/ 
BioPerl-Run-1.007003
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Alignment::Gmap

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() . "\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.

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.