Bio::M...::masta(3pm)

💖 Bio::M...::masta 💖

okay bestie, buckle up, because this is Bio::Matrix::PSM::IO::masta (3pm), a.k.a. the motif fasta format parser — straight from the User Contributed Perl Documentation. she's giving bioinformatics, she's giving matrices, she's giving ✨tab-delimited realness✨. let's get into it 🫶

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🌸 NAME 🌸

Bio::Matrix::PSM::IO::masta — the motif fasta format parser. periodt. 💅

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✨ SYNOPSIS ✨

MASTA is a position frequency matrix format that's basically fasta's cousin who went to art school. It's got one ID row, just like fasta, and then the actual data, which is tab delimited, like so:

  0.1   0.62    .017    0.11
  0.22  0.13    0.54    0.11

Orrr, plot twist, A, C, G and T could be horizontally positioned instead — positioning gets automatically detected, no cap. 🙈

lowkey important: please note masta will parse only DNA at the moment. that's it. that's the limit. don't come for her about it.

She will also convert a set of aligned sequences:

ACATGCAT ACAGGGAT ACAGGCAT ACCGGCAT

...into a PFM (SiteMatrix object). slay. 🎀

And when writing, if you supply SEQ, she will write 10 random instances, which correctly represent the frequency and can be used as an input for weblogo creation purposes. iconic behavior honestly.

See Bio::Matrix::PSM::IO for detailed documentation on how to use the masta parser. 📚

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🦋 DESCRIPTION 🦋

Parser for meme. 💀 (that's it, that's the description, we love a minimal queen)

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💌 FEEDBACK 💌

Mailing Lists 📬

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. 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. Many experienced and responsive 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. give them the whole picture bestie, they're not mind readers 💖

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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👑 AUTHOR - Stefan Kirov 👑

Email skirov@utk.edu — yes, the icon himself. 💜

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🌈 APPENDIX 🌈

⭐ new

• Title : new
• Usage :

my $psmIO =  Bio::Matrix::PSM::IO->new(-format=> 'masta',
                                       -file  => $file,
                                       -mtype => 'PWM');

• Function: Associates a file with the appropriate parser
• Throws :
• Example :
• Args : hash
• Returns : "Bio::Matrix::PSM::$format"->new(@args);

🧚 write_psm

• Title : write_psm
• Usage :
• Function: writes a pfm/pwm/raw sequence in a simple masta format
• Throws :
• Example :
• Args : SiteMatrix object, type (optional string: PWM, SEQ or PFM)
• Returns :

🌸 next_matrix

• Title : next_matrix
• Usage : my $matrix = $psmio->next_matrix;
• Function: Alias of next_psm function

💅 next_psm

• Title : next_psm
• Usage : my $matrix=$psmio->next_psm;
• Function: returns the next matrix in the stream
• Throws : If there is you mix different types, for example weights and frequencies occur in the same entry. You can mix weights, but these should be designated by different ID lines
• Example :
• Args :
• Returns : Bio::Matrix::PSM::SiteMatrix

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bestie realness check: don't mix your types in one entry unless you know what you're doing — weights need their own ID lines. the matrix said what she said. 💀

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and that's the whole page, we ate and left no crumbs 🍓

perl v5.32.1 · 2021-08-15 · mwah, xoxo, go parse some motifs 💖✨🎀🦋