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Summary

Bio::Tools::Run::Samtools - a run wrapper for the samtools suite *BETA*

Package variables

Included modules

Inherit

Bio::Root::Root Bio::Tools::Run::WrapperBase

Synopsis

 # convert a sam to a bam
 $samt = Bio::Tools::Run::Samtools( -command => 'view', 
                                    -sam_input => 1,
                                    -bam_output => 1 );
 $samt->run( -bam => "mysam.sam", -out => "mysam.bam" );
 # sort it
 $samt = Bio::Tools::Run::Samtools( -command => 'sort' );
 $samt->run( -bam => "mysam.bam", -pfx => "mysam.srt" );
 # now create an assembly
 $assy = Bio::IO::Assembly->new( -file => "mysam.srt.bam",
                                 -refdb => "myref.fas" );

Description

This is a wrapper for running samtools, a suite of large-alignment
reading and manipulation programs available at
http://samtools.sourceforge.net/.

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::Tools::Run::Samtools();
 Function: Builds a new Bio::Tools::Run::Samtools object
 Returns : an instance of Bio::Tools::Run::Samtools
 Args    :

Methods code

sub new {

     my ($class, @args) = @_;
    $program_dir ||= $ENV{SAMTOOLSDIR};
    my $self = $class->SUPER::new(@args);
    return $self;

}

General documentation

To run a samtools
command, construct a run factory, specifying the desired command using
the -command argument in the factory constructor, along with
options specific to that command (see /OPTIONS):

 $samt = Bio::Tools::Run::Samtools->new( -command => 'view',
                                         -sam_input => 1,
                                         -bam_output => 1);

To execute, use the run() method. Input and output files are
specified in the arguments of run() (see /FILES):

 $samt->run( -bam => "mysam.sam", -out => "mysam.bam" );

samtools is complex, with many subprograms (commands) and command-line
options and file specs for each. This module attempts to provide
commands and options comprehensively. You can browse the choices like so:

 $samt = Bio::Tools::Run::Samtools->new( -command => 'pileup' );
 # all samtools commands
 @all_commands = $samt->available_parameters('commands'); 
 @all_commands = $samt->available_commands; # alias
 # just for pileup
 @pup_params = $samt->available_parameters('params');
 @pup_switches = $samt->available_parameters('switches');
 @pup_all_options = $samt->available_parameters();

Reasonably mnemonic names have been assigned to the single-letter
command line options. These are the names returned by
available_parameters, and can be used in the factory constructor
like typical BioPerl named parameters.
See http://samtools.sourceforge.net/samtools.shtml for the gory details.

When a command requires filenames, these are provided to the
run() method, not the constructor (new()). To see the set of
files required by a command, use available_parameters('filespec')
or the alias filespec():

  $samt = Bio::Tools::Run::Samtools->new( -command => 'view' );
  @filespec = $samt->filespec;

This example returns the following array:

 bam
 >out

This indicates that the bam/sam file (bam) and the output file (out)
MUST be specified in the run() argument list:

 $samt->run( -bam => 'mysam.sam', -out => 'mysam.cvt' );

If files are not specified per the filespec, text sent to STDOUT and
STDERR is saved and is accessible with $bwafac-stdout()> and
$bwafac-stderr()>.

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

Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

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/

Email maj -at- fortinbras -dot- us

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