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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Run::BEDTools 3pm"
.TH Bio::Tools::Run::BEDTools 3pm "2023-01-22" "perl v5.36.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Tools::Run::BEDTools \- Run wrapper for the BEDTools suite of programs *BETA*
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\& # use a BEDTools program
\& $bedtools_fac = Bio::Tools::Run::BEDTools\->new( \-command => \*(Aqsubtract\*(Aq );
\& $result_file = $bedtools_fac\->run( \-bed1 => \*(Aqgenes.bed\*(Aq, \-bed2 => \*(Aqmask.bed\*(Aq );
\& 
\& # if IO::Uncompress::Gunzip is available...
\& $result_file = $bedtools_fac\->run( \-bed1 => \*(Aqgenes.bed.gz\*(Aq, \-bed2 => \*(Aqmask.bed.gz\*(Aq );
\& 
\& # 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 => \*(AqBio::SeqFeature::Collection\*(Aq );
.Ve
.SH "DEPRECATION WARNING"
.IX Header "DEPRECATION WARNING"
Most executables from BEDTools v>=2.10.1 can read \s-1GFF\s0 and \s-1VCF\s0 formats
in addition to \s-1BED\s0 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.
.PP
This behaviour breaks existing scripts.
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This module provides a wrapper interface for Aaron R. Quinlan and Ira M. Hall's
utilities \f(CW\*(C`BEDTools\*(C'\fR that allow for (among other things):
.IP "\(bu" 4
Intersecting two \s-1BED\s0 files in search of overlapping features.
.IP "\(bu" 4
Merging overlapping features.
.IP "\(bu" 4
Screening for paired-end (\s-1PE\s0) overlaps between \s-1PE\s0 sequences and existing genomic features.
.IP "\(bu" 4
Calculating the depth and breadth of sequence coverage across defined \*(L"windows\*(R" in a genome.
.PP
(see <http://code.google.com/p/bedtools/> for manuals and downloads).
.SH "OPTIONS"
.IX Header "OPTIONS"
\&\f(CW\*(C`BEDTools\*(C'\fR is a suite of 17 commandline executable. This module attempts to 
provide and options comprehensively. You can browse the choices like so:
.PP
.Vb 1
\& $bedtools_fac = Bio::Tools::Run::BEDTools\->new;
\&
\& # all bowtie commands
\& @all_commands = $bedtools_fac\->available_parameters(\*(Aqcommands\*(Aq);
\& @all_commands = $bedtools_fac\->available_commands; # alias
\&
\& # just for default command (\*(Aqbam_to_bed\*(Aq)
\& @btb_params = $bedtools_fac\->available_parameters(\*(Aqparams\*(Aq);
\& @btb_switches = $bedtools_fac\->available_parameters(\*(Aqswitches\*(Aq);
\& @btb_all_options = $bedtools_fac\->available_parameters();
.Ve
.PP
Reasonably mnemonic names have been assigned to the single-letter
command line options. These are the names returned by
\&\f(CW\*(C`available_parameters\*(C'\fR, and can be used in the factory constructor
like typical BioPerl named parameters.
.PP
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.
.PP
See <http://code.google.com/p/bedtools/> for details of BEDTools options.
.SH "FILES"
.IX Header "FILES"
When a command requires filenames, these are provided to the \f(CW\*(C`run\*(C'\fR method, not
the constructor (\f(CW\*(C`new()\*(C'\fR). To see the set of files required by a command, use
\&\f(CW\*(C`available_parameters(\*(Aqfilespec\*(Aq)\*(C'\fR or the alias \f(CW\*(C`filespec()\*(C'\fR:
.PP
.Vb 2
\&  $bedtools_fac = Bio::Tools::Run::BEDTools\->new( \-command => \*(Aqpair_to_bed\*(Aq );
\&  @filespec = $bedtools_fac\->filespec;
.Ve
.PP
This example returns the following array:
.PP
.Vb 4
\& #bedpe
\& #bam
\& bed
\& #out
.Ve
.PP
This indicates that the bed (\f(CW\*(C`BEDTools\*(C'\fR \s-1BED\s0 format) file \s-1MUST\s0 be
specified, and that the out, bedpe (\f(CW\*(C`BEDTools\*(C'\fR \s-1BEDPE\s0 format) and bam 
(\f(CW\*(C`SAM\*(C'\fR binary format) file \s-1MAY\s0 be specified (Note that in this case you
\&\s-1MUST\s0 provide \s-1ONE\s0 of bedpe \s-1OR\s0 bam, the module at this stage does not allow
this information to be queried). Use these in the \f(CW\*(C`run\*(C'\fR call like so:
.PP
.Vb 3
\& $bedtools_fac\->run( \-bedpe => \*(Aqpaired.bedpe\*(Aq,
\&                     \-bgv => \*(Aqgenes.bed\*(Aq,
\&                     \-out => \*(Aqoverlap\*(Aq );
.Ve
.PP
The object will store the programs \s-1STDERR\s0 output for you in the \f(CW\*(C`stderr()\*(C'\fR 
attribute:
.PP
.Vb 1
\& handle_bed_warning($bedtools_fac) if ($bedtools_fac\->stderr =~ /Usage:/);
.Ve
.PP
For the commands 'fasta_from_bed' and 'mask_fasta_from_bed' \s-1STDOUT\s0 will also
be captured in the \f(CW\*(C`stdout()\*(C'\fR attribute by default and all other commands
can be forced to capture program output in \s-1STDOUT\s0 by setting the \-out
filespec parameter to '\-'.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
bioperl\-l@bioperl.org
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Dan Kortschak"
.IX Header "AUTHOR - Dan Kortschak"
.Vb 1
\& Email dan.kortschak adelaide.edu.au
.Ve
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Additional contributors names and emails here
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "\fBnew()\fP"
.IX Subsection "new()"
.Vb 5
\& 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    :
.Ve
.SS "\fBrun()\fP"
.IX Subsection "run()"
.Vb 9
\& 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 => \*(Aq(raw|format|<object_class>)\*(Aq \- see want().
