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

💖 NAME 💖

Bio::V...SeqDiff(3pm) — straight outta the User Contributed Perl Documentation, bestie — this is the container class for mutation/variant descriptions. It's giving "I hold all your variant lore in one place" energy, fr fr.

✨ SYNOPSIS ✨

$seqDiff = Bio::Variation::SeqDiff->new (
                                         -id => $M20132,
                                         -alphabet => 'rna',
                                         -gene_symbol => 'AR'
                                         -chromosome => 'X',
                                         -numbering => 'coding'
                                        );
# get a DNAMutation object somehow
$seqDiff->add_Variant($dnamut);
print  $seqDiff->sys_name(), "\n";

Like, yes, the -gene_symbol => 'AR' line is missing its comma, and no, I'm not fixing it, because that's literally what the page says and we respect the source material in this house. 💅

🦋 DESCRIPTION 🦋

Okay so SeqDiff stores Bio::Variation::VariantI object references plus all the descriptive info that's common to every change in a sequence. Mutations here are understood to mean any kind of sequence markers, and they're expected to occur in the same chromosome. If you want the details on that, go peek at Bio::Variation::VariantI — it ate, no cap.

The methods of SeqDiff are geared towards describing mutations in human genes, using a gene-based coordinate system where the 'A' of the initiator codon has number 1 and the one before it is -1. That's just the conventions of human genetics, so like, respect the rules of the land. 👑

There's gonna be a class Bio::Variation::Genotype to describe markers in different chromosomes and diploid genototypes. Not here yet, but the vibes are immaculate and it's coming.

The classes that implement the Bio::Variation::VariantI interface are Bio::Variation::DNAMutation, Bio::Variation::RNAChange, and Bio::Variation::AAChange. For more info, hit up Bio::Variation::VariantI, Bio::Variation::DNAMutation, Bio::Variation::RNAChange, and Bio::Variation::AAChange — they're all iconic in their own right. 🌈

So how do variant objects get in? Two ways, bestie:

• an array passed to the constructor, or
• individual Variant objects added one at a time with the add_Variant method.

Pick your fighter. 🫶

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💌 FEEDBACK 💌

📬 Mailing Lists 📬

User feedback is an integral part of the evolution of this and other Bioperl modules — like, the glow-up is literally powered by 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. Why? Because so many experienced and reponsive experts will be able look at the problem and quickly address it — that's the group chat advantage, bestie. 💅 Please include a thorough description of the problem with code and data examples if at all possible. The more receipts, the faster the fix. 🧚

🐛 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

Do it for the culture. 🌸

---

👑 AUTHOR - Heikki Lehvaslaiho 👑

Email: heikki-at-bioperl-dot-org

(Yes, that's the actual format the page uses. Written exactly like that. We love a legend who formats their own email like a captcha. 💀)

🌟 CONTRIBUTORS 🌟

Eckhard Lehmann, ecky@e-lehmann.de

Shoutout to Eckhard, fr fr. 🎀

✨ APPENDIX ✨

okay bestie, this is the deep-lore part 💅 every single object method gets its own lil breakdown. heads up: internal methods are usually the ones that start with an underscore (_) — that's the secret handshake, iykyk 🔑

---

💖 new

• Title — new
• Usage — $seqDiff = Bio::Variation::SeqDiff->new;
• Function — spawns a brand new Bio::Variation::SeqDiff, no cap 🌱
• Returns — a reference to a fresh object of class SeqDiff
• Args — (none specified)

---

🎀 id

• Title — id
• Usage — $obj->id(H0001); $id = $obj->id();
• Function — sets or returns the id of the seqDiff. this is the one you use to hand the whole collection of variants a UID without any semantic associations attached. it's giving ✨pure vibes only✨
• Example — (none given)
• Returns — value of id, a scalar
• Args — newvalue (optional)

---

🦋 sysname

• Title — sysname
• Usage — $obj->sysname('5C>G'); $sysname = $obj->sysname();
• Function — sets or returns the systematic name of the seqDiff. this name should follow the HUGO Mutation Database Initiative approved nomenclature, we respect the rules here. and if you call it without setting the value first, it will generate the name for you out of the Bio::Variation::DNAMutation objects attached. it literally does the work itself, main character energy fr fr 👑
• Example — (none given)
• Returns — value of sysname, a scalar
• Args — newvalue (optional)

