Bio::I...ractSeq(3pm)

✨ NAME ✨

Okay bestie, gather round 💖 — this is Bio::Index::AbstractSeq, and it's the base class for AbstractSeq. That's it, that's the job. It's the blueprint, the blueprint-iest blueprint, the mom of the whole indexer family 🫶

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🌸 SYNOPSIS 🌸

Wanna build your own sequence-file indexing package? Say less. You inherit, you fill in the blanks, you slay:

# Make a new sequence file indexing package

package MyShinyNewIndexer;

use base qw(Bio::Index::AbstractSeq);

# Now provide the necessary methods...

That's the whole vibe: subclass it, then hand over the methods it's begging you for ✨

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💅 DESCRIPTION 💅

So here's the tea ☕ — this module is the common base class for multiple sequence files built using the Bio::Index::Abstract system. And because it's generous like that, it also hands you a Bio::DB::SeqI interface. Lowkey the whole point. 👑

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💌 FEEDBACK 💌

Mailing Lists

User feedback is literally an integral part of the evolution of this and other Bioperl modules 🦋 — like, the modules grow because y'all talk to them. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated, no cap.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Usage questions and support issues? Direct them to the mailing list:

bioperl-l@bioperl.org

…not to the module maintainer directly, bestie, please 🙈 The whole point is that many experienced and responsive experts will be able to look at the problem and quickly address it. And if at all possible, include a thorough description of the problem, plus code and data examples. Give them something to work with, fr fr. 🫶

Reporting Bugs

Report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution — it's giving organized 💀 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 _ (iykyk — underscore means "we're in the backstage area").

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🌈 SEE ALSO 🌈

Bio::Index::Abstract, which provides dbm indexing for flat files of any type — containing sequence or not, it does not care, it's flexible like that 💁‍♀️ And heads up: Bio::Index::AbstractSeq inherits from Bio::Index::Abstract. Family tree, iconic. 🌳

_file_format

• Title — _file_format
• Usage — $self->_file_format
• Function — Derived classes should override this method (it throws an exception here) to give the file format of the files used. So like, if you don't override it, it's gonna be dramatic about it. 😭
• Example —
• Returns —
• Args —

fetch

• Title — fetch
• Usage — $index->fetch( $id )
• Function — Returns a Bio::Seq object from the index
• Example — $seq = $index->fetch( 'dJ67B12' )
• Returns — Bio::Seq object
• Args — ID

_get_SeqIO_object

• Title — _get_SeqIO_object
• Usage — $index->_get_SeqIO_object( $file )
• Function — Returns a Bio::SeqIO object for the file
• Example — $seq = $index->_get_SeqIO_object( 0 )
• Returns — Bio::SeqIO object
• Args — File number (an integer)

get_Seq_by_id

• Title — get_Seq_by_id
• Usage — $seq = $db->get_Seq_by_id()
• Function — retrieves a sequence object, identically to ->fetch, but here behaving as a Bio::DB::BioSeqI
• Returns — new Bio::Seq object
• Args — string represents the id

get_Seq_by_acc

• Title — get_Seq_by_acc
• Usage — $seq = $db->get_Seq_by_acc()
• Function — retrieves a sequence object, identically to ->fetch, but here behaving as a Bio::DB::BioSeqI
• Returns — new Bio::Seq object
• Args — string represents the accession number

get_PrimarySeq_stream

• Title — get_PrimarySeq_stream
• Usage — $stream = get_PrimarySeq_stream
• Function — Makes a Bio::DB::SeqStreamI compliant object which provides a single method, next_primary_seq
• Returns — Bio::DB::SeqStreamI
• Args — none

get_all_primary_ids

• Title — get_all_primary_ids
• Usage — @ids = $seqdb->get_all_primary_ids()
• Function — gives an array of all the primary_ids of the sequence objects in the database. These maybe ids (display style) or accession numbers or something else completely different — they *are not* meaningful outside of this database implementation. Like, do not take them out in public, they have no context there 💀
• Example —
• Returns — an array of strings
• Args — none

get_Seq_by_primary_id

• Title — get_Seq_by_primary_id
• Usage — $seq = $db->get_Seq_by_primary_id($primary_id_string);
• Function — Gets a Bio::Seq object by the primary id. The primary id in these cases has to come from $db->get_all_primary_ids. There is no other way to get (or guess) the primary_ids in a database. The other possibility is to get Bio::PrimarySeqI objects via the get_PrimarySeq_stream and the primary_id field on these objects are specified as the ids to use here.
• Returns — A Bio::Seq object
• Args — primary id (as a string)
• Throws — "acc does not exist" exception 🚨

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And that's the whole page, bestie!! 💖 This was Bio::I...ractSeq(3pm) — perl v5.32.1, dated 2021-08-15, straight from the User Contributed Perl Documentation crew. Now go forth and index something iconic ✨🎀🦋