NAME¶
Bio::Tools::Run::Samtools - a run wrapper for the samtools suite *BETA*
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/>.
RUNNING COMMANDS¶
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" );
OPTIONS¶
"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.
FILES¶
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()>.
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
Support¶
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.
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 - Mark A. Jensen¶
Email maj -at- fortinbras -dot- us
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::Samtools();
Function: Builds a new Bio::Tools::Run::Samtools object
Returns : an instance of Bio::Tools::Run::Samtools
Args :