Bio::V...utation(3pm)

✨ NAME ✨

Bio::Variation::DNAMutation — the DNA level mutation class, bestie 💖

(also, hi, this whole thing lives in the User Contributed Perl Documentation manual set, so you know it's the real deal ✨)

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🌸 SYNOPSIS 🌸

okay so this is literally how you use it:

$dnamut = Bio::Variation::DNAMutation->new
    ('-start'         => $start,
     '-end'           => $end,
     '-length'        => $len,
     '-upStreamSeq'   => $upflank,
     '-dnStreamSeq'   => $dnflank,
     '-proof'         => $proof,
     '-isMutation'    => 1,
     '-mut_number'    => $mut_number
    );
$a1 = Bio::Variation::Allele->new;
$a1->seq('a');
$dnamut->allele_ori($a1);
my $a2 = Bio::Variation::Allele->new;
$a2->seq('t');
$dnamut->add_Allele($a2);

print "Restriction changes are ", $dnamut->restriction_changes, "\n";

# add it to a SeqDiff container object
$seqdiff->add_Variant($dnamut);

no notes, that's the whole vibe 💅

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🦋 DESCRIPTION 🦋

Bio::Variation::DNAMutation is an instantiable class (yes, you can actually make objects out of it, slay 👑) and it describes basic sequence changes at the genomic DNA level. It gets a bunch of its powers from its superclass, Bio::Variation::VariantI — go read Bio::Variation::VariantI for the details, iykyk 💜

If the variation your DNAMutation object is describing gets transcibed (yes bestie, the original really did spell it that way, we respect the typo, it's iconic 💀), then you link the matching Bio::Variation::RNAChange object to it with the method RNAChange(). Peep Bio::Variation::RNAChange for more info 🌈

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💌 FEEDBACK 💌

📬 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules — fr fr, they literally said it, not me. Send your comments and suggestions preferably to the Bioperl mailing lists, and 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 to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. If at all possible, please include a thorough description of the problem with code and data examples, because the more context you give, the faster someone can help you 🙏

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

do it bestie, the bugs are not gonna fix themselves ✨

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🌟 AUTHOR - Heikki Lehvaslaiho 🌟

Email: heikki-at-bioperl-dot-org 💖

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ 👀

🧬 CpG

• Title: CpG
• Usage: $obj->CpG()
• Function: sets and returns boolean values for variation hitting a CpG site. Unset value return -1.
• Example: $obj->CpG()
• Returns: boolean
• Args: optional true of false value

🔗 RNAChange

• Title: RNAChange
• Usage:

$mutobj = $obj->RNAChange;
$mutobj = $obj->RNAChange($objref);

• Function: Returns or sets the link-reference to a mutation/change object. If there is no link, it will return undef
• Returns: an obj_ref or undef

🏷️ label

• Title: label
• Usage: $obj->label();
• Function:

Sets and returns mutation event label(s). If value is not set, or no argument is given returns false. Each instantiable subclass of L<Bio::Variation::VariantI> needs to implement this method. Valid values are listed in 'Mutation event controlled vocabulary' in http://www.ebi.ac.uk/mutations/recommendations/mutevent.html.

• Example: (nothing here bestie, that's just how it is 🙈)
• Returns: string
• Args: string

🧾 sysname

• Title: sysname
• Usage: $self->sysname
• Function:

This subroutine creates a string corresponding to the 'systematic name' of the mutation. Systematic name is specified in Antonorakis & MDI Nomenclature Working Group: Human Mutation 11:1-3, 1998.

• Returns: string

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and that's the whole page, bestie 🎀 this was perl v5.32.1, dated 2021-12-02, from the Bio::V...utation(3pm) page — go forth and mutate responsibly 💅✨