\& Note    : gzipped inputs are allowed if IO::Uncompress::Gunzip
\&           is available
.Ve
.PP
.Vb 1
\&           Command                      <in>                    <out>
\&
\&           annotate             bgv             ann(s)          #out
.Ve
.PP
.Vb 1
\&           graph_union          bg_files                        #out
.Ve
.PP
.Vb 1
\&           fasta_from_bed       seq             bgv             #out
\&
\&           mask_fasta_from_bed  seq             bgv             #out
.Ve
.PP
.Vb 1
\&           bam_to_bed           bam                             #out
.Ve
.PP
.Vb 1
\&           bed_to_IGV           bgv                             #out
\&
\&           merge                bgv                             #out
\&
\&           sort                 bgv                             #out
\&
\&           links                bgv                             #out
.Ve
.PP
.Vb 1
\&           b12_to_b6            bed                             #out
\&
\&           overlap              bed                             #out
\&
\&           group_by             bed                             #out
.Ve
.PP
.Vb 1
\&           bed_to_bam           bgv                             #out
\&
\&           shuffle              bgv             genome          #out
\&
\&           slop                 bgv             genome          #out
\&
\&           complement           bgv             genome          #out
.Ve
.PP
.Vb 1
\&           genome_coverage      bed             genome          #out
.Ve
.PP
.Vb 1
\&           window               bgv1            bgv2            #out
\&
\&           closest              bgv1            bgv2            #out
\&
\&           coverage             bgv1            bgv2            #out
\&
\&           subtract             bgv1            bgv2            #out
.Ve
.PP
.Vb 1
\&           pair_to_pair         bedpe1          bedpe2          #out
.Ve
.PP
.Vb 1
\&           intersect            bgv1|bam        bgv2            #out
.Ve
.PP
.Vb 1
\&           pair_to_bed          bedpe|bam       bgv             #out
\&
\&           bgv* signifies any of BED, GFF or VCF. ann is a bgv.
\&           
\&           NOTE: Replace \*(Aqbgv\*(Aq with \*(Aqbed\*(Aq unless $use_bgv is set.
.Ve
.SS "\fBwant()\fP"
.IX Subsection "want()"
.Vb 10
\& Title   : want
\& Usage   : $bowtiefac\->want( $class )
\& Function: make factory return $class, or \*(Aqraw\*(Aq results in file
\&           or \*(Aqformat\*(Aq 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
.Ve
.SS "\fBresult()\fP"
.IX Subsection "result()"
.Vb 7
\& 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()
.Ve
.SS "\fB_determine_format()\fP"
.IX Subsection "_determine_format()"
.Vb 5
\& 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
.Ve
.SS "\fB_read_bed()\fP"
.IX Subsection "_read_bed()"
.Vb 5
\& Title   : _read_bed()
\& Usage   : $bedtools_fac\->_read_bed
\& Function: return a Bio::SeqFeature::Collection object from a BED file 
\& Returns : Bio::SeqFeature::Collection
\& Args    :
.Ve
.SS "\fB_read_bedpe()\fP"
.IX Subsection "_read_bedpe()"
.Vb 5
\& Title   : _read_bedpe()
\& Usage   : $bedtools_fac\->_read_bedpe
\& Function: return a Bio::SeqFeature::Collection object from a BEDPE file 
\& Returns : Bio::SeqFeature::Collection
\& Args    :
.Ve
.SS "\fB_validate_file_input()\fP"
.IX Subsection "_validate_file_input()"
.Vb 5
\& 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
.Ve
.SS "\fBversion()\fP"
.IX Subsection "version()"
.Vb 4
\& Title   : version
\& Usage   : $version = $bedtools_fac\->version()
\& Function: Returns the program version (if available)
\& Returns : string representing location and version of the program
.Ve