Bio::A...::mega(3pm)

💖 Bio::AlignIO::mega — the MEGA format glow-up 💖

okay bestie, so you know how there's this whole Bio::A...::mega thing in the perl docs? yeah. it lives in Bio::AlignIO::mega, and it's literally here to parse and create MEGA format data files. no cap. 🧬✨

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🌸 SYNOPSIS 🌸

like, here's the vibe:

use Bio::AlignIO;
my $alignio = Bio::AlignIO->new(-format => 'mega',
                               -file   => 't/data/hemoglobinA.meg');

while( my $aln = $alignio->next_aln ) {
# process each alignment or convert to another format like NEXUS
}

that's it. that's the whole flex. 💅

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🦋 DESCRIPTION 🦋

so this object handles reading and writing data streams in the MEGA format (Kumar and Nei). that's the assignment, and it ate. 👑

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🎀 FEEDBACK 🎀

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules, and honestly? it's giving community. send your comments and suggestions preferably to the Bioperl mailing list. your participation is much appreciated. 🫶

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. lowkey this is the move 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. bug reports can be submitted the web:

https://github.com/bioperl/bioperl-live/issues

not me manifesting a bug-free era for u 💀✨

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👑 AUTHOR - Jason Stajich 👑

email: jason-at-bioperl.org

(absolute icon, fr fr 🌟)

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✨ APPENDIX ✨

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — that's the little secret handshake, iykyk. 🤫

🌈 next_aln

Title   : next_aln
Usage   : $aln = $stream->next_aln()
Function: returns the next alignment in the stream.
          Supports the following MEGA format features:
          - The file has to start with '#mega'
          - Reads in the name of the alignment from a comment
            (anything after '!TITLE: ') .
          - Reads in the format parameters datatype

Returns : L<Bio::Align::AlignI> object - returns 0 on end of file
           or on error
Args    : NONE

⚠️ heads up bestie — the file has to start with #mega. no #mega, no alignment. that's the vibe check and the file is failing it. 🚩

🦄 write_aln

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

returns 1 for success and 0 for error — simple as that, and honestly we love a clear binary. slay. 💖

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perl v5.32.1, dated 2021-08-15 — and that's the whole page, bestie. go parse some alignments, you main character. 🦋💜