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

💖 Bio::Tools::Run::RepeatMasker — bestie edition 💖

okay so this is the perl doc page for Bio::Tools::Run::RepeatMasker, aka Bio::T...tMasker(3pm) from the User Contributed Perl Documentation. it's a wrapper. it wraps RepeatMasker. slay. let's go 🦋

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✨ NAME ✨

Bio::Tools::Run::RepeatMasker — a Wrapper for the RepeatMasker Program 💅

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✨ SYNOPSIS ✨

use Bio::Tools::Run::RepeatMasker;

my @params=("mam" => 1,"noint"=>1);
my $factory = Bio::Tools::Run::RepeatMasker->new(@params);
$in  = Bio::SeqIO->new(-file => "contig1.fa",
                       -format => 'fasta');
my $seq = $in->next_seq();

#return an array of Bio::SeqFeature::FeaturePair objects
my @feats = $factory->run($seq);

# or

$factory->run($seq);
my @feats = $factory->repeat_features;

#return the masked sequence, a Bio::SeqI object
my $masked_seq = $factory->run;

look at her. she's doing so much. three whole vibes in one synopsis 🫶

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✨ DESCRIPTION ✨

so to even use this module, bestie, the RepeatMasker program (and probably its database too) has to be installed on your machine. no install, no service 💀

and what does RepeatMasker even do? it screens DNA sequences for interspersed repeats that are known to exist in mammalian genomes — and for low complexity DNA sequences. iconic behavior honestly. for more info on the program and how to use it, go peek at http://www.repeatmasker.org/. 🧚

okay so once RepeatMasker is installed, you gotta let Bioperl know where it lives. there are (at least) three ways to do that:

1. just make sure the RepeatMasker executable is chillin' in your path. easy. ✨
2. define an environmental variable REPEATMASKERDIR that points to a directory containing the RepeatMasker executable: in bash:

export REPEATMASKERDIR=/home/username/RepeatMasker/

in csh/tcsh:

setenv REPEATMASKERDIR /home/username/RepeatMasker/

3. include a definition of the environmental variable REPEATMASKERDIR in every single script that's gonna use this RepeatMasker wrapper module, like:

BEGIN { $ENV{REPEATMASKERDIR} = '/home/username/RepeatMasker/' }
use Bio::Tools::Run::RepeatMasker;

three options, pick your fighter 🎀

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✨ FEEDBACK ✨

🌸 Mailing Lists 🌸

user feedback is, like, an integral part of the evolution of this and other Bioperl modules. literally. send your comments and suggestions preferably to one of the Bioperl mailing lists. 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 going straight to the module maintainer, bestie. there are so many experienced and responsive experts there who will be able to look at the problem and quickly address it. and please include a thorough description of the problem with code and data examples if at all possible. the more context the better, fr fr 🙏

🌸 Reporting Bugs 🌸

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. bug reports can be submitted via the web:

http://redmine.open-bio.org/projects/bioperl/

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✨ AUTHOR - Shawn Hoon ✨

Email: shawnh@fugu-sg.org

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✨ APPENDIX ✨

the rest of this documentation goes into detail on each of the object methods. internal methods are usually preceded with a _ (iykyk 👀).

🎀 program_name 🎀

• Title : program_name
• Usage : $factory>program_name()
• Function: holds the program name
• Returns: string
• Args : None

🎀 program_dir 🎀

• Title : program_dir
• Usage : $factory->program_dir(@params)
• Function: returns the program directory, obtained from ENV variable.
• Returns: string
• Args :

🎀 new 🎀

• Title : new
• Usage : $rm->new($seq)
• Function: creates a new wrapper
• Returns: Bio::Tools::Run::RepeatMasker
• Args : self

🎀 version 🎀

• Title : version
• Usage :
• Function: Determine the version number of the program
• Example :
• Returns : float or undef
• Args : none

🎀 run 🎀

• Title : run
• Usage : $rm->run($seq);
• Function: Run Repeatmasker on the sequence set as the argument
• Returns : an array of repeat features that are Bio::SeqFeature::FeaturePairs
• Args : Bio::PrimarySeqI compliant object

🎀 mask 🎀

• Title : mask
• Usage : $rm->mask($seq)
• Function: This method is deprecated. Call run() instead
• Example :
• Returns : an array of repeat features that are Bio::SeqFeature::FeaturePairs
• Args : Bio::PrimarySeqI compliant object

⚠️ bestie listen to me. this one is deprecated. do not build your whole personality around it. call run() instead. periodt.

🎀 _run 🎀

• Title : _run
• Usage : $rm->_run ($filename,$param_string)
• Function: internal function that runs the repeat masker
• Example :
• Returns : an array of repeat features
• Args : the filename to the input sequence and the parameter string

🎀 masked_seq 🎀

• Title : masked_seq
• Usage : $rm->masked_seq($seq)
• Function: get/set for masked sequence
• Example :
• Returns : the masked sequence
• Args : Bio::Seq object

🎀 repeat_features 🎀

• Title : repeat_features
• Usage : $rm->repeat_features(\@rf)
• Function: get/set for repeat features array
• Example :
• Returns : the array of repeat features
• Args :

🎀 _setparams() 🎀

• Title : _setparams
• Usage : Internal function, not to be called directly
• Function: Create parameter inputs for repeatmasker program
• Example :
• Returns : parameter string to be passed to repeatmasker
• Args : name of calling object

🎀 _setinput() 🎀

• Title : _setinput
• Usage : Internal function, not to be called directly
• Function: writes input sequence to file and return the file name
• Example :
• Returns : string
• Args : a Bio::PrimarySeqI compliant object

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✨ Bio::Tools::Run::Wrapper methods ✨

🦋 no_param_checks 🦋

• Title : no_param_checks
• Usage : $obj->no_param_checks($newval)
• Function: Boolean flag as to whether or not we should trust the sanity checks for parameter values
• Returns : value of no_param_checks
• Args : newvalue (optional)

🦋 save_tempfiles 🦋

• Title : save_tempfiles
• Usage : $obj->save_tempfiles($newval)
• Function:
• Returns : value of save_tempfiles
• Args : newvalue (optional)

🦋 outfile_name 🦋

• Title : outfile_name
• Usage : my $outfile = $codeml->outfile_name();
• Function: Get/Set the name of the output file for this run (if you wanted to do something special)
• Returns : string
• Args : [optional] string to set value to

🦋 tempdir 🦋

• Title : tempdir
• Usage : my $tmpdir = $self->tempdir();
• Function: Retrieve a temporary directory name (which is created)
• Returns : string which is the name of the temporary directory
• Args : none

🦋 cleanup 🦋

• Title : cleanup
• Usage : $codeml->cleanup();
• Function: Will cleanup the tempdir directory
• Returns : none
• Args : none

🦋 io 🦋

• Title : io
• Usage : $obj->io($newval)
• Function: Gets a L<Bio::Root::IO> object
• Returns : L<Bio::Root::IO>
• Args : none

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and that's the whole page, bestie!! 🎉 this doc ships as part of perl v5.36.0, dated 2023-01-22, from the User Contributed Perl Documentation collection — the Bio::T...tMasker(3pm) page itself. go mask some repeats, you absolute icon 👑💜✨