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

💖 Bio::Variation::AAChange 💖

okay bestie, welcome to Bio::Variation::AAChange — the Sequence change class for polypeptides ✨ (that's the NAME, and yes it's giving protein-level main character energy 🧬👑

It lives in the User Contributed Perl Documentation part of the Bio::V...Change(3pm) manual. We're so back.

---

🌸 SYNOPSIS 🌸

here's the vibe, copy-paste approved:

$aamut = Bio::Variation::AAChange->new
    ('-start'         => $start,
     '-end'           => $end,
     '-length'        => $len,
     '-proof'         => $proof,
     '-isMutation'    => 1,
     '-mut_number'    => $mut_number
     );

my $a1 = Bio::Variation::Allele->new;
$a1->seq($ori) if $ori;
$aamut->allele_ori($a1);
my $a2 = Bio::Variation::Allele->new;
$a2->seq($mut) if $mut;
$aachange->add_Allele($a2);
$aachange->allele_mut($a2);

print  "\n";

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

# and create links to and from RNA level variant objects
$aamut->RNAChange($rnachange);
$rnachange->AAChange($rnachange);

yes, print "\n"; is in there. iconic behaviour honestly. we don't question it 💅

---

🦋 DESCRIPTION 🦋

So the instantiable class Bio::Variation::RNAChange describes basic sequence changes at polypeptide level. It uses methods defined in superclass Bio::Variation::VariantI — go read Bio::Variation::VariantI for the details, bestie, it's where all the lore lives 📚✨

If the variation described by a AAChange object has a known Bio::Variation::RNAAChange object, you create the link with method AAChange(). See Bio::Variation::AAChange for more information 👀

---

🫶 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 lists — 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. Many experienced and responsive 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 — the more context you give, the faster someone can slay your bug 🐛💥

🐞 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

---

👑 AUTHOR - Heikki Lehvaslaiho 👑

Email: heikki-at-bioperl-dot-org

(the -at- and -dot- are doing the anti-spam censor thing, you got this 💖)

---

🎀 APPENDIX 🎀

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (iykyk — underscore = backstage, don't touch unless you're built different).

✨ RNAChange

• Title — RNAChange
• Usage —

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

• Function — Returns or sets the link-reference to a mutation/change object. If there is no link, it will return undef (so like, no link, no vibes, 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 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 —
• Returns — string
• Args — string

✨ similarity_score

• Title — similarity_score
• Usage — $self->similarity_score
• Function — Measure for evolutionary conservativeness of single amino substitutions. Uses BLOSUM62. Negative numbers are noncoservative changes.
• Returns — integer, undef if not single amino acid change

✨ trivname

• Title — trivname
• Usage — $self->trivname
• Function — Given a Bio::Variation::AAChange object with linked Bio::Variation::RNAChange and Bio::Variation::DNAMutation objects, this subroutine creates a string corresponding to the 'trivial name' of the mutation. Trivial name is specified in Antonorakis & MDI Nomenclature Working Group: Human Mutation 11:1-3, 1998.
• Returns — string

---

🎀 that's the whole page bestie, no notes, every flag accounted for, we ate and left absolutely no crumbs 💅

okay and for the cute sign-off: this page is from perl v5.32.1, dated 2021-12-02 🌸 that's the source/version and the date, tucked in right where the footer would be, mwah 💖✨🦋