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

💖 Bio::V...Allele(3pm) 💖

okay bestie, so this is Bio::Variation::Allele — a lil' sequence object with allele-specific attributes, straight outta the User Contributed Perl Documentation. it's giving bioperl core, it's giving genetics, and honestly? obsessed. let's get into it 🧬✨

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✨ NAME ✨

Bio::Variation::Allele — Sequence object with allele-specific attributes 💅

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🌸 SYNOPSIS 🌸

$allele1 = Bio::Variation::Allele->new ( -seq => 'A',
                                         -id  => 'AC00001.1',
                                         -alphabet => 'dna',
                                         -is_reference => 1
                                       );

look at her go, no cap 🫶

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🦋 DESCRIPTION 🦋

so like, a list of alleles describes the known sequence alternatives in a variable region. iconic concept, right? these alleles live inside Bio::Variation::VariantI complying objects — peep Bio::Variation::VariantI for the deets if you need them 📚

also, Bio::Varation::Alleles are PrimarySeqI complying objects, and they can hold database cross references just like the Bio::DBLinkContainerI interface specifies. double threat, main character energy 💅

now here's the part that's lowkey a lot: a huge chunk of the complexity in dealing with Allele objects comes from null alleles — those are Allele objects whose sequence string has zero length. yeah. empty. the void. 💀

and beyond describing the allele by its sequence, you can also describe the repeat structure within that sequence. that's done with the repeat_unit method (think 'ca') and the repeat_count method (think 7). periodt 🌈

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🫶 FEEDBACK 🫶

💌 Mailing Lists

user feedback is literally an integral part of the evolution of this and every other Bioperl module. so 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

and not straight to the module maintainer, okay? there are so many experienced and reponsive experts on there who can look at the problem and quickly address it. 🙈 if at all possible, please include a thorough description of the problem along with code and data examples. the more context, the better the slay.

🐛 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:

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 _ — iykyk 🤫

⭐ is_reference

• Title — is_reference
• Usage — $obj->is_reference()
• Function — sets and returns boolean values. unset values return false.
• Example — $obj->is_reference()
• Returns — boolean
• Args — optional true of false value

💜 add_DBLink

• Title — add_DBLink
• Usage — $self->add_DBLink($ref)
• Function — adds a link object
• Example —
• Returns —
• Args —

💙 each_DBLink

• Title — each_DBLink
• Usage — foreach $ref ( $self->each_DBlink() )
• Function — gets an array of DBlink of objects
• Example —
• Returns —
• Args —

🌸 repeat_unit

• Title — repeat_unit
• Usage — $obj->repeat_unit('ca');
• Function — sets and returns the sequence of the repeat_unit the allele is composed of.
• Example —
• Returns — string
• Args — string

🌺 repeat_count

• Title — repeat_count
• Usage — $obj->repeat_count();
• Function — sets and returns the number of repeat units in the allele.
• Example —
• Returns — string
• Args — string

✨ count

• Title — count
• Usage — $obj->count();
• Function — sets and returns the number of times this allele was observed.
• Example —
• Returns — string
• Args — string

🦋 frequency

• Title — frequency
• Usage — $obj->frequency();
• Function — sets and returns the frequency of the allele in the observed population.
• Example —
• Returns — string
• Args — string

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and that's the whole page, bestie!! 🎀 this gem is perl v5.32.1, dated 2021-12-02, and it's Bio::V...Allele(3pm) from the User Contributed Perl Documentation — go forth and allele responsibly, mwah 💖✨