Bio::SeqIO::pir(3pm)

💖 Bio::SeqIO::pir — PIR sequence input/output stream 💖

okay bestie, so this is Bio::SeqIO::pir(3pm) from the User Contributed Perl Documentation, and it's literally the little PIR-shaped door into your sequence data. let's get into it 🦋

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✨ NAME ✨

Bio::SeqIO::pir — PIR sequence input/output stream. that's it, that's the whole vibe. input. output. stream. 💅

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🌸 SYNOPSIS 🌸

not me about to tell you the most important thing first: do not use this module directly.

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

fr fr. Bio::SeqIO is the main character here, this module is the supporting cast. you go through Bio::SeqIO, always. 👑

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🎀 DESCRIPTION 🎀

okay so here's what this object does: it can transform Bio::Seq objects to and from pir flat file databases. round trip, both directions, slay. 🔥

note (important, don't skip this one): this does not completely preserve the PIR format. quality information about sequence is currently discarded, since bioperl does not have a mechanism for handling these encodings in sequence data. 💀 so like, some data goes in and doesn't come back out. it's giving "we tried" but the bioperl infrastructure just isn't there yet.

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💌 FEEDBACK 💌

📬 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules. no cap. send your comments and suggestions preferably to one of the Bioperl mailing lists — your participation is much appreciated, bestie 🫶

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. there are so many experienced and responsive experts who will be able to look at the problem and quickly address it — let them cook. please include a thorough description of the problem with code and data examples if at all possible. the more deets, the faster the fix. 🙈

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

go off, file that issue, you're doing amazing. ⭐

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🌈 AUTHORS 🌈

absolute icons, all three of them:

• Aaron Mackey <amackey@virginia.edu>
• Lincoln Stein <lstein@cshl.org>
• Jason Stajich <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 _ (iykyk, that underscore means it's private, don't touch it unless you know what you're doing 💅).

🦋 next_seq

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

lowkey the simplest one: you call it, you get the next sequence in the stream, packaged as a Bio::Seq object. zero arguments, zero drama. ✨

🍓 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

you hand it an array of Bio::PrimarySeqI objects and it writes them into the stream. returns 1 for success and 0 for error — so check that return value, bestie, it's literally telling you how it went. 👑

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that's the whole page, periodt. this was Bio::SeqIO::pir(3pm) from perl v5.32.1, dated 2021-08-15 — sending you love and clean sequence streams, mwah 💖🌈