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

💖 Bio::A...::meme 💖

okay so bestie, welcome to the manual page for Bio::A...::meme(3pm) — that's the User Contributed Perl Documentation version, iykyk. This is the meme sequence input/output stream, and it's lowkey one of the cutest little parsers in Bioperl. Let's get into it. 🎀

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✨ NAME ✨

Bio::AlignIO::meme — meme sequence input/output stream 🦋

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🌸 SYNOPSIS 🌸

Not me about to say the most important thing first: do not use this module directly. Fr fr. Use it via the Bio::AlignIO class, that's the whole vibe. 👑

use Bio::AlignIO;
# read in an alignment from meme
my $in = Bio::AlignIO->new(-format => 'meme',
                           -file   => 'meme.out');
while( my $aln = $in->next_aln ) {
   # do something with the alignment
}

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💅 DESCRIPTION 💅

So this object takes the "sites sorted by position p-value" sections of a meme (text) output file and transforms them into a whole series of Bio::SimpleAlign objects. ✨

Each Bio::SimpleAlign object contains Bio::LocatableSeq objects, and those represent the individual aligned sites — as defined by the central portion of the "site" field in the meme file. The start and end coordinates are derived from the "Start" field. If you want the full tea on those, go peek at Bio::SimpleAlign and Bio::LocatableSeq.

🚨 real talk: this module can only parse MEME version 3 and 4. Previous versions have output formats that are more difficult to parse correctly. If the meme output file is not version 3.0 or greater, we signal an error. no cap, that's the boundary.

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🫶 FEEDBACK 🫶

Support 💌

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

…rather than to the module maintainer directly. Bestie, there are so many experienced and responsive experts on there who can look at your 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, the more they can slay your bug. 🐛

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 via the web:

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

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👑 AUTHORS - Benjamin Berman 👑

• Based on the Bio::SeqIO modules by Ewan Birney and others
• Email: benb@fruitfly.berkeley.edu

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🧚 APPENDIX 🧚

The rest of the documentation details each of the object methods. Internal methods are usually preceded with an underscore. iykyk.

next_aln

• Title : next_aln
• Usage : $aln = $stream->next_aln()
• Function: returns the next alignment in the stream
• Returns : Bio::SimpleAlign object with the score() set to the evalue of the motif.
• Args : NONE

write_aln

• Title : write_aln
• Usage : $stream->write_aln(@aln)
• Function: Not implemented 🙈
• Returns : 1 for success and 0 for error
• Args : Bio::SimpleAlign object

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and that's the whole page, bestie!! 💖 this one's running on perl v5.32.1, dated 2021-08-15, and it's giving main character energy in the Bio::A...::meme(3pm) slot. go read your alignments, periodt. ✨🎀🦋