Bio::SeqIO::raw(3pm)

💖 Bio::SeqIO::raw 💖

okay so bestie, welcome to the manual page for Bio::SeqIO::raw, which is a raw sequence file input/output stream that lives in the User Contributed Perl Documentation section of your friendly neighbourhood man command. she's a 3pm girlie. 💅

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✨ NAME ✨

Bio::SeqIO::raw — raw sequence file input/output stream. that's it, that's the name, short and sweet, main character energy fr.

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🌸 SYNOPSIS 🌸

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

no like literally do not use this module directly, bestie. go through the Bio::SeqIO class like a civilized icon. 🎀

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🦋 DESCRIPTION 🦋

so this object can transform Bio::Seq objects to and from raw flat file databases. that's the whole vibe. it's giving translator, it's giving glow-up pipeline. ✨

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💌 FEEDBACK 💌

📬 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules, and honestly? your participation is much appreciated, periodt. send your comments and suggestions preferably to one of the Bioperl mailing lists:

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. the way that many experienced and reponsive experts will be able look at the problem and quickly address it — iconic behaviour honestly. please include a thorough description of the problem with code and data examples if at all possible. the more deets the better, bestie. 🧚

🐛 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   E<lt>birney@ebi.ac.ukE<gt>
Lincoln Stein E<lt>lstein@cshl.orgE<gt>

🌈 CONTRIBUTORS 🌈

Jason Stajich E<lt>jason@bioperl.org<gt>

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🔥 APPENDIX 🔥

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk). 🔍

🌟 next_seq

Title   : next_seq
Usage   : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args    :

gives you the next sequence in the stream, returns a Bio::Seq object, takes no args. slay. 💖

⭐ 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 Bio::PrimarySeqI objects

writes the $seq object into the stream. returns 1 for success and 0 for error. args? an array of Bio::PrimarySeqI objects, bestie. 🎀

💫 write_qual

Title   : write_qual
Usage   : $stream->write_qual($seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args    : Bio::Seq::Quality object

writes the $seq object into the stream (yes, same energy as write_seq). returns 1 for success and 0 for error. args? a Bio::Seq::Quality object. quality girlies rise. ✨

💅 variant

Title   : variant
Usage   : $format  = $obj->variant();
Function: Get and set method for the sequence variant.  For raw sequence, this
          indicates whether to treat the input as multiple sequences (the
          default) or as a single sequence.

current values accepted are:

'single'    single sequence
'multiple'  multiple sequences (default)

Returns : string
Args    : new value, string

get-and-set method for the sequence variant. for raw sequence, this tells you whether to treat the input as multiple sequences (that's the default, no cap) or as a single sequence. returns a string, takes a new value which is also a string. 🔥

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heads up bestie: the defaults are the defaults, don't come for me, I'm just the messenger. 💀

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and that's the page!! brought to you by perl v5.32.1, dated 2021-08-15, from the Bio::SeqIO::raw(3pm) manpage herself. go forth and sequence, you absolute legend. 🦋✨💖