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

💖 Bio::SeqIO::metafasta 💖

okay bestie, welcome to the <pink>Bio::S...tafasta(3pm)</pink> era ✨ this is the manual page for Bio::SeqIO::metafasta and she's giving metafasta sequence input/output stream realness, no cap. sit down, grab a boba, let's go 🧋

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🌸 NAME 🌸

Bio::SeqIO::metafasta — metafasta sequence input/output stream 💅

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✨ SYNOPSIS ✨

okay so listen, do NOT use this module directly — that's the rule, that's the vibe check, we don't do that here. you use it via the Bio::SeqIO class, periodt 🫶

use Bio::SeqIO;

# read the metafasta file
$io = Bio::SeqIO->new(-file => "test.metafasta",
                      -format => "metafasta" );

$seq = $io->next_seq;

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🦋 DESCRIPTION 🦋

so what does she even do? this object can transform Bio::Seq::Meta objects to and from metafasta flat file databases. iconic, honestly 💖

for the sequence part, the code is an exact copy of the Bio::SeqIO::fasta module — like, literally copy-paste energy. the only added bits deal with meta data IO. that's it, that's the whole plot 🎀

the format of a metafasta file is:

>test
ABCDEFHIJKLMNOPQRSTUVWXYZ
&charge
NBNAANCNJCNNNONNCNNUNNXNZ
&chemical
LBSAARCLJCLSMOIMCHHULRXRZ

where the sequence block is followed by one or several meta blocks 🌈

each meta block starts with the ampersand character '&' in the first column and is immediately followed by the name of the meta data, which continues until the new line. the meta data follows it. all characters, except new line, are important in meta data — like, every single one, don't be skipping anything 👑

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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 💜

🐛 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 - Heikki Lehvaslaiho 👑

Email heikki-at-bioperl-dot-org

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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    : NONE

💫 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 to n Bio::PrimarySeqI objects

💫 width

Title   : width
Usage   : $obj->width($newval)
Function: Get/Set the line width for METAFASTA output
Returns : value of width
Args    : newvalue (optional)

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and that's the whole page bestie!! 🎀✨ this lil manual is running on perl v5.32.1, dated 2021-08-15, and yes, she's still out here under the name Bio::S...tafasta(3pm) 💖 mwah, go read some sequences, you ate 🫶🌈