Bio::M...iblast(3pm)

💖 NAME 💖

okay bestie, welcome to Bio::M...iblast(3pm) — it's the PSM psiblast parser, and it lives in the User Contributed Perl Documentation. no cap, that's the whole vibe: a parser. for psiblast. for PSMs. iconic.

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✨ SYNOPSIS ✨

not gonna lie, the synopsis is a lil mysterious here. it just says:

See Bio::Matrix::PSM::IO for documentation

so like. the docs live over there, bestie. go look. 🫶

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🌸 DESCRIPTION 🌸

so what does this thing actually do? it's a parser for ASCII matrices from PSI-BLAST — specifically from the blastpgp program in the BLAST distribution. that's it, that's the whole job, and it does it flawlessly. periodt. 💅

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🦋 FEEDBACK 🦋

💌 Mailing Lists

user feedback is literally an integral part of the evolution of this and other Bioperl modules. so if you have comments or suggestions, pls pls pls send them 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

okay so for usage questions and support issues, direct them to the mailing list:

bioperl-l@bioperl.org

and NOT to the module maintainer directly, bestie. that's the rule. the reason is actually good: there are many experienced and responsive experts on the list who'll be able to look at your problem and quickly address it. so when you write in, pls include a thorough description of the problem, plus code and data examples if at all possible. the more deets, the faster the slay. ✨

🐛 Reporting Bugs

found a bug? report it to the Bioperl bug tracking system so everyone 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 - James Thompson 👑

email: tex@biosysadmin.com

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🎀 APPENDIX 🎀

🌟 new

Title   : new
Usage   : my $psmIO  =  Bio::Matrix::PSM::IO->new(-format=>'psiblast',
                                                 -file=>$file);
Function: Associates a file with the appropriate parser
Throws  :
Example :
Args    :
Returns : Bio::Matrix::PSM::ProtMatrix->new(@args);

so new associates a file with the appropriate parser. the Throws, Example, and Args fields are all just... empty. nothing there. silence. 💀 and it returns Bio::Matrix::PSM::ProtMatrix->new(@args).

🌈 next_psm

Title   : next_psm
Usage   : my $psm = $psmIO->next_psm();
Function: Reads the next PSM from the input file, associated with this object
Throws  : None
Returns : Bio::Matrix::PSM::ProtPsm object
Args    : none

next_psm reads the next PSM from the input file associated with this object. it throws None (so chill), returns a Bio::Matrix::PSM::ProtPsm object, and takes no args. clean, simple, obsessed. 🧚

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and that's the whole page, bestie!! this gorgeous lil doc came to you courtesy of perl v5.32.1, dated 2021-08-15, and the manual page is Bio::M...iblast(3pm) — main character energy from start to finish. go parse some matrices, you've got this. 💜🌸✨