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Bio::Tools::Run::WrapperBase.3pm

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.

   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:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

CONTRIBUTORS

Sendu Bala, bix@sendu.me.uk

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:EThis must be set to the desired value PRIOR to first creating
            a temp dir with tempdir().
  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