/ 
BioPerl-Run-1.007001
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::BEDTools

NAME

Bio::Tools::Run::BEDTools - Run wrapper for the BEDTools suite of programs *BETA*

SYNOPSIS

# use a BEDTools program
$bedtools_fac = Bio::Tools::Run::BEDTools->new( -command => 'subtract' );
$result_file = $bedtools_fac->run( -bed1 => 'genes.bed', -bed2 => 'mask.bed' );

# if IO::Uncompress::Gunzip is available...
$result_file = $bedtools_fac->run( -bed1 => 'genes.bed.gz', -bed2 => 'mask.bed.gz' );

# be more strict
$bedtools_fac->set_parameters( -strandedness => 1 );

# and even more...
$bedtools_fac->set_parameters( -minimum_overlap => 1e-6 );

# create a Bio::SeqFeature::Collection object
$features = $bedtools_fac->result( -want => 'Bio::SeqFeature::Collection' );

DEPRECATION WARNING

Most executables from BEDTools v>=2.10.1 can read GFF and VCF formats in addition to BED format. This requires the use of a new input file param, shown in the following documentation, '-bgv', in place of '-bed' for the executables that can do this.

This behaviour breaks existing scripts.

DESCRIPTION

This module provides a wrapper interface for Aaron R. Quinlan and Ira M. Hall's utilities BEDTools that allow for (among other things):

  • Intersecting two BED files in search of overlapping features.

  • Merging overlapping features.

  • Screening for paired-end (PE) overlaps between PE sequences and existing genomic features.

  • Calculating the depth and breadth of sequence coverage across defined "windows" in a genome.

(see http://code.google.com/p/bedtools/ for manuals and downloads).

OPTIONS

BEDTools is a suite of 17 commandline executable. This module attempts to provide and options comprehensively. You can browse the choices like so:

$bedtools_fac = Bio::Tools::Run::BEDTools->new;

# all bowtie commands
@all_commands = $bedtools_fac->available_parameters('commands');
@all_commands = $bedtools_fac->available_commands; # alias

# just for default command ('bam_to_bed')
@btb_params = $bedtools_fac->available_parameters('params');
@btb_switches = $bedtools_fac->available_parameters('switches');
@btb_all_options = $bedtools_fac->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.

As a number of options are mutually exclusive, and the interpretation of intent is based on last-pass option reaching bowtie with potentially unpredicted results. This module will prevent inconsistent switches and parameters from being passed.

See http://code.google.com/p/bedtools/ for details of BEDTools options.

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():

$bedtools_fac = Bio::Tools::Run::BEDTools->new( -command => 'pair_to_bed' );
@filespec = $bedtools_fac->filespec;

This example returns the following array:

#bedpe
#bam
bed
#out

This indicates that the bed (BEDTools BED format) file MUST be specified, and that the out, bedpe (BEDTools BEDPE format) and bam (SAM binary format) file MAY be specified (Note that in this case you MUST provide ONE of bedpe OR bam, the module at this stage does not allow this information to be queried). Use these in the run call like so:

$bedtools_fac->run( -bedpe => 'paired.bedpe',
                    -bgv => 'genes.bed',
                    -out => 'overlap' );

The object will store the programs STDERR output for you in the stderr() attribute:

handle_bed_warning($bedtools_fac) if ($bedtools_fac->stderr =~ /Usage:/);

For the commands 'fasta_from_bed' and 'mask_fasta_from_bed' STDOUT will also be captured in the stdout() attribute by default and all other commands can be forced to capture program output in STDOUT by setting the -out filespec parameter to '-'.

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 - Dan Kortschak

Email dan.kortschak adelaide.edu.au

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::BEDTools();
Function: Builds a new Bio::Tools::Run::BEDTools object
Returns : an instance of Bio::Tools::Run::BEDTools
Args    :

run()

Title   : run
Usage   : $result = $bedtools_fac->run(%params);
Function: Run a BEDTools command.
Returns : Command results (file, IO object or Bio object)
Args    : Dependent on filespec for command. 
          See $bedtools_fac->filespec and BEDTools Manual.
          Also accepts -want => '(raw|format|<object_class>)' - see want().
Note    : gzipped inputs are allowed if IO::Uncompress::Gunzip
          is available
Command              	<in>			<out>

annotate             bgv		ann(s)		#out
graph_union	        bg_files			#out
fasta_from_bed       seq		bgv		#out

mask_fasta_from_bed  seq		bgv		#out
bam_to_bed           bam 				#out
bed_to_IGV           bgv 				#out

merge                bgv 				#out

sort                 bgv 				#out

links                bgv 				#out
b12_to_b6            bed 				#out

overlap              bed 				#out

group_by             bed 				#out
bed_to_bam           bgv 				#out

shuffle              bgv 		genome		#out

slop                 bgv 		genome		#out

complement           bgv 		genome		#out
genome_coverage      bed 		genome		#out
window               bgv1		bgv2		#out

closest              bgv1		bgv2		#out

coverage             bgv1		bgv2		#out

subtract             bgv1		bgv2		#out
pair_to_pair         bedpe1		bedpe2		#out
intersect            bgv1|bam	bgv2		#out
pair_to_bed          bedpe|bam	bgv		#out

bgv* signifies any of BED, GFF or VCF. ann is a bgv.

NOTE: Replace 'bgv' with 'bed' unless $use_bgv is set.

want()

Title   : want
Usage   : $bowtiefac->want( $class )
Function: make factory return $class, or 'raw' results in file
          or 'format' for result format
          All commands can return Bio::Root::IO
          commands returning:       can return object:
          - BED or BEDPE            - Bio::SeqFeature::Collection
          - sequence                - Bio::SeqIO
Returns : return wanted type
Args    : [optional] string indicating class or raw of wanted result

result()

Title   : result
Usage   : $bedtoolsfac->result( [-want => $type|$format] )
Function: return result in wanted format
Returns : results
Args    : [optional] hashref of wanted type
Note    : -want arg does not persist between result() call when
          specified in result(), for persistence, use want()

_determine_format()

Title   : _determine_format( $has_run )
Usage   : $bedtools-fac->_determine_format
Function: determine the format of output for current options
Returns : format of bowtie output
Args    : [optional] boolean to indicate result exists

_read_bed()

Title   : _read_bed()
Usage   : $bedtools_fac->_read_bed
Function: return a Bio::SeqFeature::Collection object from a BED file 
Returns : Bio::SeqFeature::Collection
Args    :

_read_bedpe()

Title   : _read_bedpe()
Usage   : $bedtools_fac->_read_bedpe
Function: return a Bio::SeqFeature::Collection object from a BEDPE file 
Returns : Bio::SeqFeature::Collection
Args    :

_validate_file_input()

Title   : _validate_file_input
Usage   : $bedtools_fac->_validate_file_input( -type => $file )
Function: validate file type for file spec
Returns : file type if valid type for file spec
Args    : hash of filespec => file_name

version()

Title   : version
Usage   : $version = $bedtools_fac->version()
Function: Returns the program version (if available)
Returns : string representing location and version of the program