Bio::A...IO::psi(3pm)

💖 Bio::A...IO::psi 💖

okay bestie, so this is the Bio::AlignIO::psi page from the User Contributed Perl Documentation, and we're gonna get you fluent in PSI-BLAST profile alignment files in like five minutes flat. no cap. 🦋

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✨ NAME ✨

Bio::AlignIO::psi — read and write PSI-BLAST profile alignment files, periodt. 💅

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🌸 SYNOPSIS 🌸

so like, this module will parse PSI-BLAST output in the format seqid XXXX. that's the vibe.

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🎀 DESCRIPTION 🎀

it's a parser for psi-blast blocks. iconic behavior honestly. ✨

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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 whole glow-up arc. send your comments and suggestions preferably to the Bioperl mailing list. 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. if at all possible, please include a thorough description of the problem with code and data examples. give them the whole lore, bestie. 📝

🐛 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

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👑 AUTHOR - 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 _ (iykyk, that underscore is the "do not touch unless you're built different" marker 🙈).

💜 new

Title   : new
Usage   : my $obj = Bio::AlignIO::psi->new();
Function: Builds a new Bio::AlignIO::psi object
Returns : Bio::AlignIO::psi
Args    :

builds a brand new Bio::AlignIO::psi object. main character origin story. ⭐ (args are empty, she arrives fully formed 💅)

💜 next_aln

Title   : next_aln
Usage   : $aln = $stream->next_aln()
Function: returns the next alignment in the stream
Returns : Bio::Align::AlignI object
Args    : NONE

returns the next alignment in the stream, no args, she just gives. 🎁

see Bio::Align::AlignI.

💜 write_aln

Title   : write_aln
Usage   : $stream->write_aln(@aln)
Function: writes the NCBI psi-format object (.aln) into the stream
Returns : 1 for success and 0 for error
Args    : Bio::Align::AlignI object

writes the NCBI psi-format object (.aln) into the stream. returns 1 for success and 0 for error — that's it, that's the whole mood. 🔥

Bio::Align::AlignI

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ok that's the whole page bestie, go forth and parse those psi-blast blocks 💖

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this little masterpiece dropped with perl v5.32.1, dated 2021-08-15, and it lives in the User Contributed Perl Documentation. slay, bye. 🌈💅✨