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)