Bio::Tools::Run::Alignment::Gmap(3pm)			User Contributed Perl Documentation		     Bio::Tools::Run::Alignment::Gmap(3pm)

NAME

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

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.

FEEDBACK

   Mailing Lists
       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

   Reporting Bugs
       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/

AUTHOR - George Hartzell
       Email hartzell@alerce.com

       Describe contact details here

CONTRIBUTORS

       Additional contributors names and emails here

APPENDIX

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

   new
	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	:

   version
	Title	: version
	Usage	: print "gmap version: " . $mapper->version() . "
";
	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.

   program_name
	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.

   program_dir
	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.

   input_file
	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.

   genome_db
	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.

   flags
	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.

   run
	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)

   _build_fasta_input_file
	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.

perl v5.12.3							    2011-06-18				     Bio::Tools::Run::Alignment::Gmap(3pm)