NAME

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

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.

FEEDBACK

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

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

AUTHOR - George Hartzell

Describe contact details here

CONTRIBUTORS

APPENDIX

 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.