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

💖 Bio::Variation::RNAChange 💖

okay bestie, this is Bio::Variation::RNAChange, a sequence change class for the RNA level, and it lives in the Perl documentation corner of your system (3pm). It's giving "genetics but make it an object" and honestly? iconic. 🧬✨

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✨ NAME ✨

Bio::Variation::RNAChange — Sequence change class for RNA level 🦋

---

🌸 SYNOPSIS 🌸

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

print "The codon change is ", $rnachange->codon_ori,
    ">", $rnachange->codon_mut, "\n";

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

# and create links to and from DNA level mutation objects
$rnachange->DNAMutation($dnamut);
$dnamut->RNAChange($rnachange);

like, you literally just make the object, hand it some alleles, print your codon glow-up, and link it up. no cap. 💅

---

💜 DESCRIPTION 💜

The instantiable class Bio::Variation::DNAMutation describes basic sequence changes at RNA molecule level. It uses methods defined in superclass Bio::Variation::VariantI. See Bio::Variation::VariantI for details.

You are normally expected to create a corresponding Bio::Variation::DNAMutation object even if mutation is defined at RNA level. The numbering follows then cDNA numbering. Link the DNAMutation object to the RNAChange object using the method DNAMutation(). If the variation described by a RNAChange object is translated, link the corresponding Bio::Variation::AAChange object to it using method AAChange(). See Bio::Variation::DNAMutation and Bio::Variation::AAChange for more information.

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🫶 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, 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. (yes the original says "reponsive", we are keeping it, it's part of the lore 😭)

🐛 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

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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 _

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⭐ codon_ori

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

Sets and returns codon_ori triplet. If value is not set, creates the codon triplet from the codon position and flanking sequences. The string has to be three characters long. The character content is not checked. 👀 (so like, she will not vibe check your letters, only your length)

• Example :
• Returns : string
• Args : string

---

⭐ codon_mut

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

Sets and returns codon_mut triplet. If value is not set, creates the codon triplet from the codon position and flanking sequences. Return undef for other than point mutations.

• Example :
• Returns : string
• Args : string

---

⭐ codon_pos

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

Sets and returns the position of the mutation start in the codon. If value is not set, returns false.

• Example :
• Returns : 1,2,3
• Args : none if get, the new value if set

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⭐ codon_table

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

Sets and returns the codon table id of the RNA. If value is not set, returns 1, 'universal' code, as the default. 🌍

• Example :
• Returns : integer
• Args : none if get, the new value if set

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⭐ DNAMutation

• Title : DNAMutation
• Usage :

$mutobj = $obj->DNAMutation;
$mutobj = $obj->DNAMutation($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

---

⭐ AAChange

• Title : AAChange
• Usage :

$mutobj = $obj->AAChange;
$mutobj = $obj->AAChange($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

---

⭐ exons_modified

• Title : exons_modified
• Usage :

$modified = $obj->exons_modified;
$modified = $obj->exons_modified(1);

• Function : Returns or sets information (example: a simple boolean flag) about the modification of exons as a result of a mutation.

---

⭐ region

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

Sets and returns the name of the sequence region type or protein domain at this location. If value is not set, returns false.

• Example :
• Returns : string
• Args : string

---

⭐ cds_end

• Title : cds_end
• Usage : $cds_end = $obj->get_cds_end();
• Function :

Sets or returns the cds_end from the beginning of the DNA sequence to the coordinate start used to describe variants. Should be the location of the last nucleotide of the terminator codon of the gene.

• Example :
• Returns : value of cds_end, a scalar
• Args :

---

⭐ 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

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⭐ _change_codon_pos

• Title : _change_codon_pos
• Usage : $newCodonPos = _change_codon_pos($myCodonPos, 5)
• Function :

Keeps track of the codon position in a changeing sequence

• Returns : codon_pos = integer 1, 2 or 3
• Args : valid codon position, signed integer offset to a new location in sequence

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💀 heads up bestie: _change_codon_pos is an internal method, which is why it starts with an underscore — that's the usual signal that you're not meant to be poking it from the outside. You've been warned. 🙈

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and that's the whole page!! 🎉 this came out of perl v5.32.1, dated 2021-12-02, so shoutout to the Perl version and the date for keeping it real 💖 thanks for reading, mwah, go forth and annotate your RNA changes 🦋✨💅