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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
 
 

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

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: 
  Returns : value of save_tempfiles
  Args    : newvalue (optional)
 
 

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