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:

  https://github.com/bioperl/bioperl-live/issues

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