Bio::V...on::SNP(3pm)

💖 Bio::Variation::SNP — submitted SNP 💖

okay bestie, gather round, because this one is the submitted SNP module from the Bioperl family and she is lowkey iconic. it's the Bio::Variation::SNP page from the User Contributed Perl Documentation, and we're gonna walk it together, no skimming, no skipping. 🧬✨

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🌸 SYNOPSIS 🌸

fr fr, this is the whole vibe:

$SNP = Bio::Variation::SNP->new ();

that's it. that's the entry point. main character energy from line one. 👑

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🦋 DESCRIPTION 🦋

so Bio::Variation::SNP inherits from Bio::Variation::SeqDiff and Bio::Variation::Allele (yes, both, she's multifaceted 💅), and then stacks on top some extra methods that are (db)SNP specific — meaning stuff like refSNP/subSNP IDs, batch IDs, and validation methods.

like. she's not just a sequence diff, she's a sequence diff with receipts. 🧾

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💌 FEEDBACK 💌

📬 Mailing Lists

ngl, user feedback is an integral part of the evolution of this and other Bioperl modules — that's a direct quote from the vibes, and it's true. send your comments and suggestions preferably to one of the Bioperl mailing lists. your participation is much appreciated, and we mean that. 🫶

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 genuinely sweet: many experienced and responsive experts will be able to look at the problem and quickly address it. so like, you get a whole group chat instead of one person's DMs. 💖

also please include a thorough description of the problem with code and data examples if at all possible. the more detail, the faster 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 ✨

Allen Day <allenday@ucla.edu>

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🎀 APPENDIX 🎀

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk, that underscore is the "don't touch unless you know what you're doing" marker 🙈).

💅 get/set-able methods

Usage   : $is = $snp->method()
Function: for getting/setting attributes
Returns : a value.  probably a scalar.
Args    : if you're trying to set an attribute, pass in the new value.

the way this works is so clean: call it with no args and she tells you a thing, call it with an arg and she becomes that thing. get/set duality, periodt. 🌈

Methods:

--------
id
type
observed
seq_5
seq_3
ncbi_build
ncbi_chr_hits
ncbi_ctg_hits
ncbi_seq_loc
ucsc_build
ucsc_chr_hits
ucsc_ctg_hits
heterozygous
heterozygous_SE
validated
genotype
handle
batch_id
method
locus_id
symbol
mrna
protein
functional_class

all 24 of them, no cuts, no skips. collect them all like they're stickers. ⭐

🔍 is_subsnp

Title   : is_subsnp
Usage   : $is = $snp->is_subsnp()
Function: returns 1 if $snp is a subSNP
Returns : 1 or undef
Args    : NONE

a little vibe check: is this thing a subSNP or not. returns 1 if yes, undef if no. no args, no drama. 🦋

🪆 subsnp

Title   : subsnp
Usage   : $subsnp = $snp->subsnp()
Function: returns the currently active subSNP of $snp
Returns : Bio::Variation::SNP
Args    : NONE

she hands you the currently active subSNP. that's the one in the spotlight rn. 🌟

➕ add_subsnp

Title   : add_subsnp
Usage   : $subsnp = $snp->add_subsnp()
Function: pushes the previous value returned by subsnp() onto a stack,
          accessible with each_subsnp().
          Sets return value of subsnp() to a new Bio::Variation::SNP
          object, and returns that object.
Returns : Bio::Varitiation::SNP
Args    : NONE

okay so this one is a lil stacked situation 📚 — it pushes the previous value returned by subsnp() onto a stack (which you can get at with each_subsnp()), then sets the return value of subsnp() to a new Bio::Variation::SNP object, and returns that object. new subSNP just dropped. 💅

note: the Returns line above says Bio::Varitiation::SNP and we are keeping it exactly as written, typos and all, because that's what the page says and we don't edit the source of truth. 💖

🎁 each_subsnp

Title   : each_subsnp
Usage   : @subsnps = $snp->each_subsnp()
Function: returns a list of the subSNPs of a refSNP
Returns : list
Args    : NONE

give her a refSNP, she gives you back the whole list of its subSNPs. list context, bestie, that's the move. ✨

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and that's the whole page, top to bottom, nothing left out. 🫶

this gem comes from the Bioperl distribution — page Bio::Variation::SNP(3pm), built with perl v5.32.1, dated 2021-12-02. ty for coming to my ted talk, go write some SNPs, mwah 💋💖