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

🌸 NAME 🌸

Bio::Tools::Run::WrapperBase</p> — bestie, it's a base object for wrappers around executables 💅

so like, if you opened the Bio::T...erBase(3pm) page looking for something you could just use... no babe, this one's the blueprint, not the house 🏠✨

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✨ SYNOPSIS ✨

do not use this object directly, it provides the following methods for its subclasses 👑

# do not use this object directly, it provides the following methods
# for its subclasses

my $errstr = $obj->error_string();
my $exe    = $obj->executable();
$obj->save_tempfiles($booleanflag)
my $outfile= $obj->outfile_name();
my $tempdir= $obj->tempdir(); # get a temporary dir for executing
my $io     = $obj->io;  # Bio::Root::IO object
my $cleanup= $obj->cleanup(); # remove tempfiles

$obj->run({-arg1 => $value});

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🦋 DESCRIPTION 🦋

okay so here's the tea ☕ this is a basic module from which to build executable wrapper modules. It's got some basic methods to help when you're implementing new modules. That's literally it — it's the group chat admin who keeps everyone organized so the actual wrapper modules can go be main characters 💖

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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 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. 🙏

🐛 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 - Jason Stajich 👑

Email jason-at-bioperl.org

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🎀 CONTRIBUTORS 🎀

Sendu Bala, bix@sendu.me.uk

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ 🌟

🌸 run

• Title: run
• Usage: $wrapper->run({ARGS HERE});
• Function: Support generic running with args passed in as a hashref
• Returns: Depends on the implementation, status OR data
• Args: hashref of named arguments

💜 error_string

• Title: error_string
• Usage: $obj->error_string($newval)
• Function: Where the output from the last analysis run is stored.
• Returns: value of error_string
• Args: newvalue (optional)

✨ arguments

• Title: arguments
• Usage: $obj->arguments($newval)
• Function: Commandline parameters
• Returns: value of arguments
• Args: newvalue (optional)

🧚 no_param_checks

• Title: no_param_checks
• Usage: $obj->no_param_checks($newval)
• Function: Boolean flag as to whether or not we should trust the sanity checks for parameter values
• Returns: value of no_param_checks
• Args: newvalue (optional)

🍓 save_tempfiles

• Title: save_tempfiles
• Usage: $obj->save_tempfiles($newval)
• Function: Get/set the choice of if tempfiles in the temp dir (see tempdir()) are kept or cleaned up. Default is '0', ie. delete temp files.
• Returns: boolean
• Args: none to get, boolean to set

🚨 bestie listen — NB: This must be set to the desired value PRIOR to first creating a temp dir with tempdir(). Any attempt to set this after tempdir creation will get a warning. So set it first, no cap 💀

💖 outfile_name

• Title: outfile_name
• Usage: my $outfile = $wrapper->outfile_name();
• Function: Get/Set the name of the output file for this run (if you wanted to do something special)
• Returns: string
• Args: [optional] string to set value to

🌈 tempdir

• Title: tempdir
• Usage: my $tmpdir = $self->tempdir();
• Function: Retrieve a temporary directory name (which is created)
• Returns: string which is the name of the temporary directory
• Args: none

🧹 cleanup

• Title: cleanup
• Usage: $wrapper->cleanup();
• Function: Will cleanup the tempdir directory
• Returns: none
• Args: none

🦋 io

• Title: io
• Usage: $obj->io($newval)
• Function: Gets a Bio::Root::IO object
• Returns: Bio::Root::IO object
• Args: none

⭐ version

• Title: version
• Usage: $version = $wrapper->version()
• Function: Returns the program version (if available)
• Returns: string representing version of the program
• Args: [Optional] value to (re)set version string

💅 executable

• Title: executable
• Usage: my $exe = $factory->executable();
• Function: Finds the full path to the executable
• Returns: string representing the full path to the exe
• Args: [optional] name of executable to set path to [optional] boolean flag whether or not warn when exe is not found

🌸 program_path

• Title: program_path
• Usage: my $path = $factory->program_path();
• Function: Builds path for executable
• Returns: string representing the full path to the exe
• Args: none

🎀 program_dir

• Title: program_dir
• Usage: my $dir = $factory->program_dir();
• Function: Abstract get method for dir of program. To be implemented by wrapper.
• Returns: string representing program directory
• Args: none

👑 program_name

• Title: program_name
• Usage: my $name = $factory->program_name();
• Function: Abstract get method for name of program. To be implemented by wrapper.
• Returns: string representing program name
• Args: none

🤫 quiet

• Title: quiet
• Usage:

$factory->quiet(1);
if ($factory->quiet()) { ... }

• Function: Get/set the quiet state. Can be used by wrappers to control if program output is printed to the console or not.
• Returns: boolean
• Args: none to get, boolean to set

🔧 _setparams()

• Title: _setparams
• Usage: $params = $self->_setparams(-params => [qw(window evalue_cutoff)])
• Function: For internal use by wrapper modules to build parameter strings suitable for sending to the program being wrapped. For each method name supplied, calls the method and adds the method name (as modified by optional things) along with its value (unless a switch) to the parameter string

Example:

$params = $self->_setparams(-params => [qw(window evalue_cutoff)],
                            -switches => [qw(simple large all)],
                            -double_dash => 1,
                            -underscore_to_dash => 1);

If window() and simple() had not been previously called, but evalue_cutoff(0.5), large(1) and all(0) had been called, $params would be ' --evalue-cutoff 0.5 --large' 🔥

• Returns: parameter string
• Args:

-params => [] or {}  # array ref of method names to call,
                       or hash ref where keys are method names and
                       values are how those names should be output
                       in the params string
-switches => [] or {}# as for -params, but no value is printed for
                       these methods
-join => string      # define how parameters and their values are
                       joined, default ' '. (eg. could be '=' for
                       param=value)
-lc => boolean       # lc() method names prior to output in string
-dash => boolean     # prefix all method names with a single dash
-double_dash => bool # prefix all method names with a double dash
-mixed_dash => bool  # prefix single-character method names with a
                     # single dash, and multi-character method names
                     # with a double-dash
-underscore_to_dash => boolean # convert all underscores in method
                                 names to dashes

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that's the whole page bestie, we ate and left no crumbs 💅✨ this one shipped as perl v5.32.1, dated 2021-08-15, and it lives in the User Contributed Perl Documentation section. go forth and wrap some executables 🫶🎀