Bio::S...chSeqI(3pm)

💖 Bio::S...chSeqI(3pm) — bestie edition 💖

okay so you found Bio::S...chSeqI(3pm), which lives in the User Contributed Perl Documentation corner of the perl universe, and honestly? she's a whole interface. let's get into it 🦋

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✨ NAME ✨

Bio::Seq::RichSeqI — it's the interface for sequences that come from rich data sources, mostly databases. rich as in data-rich, not rich as in trust fund, but also, slay 💅

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🌸 SYNOPSIS 🌸

    @secondary   = $richseq->get_secondary_accessions;
    $division    = $richseq->division;
    $mol         = $richseq->molecule;
    @dates       = $richseq->get_dates;
    $seq_version = $richseq->seq_version;
    $pid         = $richseq->pid;
    @keywords    = $richseq->get_keywords;

like… that's the whole vibe check right there. seven little calls and you know everything about a sequence's ~backstory~ 😌

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👑 DESCRIPTION 👑

so this interface extends the Bio::SeqI interface, and the way it does that is by handing extra functionality to sequences whose data sources are richer than your average bear — specifically database sequences (we're talking EMBL, GenBank and Swissprot). for a general implementation, bestie, please go see the documentation for Bio::Seq::RichSeq. that's where the actual doing-it lives. this page is the promise, that page is the follow-through ✨

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🫶 FEEDBACK 🫶

💌 Mailing Lists 💌

user feedback is, and I quote, an integral part of the evolution of this and other Bioperl modules. so send your comments and suggestions, preferably to one of the Bioperl mailing lists. your participation is much appreciated — genuinely, they mean it 🥹

  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 to the module maintainer directly, okay? bc there are so many experienced and reponsive experts on there who will be able to look at the problem and quickly address it. (yes the original says "reponsive", we're keeping it, it's canon now 💀)

also: please include a thorough description of the problem with code and data examples if at all possible. the more receipts you bring, the faster someone can help 🧚

🐛 Reporting Bugs 🐛

report bugs to the Bioperl bug tracking system, it helps them keep track of the bugs and their resolution (which is the whole point, fr fr). bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

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✍️ AUTHOR - Ewan Birney ✍️

Email birney@ebi.ac.uk — icon, legend, the moment 💜

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📖 APPENDIX 📖

the rest of the documentation here details each of the object methods, one by one. internal methods are usually preceded with a _ (iykyk, that's the secret menu).

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🔥 get_secondary_accessions 🔥

• Title : get_secondary_accessions
• Usage :
• Function: get the secondary accessions for a sequence.

an implementation that allows modification of this array property should provide the methods add_secondary_accession and remove_secondary_accessions, with obvious purpose. (yes, one is singular and one is plural, that's just how it is, don't look at me 🙈)

• Example :
• Returns : an array of strings
• Args : none

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🌱 division 🌱

• Title : division
• Usage :
• Function: get (and set, depending on the implementation) the division for a sequence.

examples from GenBank are PLN (plants), PRI (primates), etc. yes, plants and primates are both "divisions", it's giving taxonomy at a dinner party 🌿🐒

• Example :
• Returns : a string
• Args :

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🧬 molecule 🧬

• Title : molecule
• Usage :
• Function: get (and set, depending on the implementation) the molecule type for the sequence.

this is not necessarily the same as Bio::PrimarySeqI::alphabet(), because it is databank-specific. so don't come for me if they disagree, they're different things on purpose 💅

• Example :
• Returns : a string
• Args :

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🆔 pid 🆔

• Title : pid
• Usage :
• Function: get (and set, depending on the implementation) the PID property for the sequence.
• Example :
• Returns : a string
• Args :

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📅 get_dates 📅

• Title : get_dates
• Usage :
• Function: get (and set, depending on the implementation) the dates the databank entry specified for the sequence.

an implementation that allows modification of this array property should provide the methods add_date and remove_dates, with obvious purpose. (again: singular, plural, chaos, love that for us 😭)

• Example :
• Returns : an array of strings
• Args :

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🔢 seq_version 🔢

• Title : seq_version
• Usage :
• Function: get (and set, depending on the implementation) the version string of the sequence.
• Example :
• Returns : a string
• Args :
• Note : this differs from Bio::PrimarySeq version() in that this explicitly refers to the sequence record version one would find in a typical sequence file. it is up to the implementation whether this is set separately or falls back to the more generic Bio::Seq::version() — so like, read your implementation's docs before you assume, bestie 🎀

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🏷️ get_keywords 🏷️

• Title : get_keywords
• Usage : $obj->get_keywords()
• Function: get the keywords for this sequence object.

an implementation that allows modification of this array property should provide the methods add_keyword and remove_keywords, with obvious purpose.

• Returns : an array of strings
• Args :

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and that's the whole page!! every method, every Returns, every little empty Args field, all of it preserved like a pressed flower 🌸

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okay bye bestie, this was perl v5.32.1 from 2021-08-15, brought to you by the absolute legends at User Contributed Perl Documentation — go forth and access your secondary accessions responsibly ✨🫶💖