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

🧬 Bio::S...::fasta(3pm) — the manual page, but make it make sense

okay bestie, so this is the page for Bio::S...::fasta(3pm) from the User Contributed Perl Documentation, and it's literally all about fasta sequence input/output streams. pull up a chair, grab a boba, we're doing this 💖

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✨ NAME ✨

Bio::SeqIO::fasta — fasta sequence input/output stream. that's it, that's the whole name, she's simple, she's iconic.

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✨ SYNOPSIS ✨

Do not use this module directly.  Use it via the Bio::SeqIO class.

bestie. LISTEN. do not use this module directly, okay?? it's giving "don't text your ex." go through the Bio::SeqIO class instead, that's the whole vibe. 🫶

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✨ DESCRIPTION ✨

this object can transform Bio::Seq objects to and from fasta flat file databases. glow-up in both directions, we love a bi-directional queen 👑

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✨ FEEDBACK ✨

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules — like, genuinely, it's the main character of the whole development arc. 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. no vague "it doesn't work" texts please, give us the receipts 📸

🐛 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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✨ AUTHORS - Ewan Birney & Lincoln Stein ✨

email: birney@ebi.ac.uk lstein@cshl.org

two absolute legends, we stan 👑

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✨ CONTRIBUTORS ✨

Jason Stajich, jason-at-bioperl.org

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✨ APPENDIX ✨

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (yes, the underscore is the "backstage pass only" marker, iykyk)

🦋 next_seq

• Title — next_seq
• Usage — $seq = $stream->next_seq()
• Function — returns the next sequence in the stream
• Returns — Bio::Seq object, or nothing if no more available
• Args — NONE

🦋 next_seq_fast

• Title — next_seq_fast
• Usage — $seq = $stream->next_seq_fast()
• Function — returns the next sequence in the stream. Favors speed over perfection.
• Returns — Bio::Seq object, or nothing if no more available
• Args — NONE

she's the speedy one. favors speed over perfection — a little messy, but she gets there fast 💅

🦋 write_seq

• Title — write_seq
• Usage — $stream->write_seq(@seq)
• Function — Writes the $seq object into the stream
• Returns — 1 for success and 0 for error
• Args — Array of 1 or more Bio::PrimarySeqI objects

🦋 width

• Title — width
• Usage — $obj->width($newval)
• Function — Get/Set the line width for FASTA output (not counting whitespace).
• Returns — value of width
• Args — newvalue (optional)

🦋 block

• Title — block
• Usage — $obj->block($newval)
• Function — Get/Set the length of each block for FASTA output. Sequence blocks will be split with a space. Configuring block, to a value of 10 for example, allows one to easily identify a position in a sequence by eye.
• Default — same value used for width.
• Returns — value of block
• Args — newvalue (optional)

the space between blocks is genuinely so helpful for counting by eye, it's giving "ruler but for nucleotides" 📏✨

🦋 preferred_id_type

• Title — preferred_id_type
• Usage — $obj->preferred_id_type('accession')
• Function — Get/Set the preferred type of identifier to use in the ">ID" position for FASTA output.
• Returns — string, one of values defined in @Bio::SeqIO::fasta::SEQ_ID_TYPES.
• Default — display
• Args — string when setting. This must be one of values defined in @Bio::SeqIO::fasta::SEQ_ID_TYPES. Allowable values: accession, accession.version, display, primary
• Throws — fatal exception if the supplied id type is not in @SEQ_ID_TYPES.

🚨 bestie WARNING: if you hand her an id type that's not in @SEQ_ID_TYPES, she throws a fatal exception. do not test her. pick from the list: accession, accession.version, display, primary. that's the whole menu, no substitutions 🍓

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and that's the whole page, no cap 💜 this was perl v5.32.1, dated 2021-08-15, and yes the manual name really is Bio::S...::fasta(3pm) — she got truncated in the header and honestly? she ate anyway 👑✨