Provided by: libbio-perl-run-perl_1.6.9-1_all
Bio::Tools::Run::Samtools - a run wrapper for the samtools suite *BETA*
# 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" );
This is a wrapper for running samtools, a suite of large-alignment reading and manipulation programs available at <http://samtools.sourceforge.net/>.
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()>.
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AUTHOR - Mark A. Jensen
Email maj -at- fortinbras -dot- us
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::Samtools(); Function: Builds a new Bio::Tools::Run::Samtools object Returns : an instance of Bio::Tools::Run::Samtools Args :