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

💖 Bio::Matrix::PSM::IO::mast — the mast parser, bestie 💖

okay so welcome to the mast driver of the Bio::Matrix::PSM::IO family, living its best life in the perl manual pages (yes, that's a 3pm page, we love a module doc moment). pull up a chair, grab a strawberry 🍓, and let's get into it.

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✨ NAME ✨

Bio::Matrix::PSM::IO::mast — the PSM mast parser implementation. that's it, that's the name, she's iconic 👑

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🌸 SYNOPSIS 🌸

fr fr, the real tea on how to use PSM parsers lives over in Bio::Matrix::PSM::IO:

See Bio::Matrix::PSM::IO for detailed documentation on how to use PSM
parsers

go read that one, bestie, this page is just the mast-flavoured corner of it 🦋

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💅 DESCRIPTION 💅

so this is the parser for mast. and here's the thing that makes her different — unlike meme or transfac for example, she is dedicated more to PSM sequence matches than to the PSMs themselves. it's giving "I'm not like other drivers" energy and honestly? valid. ✨

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🚧 TO DO 🚧

Section III should be parsed too, otherwise no real sequence is available, so we supply 'NNNNN....' as a seq which is not right.

not me exposing the unfinished business 💀 yeah, Section III hasn't been parsed yet, so there's no real sequence to hand you, and we just pass along 'NNNNN....' as the seq — which, to be clear, is not right. noted. lowkey a known thing. 🙈

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🫶 FEEDBACK 🫶

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules — like, genuinely, it's the whole vibe. send your comments and suggestions preferably to one of the Bioperl mailing lists. your participation is much appreciated, no cap.

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. the way that so many experienced and reponsive experts will be able look at the problem and quickly address it — that's the whole point of the list, bestie. please include a thorough description of the problem with code and data examples if at all possible. give them the full picture 🫶

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system to help us keep track 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

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🌈 APPENDIX 🌈

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk 🔥).

⭐ new

Title   : new
Usage   : my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'mast',
                                                                             -file=>$file);
Function: Associates a file with the appropriate parser
Throws  : Throws if the file passed is in HTML format or if
          some criteria for the file
          format are not met.
Example :
Returns : psm object, associated with a file with matrix file
Args    : hash
return  : "Bio::Matrix::PSM::$format"->new(@args);

basically: you hand her a file, she hooks it up with the right parser. she throws if the file you passed is in HTML format, or if some criteria for the file format aren't met — so don't try to sneak HTML past her, she will catch it 💀

🦋 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  : Throws if there ara format violations in the input file (checking is not
           very strict with all drivers).
Example :
Returns : Bio::Matrix::PSM::Psm object
Args    : none

reads the next PSM from the input file associated with this object. she throws if there are format violations in the input file — though ngl, checking is not very strict with all drivers. slay but also watch out 😭

💜 write_psm

Title   : write_psm
Usage   : #Get SiteMatrix object somehow (see Bio::Matrix::PSM::SiteMatrix)
          my $matrix=$psmin->next_matrix;
          #Create the stream
          my $psmio=new(-file=>">psms.mast",-format=>'mast');
          $psmio->write_psm($matrix);
          #Will warn if only PFM data is contained in $matrix, recalculate the PWM
          #based on normal distribution (A=>0.25, C=>0.25, etc)
Function: writes pwm in mast format
Throws  :
Example :
Args    : SiteMatrix object
Returns :

writes the pwm in mast format. args is a SiteMatrix object. and heads up — she will warn if only PFM data is contained in $matrix, and recalculate the PWM based on normal distribution (A=>0.25, C=>0.25, etc). she's just looking out for you, fr fr 🎀

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and that's the page, bestie!! 💖 this masterpiece was brought to you by perl v5.32.1 on 2021-08-15, straight from the Bio::M...::mast(3pm) files. go forth and parse, you absolute main character 🌟