The London Perl and Raku Workshop takes place on 26th Oct 2024. If your company depends on Perl, please consider sponsoring and/or attending.
 / 
BioPerl-1.7.8
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Tools::Run::WrapperBase

NAME

Bio::Tools::Run::WrapperBase - A Base object for wrappers around executables

SYNOPSIS

# 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});

DESCRIPTION

This is a basic module from which to build executable wrapper modules. It has some basic methods to help when implementing new modules.

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.

[email protected]                  - General discussion
https://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

CONTRIBUTORS

Sendu Bala, [email protected]

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.
          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.
Returns : boolean
Args    : none to get, boolean to set

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