename = $mapper->input_file();
 Function: sets/gets the name of a file containing sequences
           to be mapped.
 Returns : string containing the name of the query sequence.
 Args    : [optional] string representing the directory path to set.

 Title   : genome_db
 Usage   : $mapper->genome_db('NHGD_R36');
           my $genome_db = $mapper->genome_db();
 Function: sets/gets the name of the genome database, this will be
           passed to gmap using its '-d' flag.
 Returns : name of the genome database.
 Args    : [optional] string representing the genome db to set.

 Title   : flags
 Usage   : $mapper->flags('-A -e -5');
           my $flags = $mapper->flags();
 Function: sets/gets the flags that will be passed to gmap.
 Returns : the current value of the flags that will be passed to gmap.
 Args    : [optional] the flags to set.

 Title   : run
 Usage   : $mapper->run()
 Function: runs gmap
 Example :
 Returns : a file handle, opened for reading, for gmap's output.
 Args    : An array of references query sequences (as Bio::Seq objects)

 Title   : _build_fasta_input_file
 Usage   : my $seq_file = $self->_build_fasta_input_file(@_);
 Function:
 Example :
 Returns : The name of the temporary file that contains the sequence.
 Args    : A reference to an array of Bio::Seq objects.

Methods code

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  $self->{_program_name} = 'gmap';
  return $self;

}

sub version {

   my ($self,@args) = @_;
   my $version;

   my $str = $self->executable;
   $str .= ' --version';
   $self->debug("gmap version command = $str\n");

   open(GMAPRUN, "$str |") || $self->throw($@);

   {
       local $/ = undef;
       my $result = <GMAPRUN>;
       ($version) = ($result =~ m|.*Part of GMAP package, version (.*).*|);
   }

   return($version);

}

sub program_name {

   my $self = shift;

   $self->{_program_name} = shift if @_;
   return $self->{_program_name};

}

sub program_dir {

  my $self = shift;

  $self->{_program_dir} = shift if @_;
  return $self->{_program_dir};

}

sub input_file {

  my $self = shift;

  $self->{_input_file} = shift if @_;
  return $self->{_input_file};

}

sub genome_db {

  my $self = shift;

  $self->{_genome_db} = shift if @_;
  return $self->{_genome_db};

}

sub flags {

  my $self = shift;

  $self->{_flags} = shift if @_;
  return $self->{_flags};

}

sub run {

  my $self = shift;

  $self->input_file( $self->_build_fasta_input_file(@_) ) if(@_);

  my $result = $self->_run();

  return $result;

}

sub _build_fasta_input_file {

  my $self = shift;
  my $seqs = shift;
  my $seq_count = 0;

  # the object returned by File::Temp->new() is magic.  Used normally
  # it behaves as a filehandle opened onto the temporary file.  Used
  # as a string it behaves as a string that is the name of the
  # temporary file.
  # It is up to the user to remove the when finished with it.
  my $file_tmp = File::Temp->new( TEMPLATE => 'mvp-gmap-tempfile-XXXXXX',
				  TMPDIR => 1,
				  UNLINK => 0,
				);
  my $seqio = Bio::SeqIO->new( -fh => $file_tmp, -format => 'Fasta' );

  if (ref($seqs) =~ /ARRAY/i) {
    foreach my $seq (@$seqs) {
      throw
	Bio::Root::BadParameter(-text =>
				"sequence args must be a Bio::SeqI subclass.",
			       )
	    unless ($seq->isa("Bio::PrimarySeqI"));

      $seqio->write_seq($seq);
      $seq_count++;
    }
  }
  if ($seq_count == 0) {
    throw
      Bio::Root::BadParameter(-text => <<EOM
You must supply a reference to an array of Bio::SeqI objects.
EOM
			     );
  }

  # pass back the filename of the temporary file (see above)
  return ("$file_tmp");

}

sub _run {

  my $self = shift;

  my $str = $self->executable;
  $str .= ' -d' . ($self->genome_db() || 'NHGD_R36');
  $str .= ' ' . ($self->flags() || '-f 9 -5 -e');
  $str .= ' ' . $self->input_file();
  $str .= ' 2> /dev/null';
  $str .= '; rm -f ' . $self->input_file();
  $self->debug("gmap command = $str\n");

  open(GMAPRUN, "$str |") || $self->throw("Can't open gmap (command =\" $str\"): $!");

  return (\*GMAPRUN);
}

1;

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:

  http://redmine.open-bio.org/projects/bioperl/

Email hartzell@alerce.com
Describe contact details here

Additional contributors names and emails here

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _