Bio::T...EDTools(3pm)

📦

version 1.7.3 · 3 versions

1.7.3 · debian bookworm, ubuntu noble (latest)
1.7.3 · ubuntu jammy
1.7.3 · debian trixie

💖 Bio::Tools::Run::BEDTools 💖

okay bestie, so this is a page from the User Contributed Perl Documentation for Bio::Tools::Run::BEDTools(3pm) — and yes the manual name is literally Bio::T...EDTools(3pm) with the middle chopped out, iconic truncation, we love her. Pull up a chair, grab a strawberry 🍓, and let's get into it.

✨ NAME ✨

Bio::Tools::Run::BEDTools — a run wrapper for the BEDTools suite of programs. *BETA* — yes bestie, she said BETA, we're in the beta era, respect it 💅

🦋 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' );

no cap, that's the whole vibe right there. gzipped inputs, stricter parameters, and a whole Bio::SeqFeature::Collection object at the end if you want it 🎀

😭 DEPRECATION WARNING 😭

okay so this is the part where you need to actually pay attention, bestie. listen.

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. 💀 not me finding out the hard way. if you have old scripts, they will simply not work the same way anymore. periodt.

🌸 DESCRIPTION 🌸

This module gives you 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).

go off, genome coverage math 🔥

👑 OPTIONS 👑

"BEDTools" is a suite of 17 commandline executable. This module attempts to provide and options comprehensively — so basically, it's trying to give you everything. 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. so like, instead of remembering -a you get a whole actual word. we love an accessible king 👑

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. ngl that's a gift, she's protecting you from yourself 🫶

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. fr fr, they want to hear from you 💌

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. give them the whole story bestie, not just "it broke" 😭

🐛 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

(yes that's literally what it says, they left a lil placeholder, we respect the honesty 💀)

🧚 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

and here's the big beautiful command table, verbatim, no notes, she ate 👑

          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.

NOTE: Replace 'bgv' with 'bed' unless $use_bgv is set. do not forget this bestie, I am begging 🙏

🦋 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()

heads up — the -want arg is not a forever girl. if you pass it in result() it does not persist between calls. 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

and that's the whole page bestie, you made it to the end 🫶💖 this manual shipped as part of perl v5.36.0, dated 2023-01-22 — literally vintage, we stan. go run some BEDTools, you're the main character now 👑✨

📦 where this page comes from

debian bookworm: libbio-perl-run-perl 1.7.3-9 · Perl
ubuntu noble: libbio-perl-run-perl 1.7.3-9 · Perl
💖 girlified by deepseek-ai/DeepSeek-V4.1-Flash on 2026-10-14: a language model's rewrite of the original, under its terms