Bio::T...rotDist(3pm)

💖 Bio::T...rotDist(3pm) — aka Bio::Tools::Phylo::Phylip::ProtDist 💖

okay bestie, welcome to the Perl User Contributed Documentation section, this one is the manual for Bio::Tools::Phylo::Phylip::ProtDist and it is exactly what it sounds like. let's get into it 🦋

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✨ NAME ✨

Bio::Tools::Phylo::Phylip::ProtDist — it's a parser for ProtDist output. that's the whole job. she parses, she serves, she does not elaborate 💅

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🌸 SYNOPSIS 🌸

like here's the vibe, literally the entire usage pattern:

use Bio::Tools::Phylo::Phylip::ProtDist;
my $parser = Bio::Tools::Phylo::Phylip::ProtDist->new(-file => 'outfile');
while( my $result = $parser->next_matrix) {
  # do something with it
}

make the parser, hand her a file, loop over the matrices, do whatever you want with them. that's it. iconic. 🎀

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🫶 DESCRIPTION 🫶

so. this module is a parser for ProtDist output, and it turns that output into a Bio::Matrix::PhylipDist object. that's the whole deal.

also go look at Bio::Matrix::IO::phylip — because heads up, this module may go away. yes bestie, she said what she said 😭 don't get too attached.

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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 not just a polite line. 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. there are lots of experienced and reponsive experts (yes, that's how the original spells it, we keep it 💀) who will be able to look at the problem and quickly address it. and please include a thorough description of the problem with code and data examples if at all possible. the more context you give, the faster someone can help you 🫡

🐛 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 - Shawn Hoon 👑

Email shawnh@fugu-sg.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, the underscore ones are the backstage crew 🧚).

🌟 new

Title   : new
Usage   : my $obj = Bio::Tools::Phylo::Phylip::ProtDist->new();
Function: Builds a new Bio::Tools::Phylo::Phylip::ProtDist object
Returns : Bio::Tools::ProtDist
Args    : -fh/-file => $val, # for initing input, see Bio::Root::IO
          -program  => 'programname' # name of the program

so new builds you a brand new Bio::Tools::Phylo::Phylip::ProtDist object, she returns a Bio::Tools::ProtDist, and you feed her args: -fh or -file with a value to init the input (peep Bio::Root::IO for that), and -program with a 'programname' — the name of the program. slay ✨

🌟 next_matrix

Title   : next_matrix
Usage   : my $matrix = $parser->next_matrix
Function: Get the next result set from parser data
Returns : L<Bio::Matrix::PhylipDist>
Args    : none

next_matrix grabs the next result set from the parser data. no args, she just gives. returns a Bio::Matrix::PhylipDist. call her in a loop and you're set 💜

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and that's the whole page bestie, no cap, every option accounted for 🎀

this little manual was brought to you by perl v5.32.1, dated 2021-08-15, and she is forever known as Bio::T...rotDist(3pm) 💅 mwah, go parse something gorgeous 🌸