Bio::A...IO::maf(3pm)

💖 Bio::AlignIO::maf(3pm) — the glow-up edition 💖

okay bestie, so this is a page from the User Contributed Perl Documentation — yep, the whole Bio::AlignIO::maf(3pm) situation. It's giving "read me before you touch MAF files", and honestly? Iconic. Let's go. ✨

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🌸 NAME 🌸

Bio::AlignIO::maf — Multiple Alignment Format sequence input stream. That's it, that's the whole vibe. It reads MAF, it does not write MAF. 🎀

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🦋 SYNOPSIS 🦋

okay so like, real talk: do not use this module directly. You go through the Bio::AlignIO class, that's the whole point. 🙈

Do not use this module directly.  Use it via the Bio::AlignIO class.

use Bio::AlignIO;

my $alignio = Bio::AlignIO->new(-fh => \*STDIN, -format => 'maf');

while(my $aln = $alignio->next_aln()){
  my $match_line = $aln->match_line;

  print $aln, "\n";

  print $aln->length, "\n";
  print $aln->num_residues, "\n";
  print $aln->is_flush, "\n";
  print $aln->num_sequences, "\n";

  $aln->splice_by_seq_pos(1);

  print $aln->consensus_string(60), "\n";
  print $aln->get_seq_by_pos(1)->seq, "\n";
  print $aln->match_line(), "\n";

  print "\n";
}

like, that's the whole loop. Read the stream, get an alignment, poke at it, print it. slay. 💅

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🌈 DESCRIPTION 🌈

So this class builds up Bio::SimpleAlign objects from an MAF-format multiple alignment file. That's its one job and it does it. ✨

Writing in MAF format? Yeah, that's currently unimplemented. Not a thing. Don't come for me. 😭

The spec for the MAF format lives right here, so go look if you wanna know the lore:

http://genome.ucsc.edu/FAQ/FAQformat

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🫶 FEEDBACK 🫶

💬 Support

okay so if you've got usage questions or support issues, please send them to the mailing list:

bioperl-l@bioperl.org

and not straight to the module maintainer, bestie. Like, the whole point is that there are many experienced and responsive experts on there who can look at your problem and sort it out fast. 🧚

If at all possible, please include a thorough description of the problem, plus code and data examples. Fr fr, the more detail the better — it's giving "help me help you". 💖

🐛 Reporting Bugs

Found a bug? Report it to the Bioperl bug tracking system so we can keep track of the bugs and their resolutions. Bug reports can be submitted via the web:

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

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👑 AUTHORS - Allen Day 👑

Email: allenday@ucla.edu

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⭐ APPENDIX ⭐

The rest of this documentation is where the details live for each of the object methods. Heads up: internal methods usually have a _ in front of them. iykyk. 💜

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🔥 new

Title   : new
Usage   : my $alignio = Bio::AlignIO->new(-format => 'maf'
                                         -file   => '>file',
                                         -idlength => 10,
                                         -idlinebreak => 1);
Function: Initialize a new L<Bio::AlignIO::maf> reader
Returns : L<Bio::AlignIO> object
Args    :

So new spins up a fresh Bio::AlignIO::maf reader for you, and what you get back is a Bio::AlignIO object. The Args list is empty, bestie — nothing to declare. 🎀

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🌟 next_aln

Title   : next_aln
Usage   : $aln = $stream->next_aln()
Function: returns the next alignment in the stream.
          Throws an exception if trying to read in PHYLIP
          sequential format.
Returns : L<Bio::SimpleAlign> object
Args    :

next_aln hands you the next alignment in the stream, and you get a Bio::SimpleAlign object back. ✨

⚠️ But bestie, listen: it throws an exception if you try to read in PHYLIP sequential format. That's a hard no, not a soft no. 💀

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okay that's the whole page, no cap. 🫶

this documentation came from perl v5.32.1, dated 2021-08-15, and it's filed under Bio::A...IO::maf(3pm) — go forth and read your alignments, main character. 👑💖