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

✨ NAME ✨

Bio::Variation::AAReverseMutate — okay so this one pulls point mutation and codon info out of single amino acid changes 🧬💅

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🌸 SYNOPSIS 🌸

$aamut = Bio::Variation::AAReverseMutate->new
             (-aa_ori => 'F',
              -aa_mut => 'S',
              -codon_ori => 'ttc', # optional
              -codon_table => '3'  # defaults to 1
              );

@points = $aamut->each_Variant;

if (scalar @points > 0 ) {
    foreach $rnachange ( @points ) {
        # $rnachange is a Bio::Variation::RNAChange object
        print " ", $rnachange->allele_ori->seq, ">",
        $rnachange->allele_mut->seq, " in ",
        $rnachange->codon_ori, ">", $rnachange->codon_mut,
        " at position ", $rnachange->codon_pos, "\n";
    }
} else  {
    print "No point mutations possible\n",
}

Like, you build the object, you ask for each_Variant, and if you get anything back each thing is a Bio::Variation::RNAChange object you can interrogate. If you get nothing back, bestie, there's just no point mutation that does it 😭

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🦋 DESCRIPTION 🦋

So Bio::Variation::AAReverseMutate objects take in reference and mutated amino acid info and deduce the potential point mutations at the RNA level that could lead to that change. The way that it works is very much detective energy 🔍

And you can narrow the vibes even more: if you tell the object what the codon is in the reference sequence, the choice gets further limited. Results come back to you as Bio::Variation::RNAChange objects. Periodt.

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💌 FEEDBACK 💌

📬 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules — no cap, they actually want to hear from you 🫶 Send your comments and suggestions preferably to 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 to the module maintainer directly. The reason is that many experienced and responsive experts will be able look at the problem and quickly address it. And pls pls pls include a thorough description of the problem with code and data examples if at all possible — it's giving helpful, and it makes everyone's life easier ✨

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help keep track of 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 _ — that underscore is the little "backstage pass" marker, iykyk 🙈

🌟 aa_ori

• Title: aa_ori
• Usage: $obj->aa_ori();
• Function: Sets and returns original aa sequence. If value is not set, returns false. Amino acid sequences are stored in upper case characters, others in lower case.
• Example: (none given)
• Returns: string
• Args: single character amino acid code

💫 aa_mut

• Title: aa_mut
• Usage: $obj->aa_mut();
• Function: Sets and returns the mutated allele sequence. If value is not set, returns false.
• Example: (none given)
• Returns: string
• Args: single character amino acid code

🌈 codon_ori

• Title: codon_ori
• Usage: $obj->codon_ori();
• Function: Sets and returns codon_ori triplet. If value is not set, returns false. The string has to be three characters long. The character content is not checked.
• Example: (none given)
• Returns: string
• Args: string

Heads up bestie: it checks the length and that's it. It does not check whether those three characters are actually a real codon. So don't come for it later 💀

🍓 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: (none given)
• Returns: integer
• Args: none if get, the new value if set

🧚 each_Variant

• Title: each_Variant
• Usage: $obj->each_Variant();
• Function: Returns a list of Variants.
• Example: (none given)
• Returns: list of Variants
• Args: none

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And that's the whole page, bestie — slay 💜 This was perl v5.32.1, dated 2021-12-02, living in the Bio::V...eMutate(3pm) page of the User Contributed Perl Documentation. Go forth and reverse-mutate, you icon 👑✨