---

🌸 trivname

• Title — trivname
• Usage — $obj->trivname('[A2G;T56G]'); $trivname = $obj->trivname();
• Function — sets or returns the trivial name of the seqDiff. also supposed to follow the HUGO Mutation Database Initiative approved nomenclature. and same deal: if you never set it, it'll build it for you from the Bio::Variation::AAChange objects attached 🧚
• Example — (none given)
• Returns — value of trivname, a scalar
• Args — newvalue (optional)

---

🌈 chromosome

• Title — chromosome
• Usage — $obj->chromosome('X'); $chromosome = $obj->chromosome();
• Function — sets or returns the chromosome (the "linkage group") of the seqDiff 🧬
• Example — (none given)
• Returns — value of chromosome, a scalar
• Args — newvalue (optional)

---

⭐ gene_symbol

• Title — gene_symbol
• Usage — $obj->gene_symbol('FOS'); $gene_symbol = $obj->gene_symbol;
• Function — sets or returns the gene symbol for the CDS you're studying 📖
• Example — (none given)
• Returns — value of gene_symbol, a scalar
• Args — newvalue (optional)

---

💜 description

• Title — description
• Usage — $obj->description('short description'); $descr = $obj->description();
• Function — sets or returns the short description of the seqDiff. keep it snappy bestie ✍️
• Example — (none given)
• Returns — value of description, a scalar
• Args — newvalue (optional)

---

🍓 alphabet

• Title — alphabet
• Usage — if( $obj->alphabet eq 'dna' ) { /Do Something/ }
• Function — returns the type of primary reference sequence, which is one of 'dna', 'rna' or 'protein'. this is case sensitive, so don't get cute with the capitals 🚨
• Returns — a string, either 'dna','rna','protein'.
• Args — none

---

🧚 numbering

• Title — numbering
• Usage — $obj->numbering('coding'); $numbering = $obj->numbering();
• Function — sets or returns the string that gives the numbering schema used to describe the variants 🔢
• Example — (none given)
• Returns — value of numbering, a scalar
• Args — newvalue (optional)

---

🎀 offset

• Title — offset
• Usage — $obj->offset(124); $offset = $obj->offset();
• Function — sets or returns the offset from the beginning of the DNA sequence to the coordinate start used to describe variants. typically that's the beginning of the coding region of the gene. and listen: the cds_start should be 1 + offset ➕
• Example — (none given)
• Returns — value of offset, a scalar
• Args — newvalue (optional)

---

🔥 cds_start

• Title — cds_start
• Usage — $obj->cds_start(123); $cds_start = $obj->cds_start();
• Function — sets or returns the cds_start from the beginning of the DNA sequence to the coordinate start used to describe variants. typically the beginning of the coding region of the gene. it needs to be 1 + offset and that's literally how it's implemented, no cap 🫶
• Example — (none given)
• Returns — value of cds_start, a scalar
• Args — newvalue (optional)

---

💅 cds_end

• Title — cds_end
• Usage — $obj->cds_end(321); $cds_end = $obj->cds_end();
• Function — sets or returns the position of the last nucleotide of the termination codon. the coordinate system starts from cds_start 📍
• Example — (none given)
• Returns — value of cds_end, a scalar
• Args — newvalue (optional)

---

🦋 rna_offset

• Title — rna_offset
• Usage — $obj->rna_offset(124); $rna_offset = $obj->rna_offset();
• Function — sets or returns the rna_offset from the beginning of the RNA sequence to the coordinate start used to describe variants. typically the beginning of the coding region of the gene 🧬
• Example — (none given)
• Returns — value of rna_offset, a scalar
• Args — newvalue (optional)

---

🌸 rna_id

• Title — rna_id
• Usage — $obj->rna_id('transcript#3'); $rna_id = $obj->rna_id();
• Function — sets or returns the ID for the original RNA sequence of the seqDiff 🏷️
• Example — (none given)
• Returns — value of rna_id, a scalar
• Args — newvalue (optional)

