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

✨ NAME ✨

okay bestie, so you're reading the manual for Bio::M...:mlagan(3pm) — and what it actually is, is Bio::Matrix::IO::mlagan, a whole parser for the mlagan substitution matrix 💅 it reads them, it writes them, it's giving very niche-but-iconic 💖

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🌸 SYNOPSIS 🌸

here's the vibe, copy-paste ready, no cap:

use Bio::Matrix::IO;
my $parser = Bio::Matrix::IO->new(-format => 'mlagan',
                                  -file   => 'nucmatrix.txt');
my $matrix = $parser->next_matrix;
my $gap_open = $parser->gap_open;
my $gap_continue = $parser->gap_continue;

like… you build the parser, you pull the matrix out, you grab gap_open and gap_continue off it. slay 🎀

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🦋 DESCRIPTION 🦋

so basically? use this to read in and write out substitution matrix files that are suitable for use by mlagan. that's the whole job. it does it well. periodt ✨

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💌 FEEDBACK 💌

🌈 Mailing Lists 🌈

user feedback is like, an integral part of the evolution of this module and all the other Bioperl modules 🫶 so if you have comments or suggestions, pls send them, preferably to the Bioperl mailing list. your participation is so appreciated fr fr 💖

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🩷 Support 🩷

if you've got a usage question or a support issue, pls pls pls direct it to the mailing list:

bioperl-l@bioperl.org

…instead of going straight to the module maintainer, okay? there are so many experienced and responsive experts on there who will look at your problem and address it fast 🔥 and if you can, include a thorough description of the problem with code and data examples. the more deets the better, iykyk 💅

💀 Reporting Bugs 💀

found a bug? report it 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 - Sendu Bala 👑

Email bix@sendu.me.uk — iconic behaviour, honestly 🌟

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📖 APPENDIX 📖

the rest of this documentation goes into the details of each of the object methods. internal methods are usually preceded with a _ (so if you see an underscore, mind your business, that's internal 🙈)

🧚 new

Title   : new
Usage   : my $obj = Bio::Matrix::IO::mlagan->new();
Function: Builds a new Bio::Matrix::IO::mlagan object
Returns : an instance of Bio::Matrix::IO::mlagan
Args    :

builds you a brand new Bio::Matrix::IO::mlagan object, hands you back an instance of Bio::Matrix::IO::mlagan, and takes no args 💖

🌟 next_matrix

Title   : next_matrix
Usage   : my $matrix = $obj->next_matrix();
Function: parses a matrix file
Returns : L<Bio::Matrix::Mlagan>
Args    : none

this one parses a matrix file 📄 and returns you a L<Bio::Matrix::Mlagan>. no args, no drama.

🎀 write_matrix

Title   : write_matrix
Usage   : $obj->write_matrix($matrix)
Function: Write out a matrix in mlagan format
Returns : n/a
Args    : L<Bio::Matrix::Generic>

writes out a matrix in mlagan format ✍️ returns n/a (so don't go looking for a return value, bestie, there isn't one 😭), and it takes a L<Bio::Matrix::Generic> as its arg.

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okay that's the whole page!! go forth and parse those matrices 💅✨

perl v5.32.1 · 2021-08-15 · Bio::M...:mlagan(3pm) — mwah, that's the version, the date and the page name, all wrapped up with a bow 🎀 byeee 🦋💜