Bio::DB::SeqI(3pm)

🦋 NAME 🦋

okay so bestie, meet Bio::DB::SeqI — the Abstract Interface for Sequence databases. That's it, that's the whole name. This is the Bio::DB::SeqI(3pm) page from the User Contributed Perl Documentation collection, and we're gonna read it together, slay. 💅

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✨ SYNOPSIS ✨

here's the vibe in code form, no edits, no cap:

# get a Bio::DB::SeqI somehow

$seq = $seqdb->get_Seq_by_id('some-id');
$seq = $seqdb->get_Seq_by_acc('some-accession-number');

@ids = $seqdb->get_all_ids();
$stream = $seqdb->get_PrimarySeq_stream();
while((my $seq = $stream->next_seq()) {
   # $seq is a PrimarySeqI compliant object
}

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🌸 DESCRIPTION 🌸

Abstract interface for a sequence database. that's the whole description, she's short and she knows it. 💜

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💌 FEEDBACK 💌

📬 Mailing Lists

User feedback is, like, an integral part of the evolution of this and other Bioperl modules — genuinely. Send your comments and suggestions preferably to one of 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 many experienced and reponsive experts will be able look at the problem and quickly address it. (the spelling is theirs, the love is mine 🌈) Please include a thorough description of the problem with code and data examples if at all possible. fr fr, examples help.

🐛 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 _. iykyk. 👀

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🧬 Methods inherited from Bio::DB::RandomAccessI

get_Seq_by_id

• Title : get_Seq_by_id
• Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
• Function: Gets a Bio::Seq object by its name
• Returns : a Bio::Seq object
• Args : the id (as a string) of a sequence
• Throws : "id does not exist" exception

get_Seq_by_acc

• Title : get_Seq_by_acc
• Usage : $seq = $db->get_Seq_by_acc('X77802')
• Function: Gets a Bio::Seq object by accession number
• Returns : A Bio::Seq object
• Args : accession number (as a string)
• Throws : "acc does not exist" exception

get_Seq_by_version

• Title : get_Seq_by_version
• Usage : $seq = $db->get_Seq_by_version('X77802.1')
• Function: Gets a Bio::Seq object by sequence version
• Returns : A Bio::Seq object
• Args : accession.version (as a string)
• Throws : "acc.version does not exist" exception

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🌟 Methods [that were] specific for Bio::DB::SeqI 🌟

get_PrimarySeq_stream

• Title : get_PrimarySeq_stream
• Usage : $stream = get_PrimarySeq_stream
• Function: Makes a Bio::SeqIO compliant object which provides a single method, next_seq
• Returns : Bio::SeqIO
• Args : none

get_all_primary_ids

• Title : get_all_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 may be ids (display style) or accession numbers or something else completely different — they are not meaningful outside of this database implementation.
• 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 : accession number (as a string)
• Throws : "acc does not exist" exception

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that's the whole page bestie, go forth and query your sequence databases 💖

and that's a wrap!! this was perl v5.32.1, dated 2021-08-15, and it's the Bio::DB::SeqI(3pm) page — periodt. 🎀✨🦋