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

🌸 Bio::S...RichSeq — the manual page, bestie edition 🌸

okay so this is Bio::S...RichSeq(3pm), from the User Contributed Perl Documentation corner of the internet, and it is genuinely iconic. let's get into it 💅

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✨ NAME ✨

Bio::Seq::RichSeq — the module that implements a sequence created from a rich sequence database entry. that's the whole vibe 🫶

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✨ SYNOPSIS ✨

See Bio::Seq::RichSeqI and the documentation of methods. that's it, that's the synopsis, she's mysterious 💖

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✨ DESCRIPTION ✨

This module implements Bio::Seq::RichSeqI, which is an interface for sequences created from — or created for — entries from/of rich sequence databanks, like EMBL, GenBank, and SwissProt. the way these methods get added on top of the Bio::SeqI interface? they're all about databank-specific information. so fancy ✨

heads up bestie: not every rich databank format may use all of the properties provided. so don't come for the module if your format is doing its own thing 🙈

For more information, please see the relevant

(yes, that sentence just ends there in the original. she said "see the relevant" and left. main character energy honestly 💀)

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🧬 Implemented Interfaces 🧬

This class implements the following interfaces. slay, look at her go ✨

• Bio::Seq::RichSeqI — note that this includes implementing Bio::PrimarySeqI and Bio::SeqI, specifically via Bio::Seq and Bio::PrimarySeq. please review the documentation for those modules on implementation details relevant to those interfaces, as well as the ones below. iykyk 🫶
• Bio::IdentifiableI
• Bio::DescribableI
• Bio::AnnotatableI

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💌 FEEDBACK 💌

📬 Mailing Lists 📬

User feedback is an integral part of the evolution of this and other Bioperl modules. send your comments and suggestions preferably to one of 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

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. give them the whole lore, not just the vibe ✨

🐛 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

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👑 AUTHOR - Ewan Birney 👑

Email birney@ebi.ac.uk

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📎 APPENDIX 📎

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _. okay so underscore means stay out unless you know what you're doing 💜

new

• Title : new
• Usage :

$seq    = Bio::Seq::RichSeq->new( -seq => 'ATGGGGGTGGTGGTACCCT',
                                  -id  => 'human_id',
                                  -accession_number => 'AL000012',
                                 );

• Function: Returns a new seq object from basic constructors, being a string for the sequence and strings for id and accession_number
• Returns : a new Bio::Seq::RichSeq object

division

• Title : division
• Usage : $obj->division($newval)
• Function:
• Returns : value of division
• Args : newvalue (optional)

molecule

• Title : molecule
• Usage : $obj->molecule($newval)
• Function:
• Returns : type of molecule (DNA, mRNA)
• Args : newvalue (optional)

add_date

• Title : add_date
• Usage : $self->add_date($datestr)
• Function: adds one or more dates

This implementation stores dates as keyed annotation, the key being 'date_changed'. You can take advantage of this fact when accessing the annotation collection directly. little insider tip, you're welcome 🍓

• Example :
• Returns :
• Args : a date string or an array of such strings

get_dates

• Title : get_dates
• Usage : my @dates = $seq->get_dates;
• Function: Get the dates of the sequence (usually, when it was created and changed.
• Returns : an array of date strings
• Args :

pid

• Title : pid
• Usage : my $pid = $seq->pid();
• Function: Get (and set, depending on the implementation) the PID property for the sequence.
• Returns : a string
• Args :

accession

• Title : accession
• Usage : $obj->accession($newval)
• Function: Whilst the underlying sequence object does not have an accession, so we need one here.

In this implementation this is merely a synonym for accession_number(). same thing, different name, we love a rebrand 💅

• Example :
• Returns : value of accession
• Args : newvalue (optional)

add_secondary_accession

• Title : add_secondary_accession
• Usage : $self->add_domment($ref)
• Function: adds a secondary_accession

This implementation stores secondary accession numbers as keyed annotation, the key being 'secondary_accession'. You can take advantage of this fact when accessing the annotation collection directly. 🎀

• Example :
• Returns :
• Args : a string or an array of strings

get_secondary_accessions

• Title : get_secondary_accessions
• Usage : my @acc = $seq->get_secondary_accessions();
• Function: Get the secondary accession numbers as strings.
• Returns : An array of strings
• Args : none

seq_version

• Title : seq_version
• Usage : $obj->seq_version($newval)
• Function: Get/set the sequence version
• Returns : value of seq_version (a scalar)
• Args : on set, new value (a scalar or undef, optional)
• 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. not the same thing bestie, do not confuse them 😭

add_keyword

• Title : add_keyword
• Usage : $obj->add_keyword($newval)
• Function: Add a new keyword to the annotation of the sequence.

This implementation stores keywords as keyed annotation, the key being 'keyword'. You can take advantage of this fact when accessing the annotation collection directly. ✨

• Returns :
• Args : value to be added (optional) (a string)

get_keywords

• Title : get_keywords
• Usage : $obj->get_keywords($newval)
• Function: Get the keywords for this sequence as an array of strings.
• Returns : an array of strings
• Args :

Private methods and synonyms for backward compatibility

these ones are not public, okay? they're here for backward compatibility. we respect them but we do not call them 💀

_add_annotation_value

• Title : _add_annotation_value
• Usage :
• Function: Adds a value to the annotation collection under the specified key. Note that this is not a public method.
• Returns :
• Args : key (a string), value(s) (one or more scalars)

_get_annotation_values

• Title : _get_annotation_values
• Usage :
• Function: Gets the values of a specific annotation as identified by the key from the annotation collection. Note that this is not a public method.
• Example :
• Returns : an array of strings
• Args : the key (a string)

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and that's the whole page, you ate it, no crumbs. 🦋 this one's from perl v5.32.1, dated 2021-08-15, and yes it lives in the Bio::S...RichSeq(3pm) manual page. go forth and annotate your sequences responsibly, bestie 💖✨🎀