Bio::T...:Match(3pm)

🌸 Bio::Tools::Run::Match — the manual, but make it cute 🌸

okay bestie, welcome to Bio::Tools::Run::Match 💖 this is the Perl doc for it, straight from the User Contributed Perl Documentation corner of the world. It's a wrapper. It's iconic. Let's go 🦋

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✨ NAME ✨

Bio::Tools::Run::Match — a wrapper for Transfac's match(TM) 🧚 no cap, that's literally the whole name.

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✨ SYNOPSIS ✨

here's the vibe, copy-paste ready 👑

use Bio::Tools::Run::Match;

# Make a Match factory
$factory = Bio::Tools::Run::Match->new(-mxlib => '/path/to/matrix.dat');

# Run Match on an sequence object
my @results = $factory->run($bio_seq);

# look at the results
foreach my $feat (@results) {
  my $seq_id = $feat->seq_id;
  my $start = $feat->start;
  my $end = $feat->end;
  my $score = $feat->score;
  my ($pvalue) = $feat->get_tag_values('pvalue');
}

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✨ DESCRIPTION ✨

so what is this? It's a wrapper for running the match(TM) program that ships with Transfac Pro distributions. periodt 💅

You can lowkey try feeding normal match command-line arguments straight into new(), like new(-b => 1), or you can call arg-named methods instead — just drop the leading hyphens, so $factory->b(1) sets the -b option to true. easy ✨

Histogram output isn't supported. 😭 But -p is supported, by using -mxprf — go peek at the docs of new() for the details, iykyk.

Also, you're gonna need to enable this match wrapper to find the match executable. There are (at least) three ways to do that:

1. Make sure match is in your path. 🫶
2. Define an environmental variable MATCHDIR which is a directory which contains the match executable:

In bash:

export MATCHDIR=/home/username/match/

In csh/tcsh:

setenv MATCHDIR /home/username/match

3. Include a definition of an environmental variable MATCHDIR in every script that will use this match wrapper module, e.g.:

BEGIN { $ENV{MATCHDIR} = '/home/username/match/' }
use Bio::Tools::Run::Match;

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💬 FEEDBACK 💬

📬 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules 🥺 so send your comments and suggestions preferably to the Bioperl mailing list. 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 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. that's the magic combo ✨

🐛 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:

http://redmine.open-bio.org/projects/bioperl/

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👑 AUTHOR - Sendu Bala 👑

Email bix@sendu.me.uk — shoutout to the legend 🫶

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ 🙈 (that's your cue that it's lowkey private, bestie).

program_name

• Title: program_name
• Usage: $factory>program_name()
• Function: holds the program name
• Returns: string
• Args: None

program_dir

• Title: program_dir
• Usage: $factory->program_dir(@params)
• Function: returns the program directory, obtained from ENV variable.
• Returns: string
• Args: None

new

• Title: new
• Usage: $factory = Bio::Tools::Run::Match->new()
• Function: creates a new MCS factory
• Returns: Bio::Tools::Run::MCS
• Args: The following args can either be supplied here or set by calling arg-named methods (eg. $factory->imcut(2) ).
  • -mxlib => path to the matrix.dat file containing Transfac matricies
  • -mxprf => path to a profile file | [core_thresh, [matrix_thresh]] (defaults to a standard one based on the mxlib provided if file not supplied, using core_thresh and matrix_thresh values if those are supplied instead)
  • -imcut => floating point number, the importance cutoff
  • -b | -u => boolean, mutually exclusive

run

• Title: run
• Usage: $result = $factory->run($bio_seqi_object);
• Function: Runs match on a sequence.
• Returns: list of Bio::SeqFeatureI feature objects
• Args: Bio::SeqI compliant object

NB: mxlib has to have been set prior to calling run(), either as an argument to new() or by calling mxlib(). don't forget it, bestie, or it's giving 💀

_setparams

• Title: _setparams
• Usage: Internal function, not to be called directly
• Function: Creates a string of params to be used in the command string
• Returns: string of params
• Args: none

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okay that's the whole page, you ate that 💅 this lil doc comes from perl v5.36.0, dated 2023-01-22 — go forth and match some matricies, main character 🌈⭐💜