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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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 hereAPPENDIX
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