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

💖 NAME 💖

Bio::SeqIO::largefasta — bestie, it does method i/o on very large fasta sequence files. That's the whole vibe. 🦋

Oh and also, hi, you're reading the manual page for Bio::S...efasta(3pm) — that's the name up top, iykyk. ✨

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🌸 SYNOPSIS 🌸

Do not use this module directly. Like, at all. Not even a little. Use it via the Bio::SeqIO class instead, bestie. That's the way. 💅

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🎀 DESCRIPTION 🎀

Okay so, real talk: this object can transform Bio::Seq objects to and from fasta flat file databases. Cute, right? 🌈

Here's where it gets spicy. This module handles very large sequence files by using the Bio::Seq::LargePrimarySeq module to store all the sequence data in a file. Which sounds slay until you realize — this can be a problem if you have limited disk space on your computer, because this will effectively cause 2 copies of the sequence file to reside on disk for the life of the Bio::Seq::LargePrimarySeq object. Two. Copies. Living rent free. 😭

The default location for this is specified by the File::Spec->tmpdir routine, which is usually /tmp on UNIX. And if a sequence file is larger than the swap space (aka the capacity of the /tmp dir) this could cause problems for the machine. Like, actual problems. 💀

But good news bestie, it IS possible to set the directory where the temporary file is located by adding the following line to your code BEFORE calling next_seq. See Bio::Seq::LargePrimarySeq for more information. 👑

$Bio::Seq::LargePrimarySeq::DEFAULT_TEMP_DIR = 'newdir';

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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, they mean it. 🫶

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. Give them the whole story, not just the vibes. ✨

🐛 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 - Jason Stajich 👑

Email: jason@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 _. Sneaky little underscore, you know the one. 🙈

🌟 next_seq

Title   : next_seq
Usage   : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : A Bio::Seq::LargePrimarySeq object
Args    : NONE

So like, it returns the next sequence in the stream, and what you get back is a Bio::Seq::LargePrimarySeq object. Args? NONE. Periodt. 💅

🌟 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    : Bio::Seq object

Writes the $seq object into the stream, and you get 1 for success and 0 for error. Binary queen behavior honestly. ✨

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And that's the whole page, bestie!! 🎀 This little masterpiece is running on perl v5.32.1, dated 2021-08-15, and it belongs to Bio::S...efasta(3pm). Go forth and sequence responsibly, mwah 💖✨🦋