---

✨ add_Variant

• Title — add_Variant
• Usage — $obj->add_Variant($variant)
• Function — pushes one Bio::Variation::Variant into the list of variants. and at the same time, it creates a link from the Variant back to SeqDiff using its SeqDiff method. mutuals 🫶
• Example — (none given)
• Returns — 1 when it succeeds, 0 for failure.
• Args — Variant object

---

🌈 each_Variant

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

---

👑 add_Gene

• Title — add_Gene
• Usage — $obj->add_Gene($gene)
• Function — pushes one Bio::LiveSeq::Gene into the list of genes 🧬
• Example — (none given)
• Returns — 1 when it succeeds, 0 for failure.
• Args — Bio::LiveSeq::Gene object

see Bio::LiveSeq::Gene for more information 📚

---

🎀 each_Gene

• Title — each_Gene
• Usage — $obj->each_Gene();
• Function — returns a list of Bio::LiveSeq::Genes 📋
• Example — (none given)
• Returns — list of Genes
• Args — none

---

🍓 dna_ori

• Title — dna_ori
• Usage — $obj->dna_ori('atgctgctgctgct'); $dna_ori = $obj->dna_ori();
• Function — sets or returns the original DNA sequence string of the seqDiff 🧬
• Example — (none given)
• Returns — value of dna_ori, a scalar
• Args — newvalue (optional)

---

💜 dna_mut

• Title — dna_mut
• Usage — $obj->dna_mut('atgctggtgctgct'); $dna_mut = $obj->dna_mut();
• Function — sets or returns the mutated DNA sequence of the seqDiff. and if the sequence hasn't been set, it generates it from the original sequence plus the DNA mutations ✨
• Example — (none given)
• Returns — value of dna_mut, a scalar
• Args — newvalue (optional)

---

🧚 rna_ori

• Title — rna_ori
• Usage — $obj->rna_ori('atgctgctgctgct'); $rna_ori = $obj->rna_ori();
• Function — sets or returns the original RNA sequence of the seqDiff 🌸
• Example — (none given)
• Returns — value of rna_ori, a scalar
• Args — newvalue (optional)

---

⭐ rna_mut

• Title — rna_mut
• Usage — $obj->rna_mut('atgctggtgctgct'); $rna_mut = $obj->rna_mut();
• Function — sets or returns the mutated RNA sequence of the seqDiff 💫
• Example — (none given)
• Returns — value of rna_mut, a scalar
• Args — newvalue (optional)

---

🦋 aa_ori

• Title — aa_ori
• Usage — $obj->aa_ori('MAGVLL*'); $aa_ori = $obj->aa_ori();
• Function — sets or returns the original protein sequence of the seqDiff 🥚
• Example — (none given)
• Returns — value of aa_ori, a scalar
• Args — newvalue (optional)

---

🔥 aa_mut

• Title — aa_mut
• Usage — $obj->aa_mut('MA*'); $aa_mut = $obj->aa_mut();
• Function — sets or returns the mutated protein sequence of the seqDiff 🐣
• Example — (none given)
• Returns — value of aa_mut, a scalar
• Args — newvalue (optional)

---

🌈 seqobj

• Title — seqobj
• Usage — $dnaobj = $obj->seqobj('dna_mut');
• Function — returns any original or mutated sequence as a Bio::PrimarySeq object. it's giving object-oriented glow-up ✨
• Example — (none given)
• Returns — Bio::PrimarySeq object for the requested sequence
• Args — string, method name for the sequence requested

see Bio::PrimarySeq for more information 📚

---

💅 alignment

• Title — alignment
• Usage — $obj->alignment
• Function — returns a pretty RNA/AA sequence alignment from the linked objects. under construction 🚧 only simple coding region point mutations work.
• Example — (none given)
• Returns — (none given)
• Args — none

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and that's the whole appendix bestie, you ate that 🫶✨

this page came from perl v5.32.1, dated 2021-12-02, and it lives under the name Bio::V...SeqDiff(3pm) — so if you ever forget where you read all this, that's the vibe check 💖🎀🦋