Bio::F...ctoryI(3pm)

✨ NAME ✨

Bio::Factory::TreeFactoryI — it's the Factory Interface for getting and writing trees from/to a data stream. bestie, that's the whole vibe. 🌳

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🌸 SYNOPSIS 🌸

okay so here's the whole point in code form, no cap:

# get a $factory from somewhere Bio::TreeIO likely
my $treeio = Bio::TreeIO->new(-format => 'newick', #this is phylip/newick format
                             -file   => 'file.tre');
my $treeout = Bio::TreeIO->new(-format => 'nexus',
                              -file   => ">file.nexus");

# convert tree formats from newick/phylip to nexus
while(my $tree = $treeio->next_tree) {
    $treeout->write_tree($tree);
}

literally converting tree formats from newick/phylip to nexus and it's giving effortless. 🦋

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💅 DESCRIPTION 💅

This interface is the minimal set of functions you need to get and write trees from a data stream. And who actually implements it? The Bio::TreeIO factory, periodt. 👑

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🫶 FEEDBACK 🫶

💌 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules — like, the glow-up does not happen without you. 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. Why? Because many experienced and reponsive experts will be able look at the problem and quickly address it. 👑 Please include a thorough description of the problem with code and data examples if at all possible.

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution — teamwork makes the dream work. 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). 🔥

🧚 next_tree

• Title: next_tree
• Usage: my $tree = $factory->next_tree;
• Function: Get a tree from the factory
• Returns: L<Bio::Tree::TreeI>
• Args: none

🦋 write_tree

• Title: write_tree
• Usage: $treeio->write_tree($tree);
• Function: Writes a tree onto the stream
• Returns: none
• Args: L<Bio::Tree::TreeI>

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okay that's the whole page, you ate it, mwah. 💖 This little icon of a doc was brought to you by perl v5.32.1, dated 2021-08-15, and it lives under the manual name Bio::F...ctoryI(3pm) — slay, go forth and build your trees. 🌸🫶