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

💖 Bio::Matrix::PSM::IO::transfac — the manual page, bestie edition 💖

okay so this is the page for Bio::Matrix::PSM::IO::transfac from the User Contributed Perl Documentation — it's the PSM transfac parser and it's here to help you parse TRANSFAC-format position-specific scoring matrices. it's giving "quiet little module that does one thing" and honestly? iconic. 💅

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✨ NAME ✨

Bio::Matrix::PSM::IO::transfac — PSM transfac parser 🧚

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🌸 SYNOPSIS 🌸

bestie, the synopsis is literally just pointing you elsewhere:

See Bio::Matrix::PSM::IO for documentation

so like, go read that one, she's the main character here. this page is the sidekick. 🫶

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🎀 DESCRIPTION 🎀

the entire description is:

#

no fr, that's it. that's the whole thing. a single hash. she said "I contain multitudes" and then contained exactly one #. not me being obsessed with the minimalism 😭✨

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💌 FEEDBACK 💌

📬 Mailing Lists

user feedback is integral to the evolution of this and other Bioperl modules, so if you've got comments or suggestions, send them to one of the Bioperl mailing lists. your participation is so appreciated, bestie, 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

and not to the module maintainer directly, okay? like, don't DM the maintainer, post in the group chat. 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 — the more context the better, periodt. 📝

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. bug reports can be submitted via the web:

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

go off, tell them what's broken. it's a public service. 👑

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👑 AUTHOR - Stefan Kirov 👑

Email skirov@utk.edu 💌

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📚 APPENDIX 📚

🆕 new

• Title — new
• Usage —

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

• Function — associates a file with the appropriate parser
• Throws — (nothing listed)
• Example — (nothing listed)
• Args — (nothing listed)
• Returns — "Bio::Matrix::PSM::$format"->new(@args);

⏭️ next_psm

• Title — next_psm
• Usage —

my $psm=$psmIO->next_psm();

• Function — reads the next PSM from the input file, associated with this object
• Throws — upon finding a line, defining the matrix, where one or more positions are not defined, see _make_matrix
• Returns — Bio::Matrix::PSM::Psm object
• Args — none

🔍 _parseMatrix

• Title — _parseMatrix
• Usage — (nothing listed)
• Function — parses a line
• Throws — (nothing listed)
• Example — internal stuff
• Returns — array (frequencies for A,C,G,T in this order).
• Args — string

🧵 _make_matrix

• Title — _make_matrix
• Usage — (nothing listed)
• Function — (nothing listed)
• Throws — if a position is undefined, for example if you have line like this in the file you are parsing: 08 4,7,,9
• Example — internal stuff
• Returns — (nothing listed)
• Args — (nothing listed)

⚠️ heads up bestie: that _make_matrix throw is the one to watch. an undefined position like 08 4,7,,9 will absolutely end your whole parsing moment, no cap.

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and that's the page!! this was documented with perl v5.32.1, dated 2021-08-15, and it lives under the User Contributed Perl Documentation umbrella. stay parsing, angel 🦋💖✨