Christopher Fields > BioPerl-Run > Bio::Tools::Run::Alignment::Gmap

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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.
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