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

💖 NAME 💖

Mdust — the Perl extension that does Mdust nucleotide filtering, bestie ✨ (it lives under Bio::Tools::Run::Mdust, iykyk)

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🦋 SYNOPSIS 🦋

use Bio::Tools::Run::Mdust;
my $mdust = Bio::Tools::Run::Mdust->new();

$mdust->run($bio_seq_object);

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🌸 DESCRIPTION 🌸

Okay so picture this: it's a Perl wrapper 🫶 for the nucleic acid complexity filtering program mdust, which you can get from TIGR over at http://www.tigr.org/tdb/tgi/software/. It takes a Bio::SeqI or Bio::PrimarySeqI object of type DNA as input. No DNA, no vibes, sorry 💅

Here's the tea on what you get back:

• If you pass in a Bio::Seq::RichSeqI, the low-complexity regions get added to the feature table of the target object as Bio::SeqFeature::Generic items with primary tag = 'Excluded' 👑
• Otherwise, a brand new target object comes back to you with the low-complexity regions masked (masked by N's, or whatever other character you set with maskchar() 🎀)

🚨 Real talk, bestie: the mdust executable must be sitting in a directory that's listed in either the PATH or the MDUSTDIR environment variable. If it's not there, this whole thing is giving nothing.

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🔥 SEE ALSO 🔥

• mdust
• Bio::PrimarySeq
• Bio::Seq::RichSeq
• Bio::SeqFeature::Generic

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💬 FEEDBACK 💬

🎀 Mailing Lists 🎀

User feedback is literally 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 💜

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. Not me being dramatic — it's just that 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, bestie, we're begging 🙏

🐛 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 ✨

Donald Jackson (donald.jackson@bms.com) — iconic, we stan 💅

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🌈 APPENDIX 🌈

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ 👀 (that's your cue that it's giving backstage, not main character energy).

🦋 new 🦋

• Title: new
• Usage: my $mdust = Bio::Tools::Run::Mdust->new( -target => $target_bioseq)
• Purpose: Create a new mdust object
• Returns: A Bio::Seq object
• Args:
  • target — Bio::Seq object for masking — alphabet MUST be DNA. No exceptions, bestie 💀
  • wsize — word size for masking (default = 3)
  • cutoff — cutoff score for masking (default = 28)
  • maskchar — character for replacing masked regions (default = N)
  • coords — boolean — indicate low-complexity regions as Bio::SeqFeature::Generic objects with primary tag 'Excluded', do not change sequence (default 0)
  • tmpdir — directory for storing temporary files
  • debug — boolean — toggle debugging output, do not remove temporary files
• Notes: All of the arguments can also be get/set with their own accessors, such as:

my $wsize = $mdust->wsize();

When processing multiple sequences, call Bio::Tools::Run::Mdust->new() once then pass each sequence as an argument to the target() or run() methods. Reusing the object is the move, lowkey efficient 🧚

⭐ run ⭐

• Title: run
• Usage: $mdust->run();
• Purpose: Run mdust on the target sequence
• Args: target (optional) — Bio::Seq object of alphabet DNA for masking
• Returns: Bio::Seq object with masked sequence or low-complexity regions added to feature table.

💜 target 💜

• Title: target
• Usage: $mdust->target($bio_seq)
• Purpose: Set/get the target (sequence to be filtered).
• Returns: Target Bio::Seq object
• Args: Bio::SeqI or Bio::PrimarySeqI object using the DNA alphabet (optional)
• Note: If coordinate parsing is selected ($mdust->coords = 1) then target MUST be a Bio::Seq::RichSeqI object. Passing a RichSeqI object automatically turns on coordinate parsing. Not optional, it just does that 💅

🌸 maskchar 🌸

• Title: maskchar
• Usage: $mdust->maskchar('N')
• Purpose: Set/get the character for masking low-complexity regions
• Returns: True on success
• Args: Either N (default), X or L (lower case)

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And that's the whole page, bestie!! This gem was documented by perl v5.36.0 on 2023-01-22, from the Bio::T...:Mdust(3pm) files themselves — go mask some low-complexity regions and slay 💖✨🎀🦋🌸