Bio::Tools::Run::WrapperBase::CommandExts(3) Extensions to WrapperBase for handling programs with commands *ALPHA*




This is a developer-focused experimental module. The main idea is to extend Bio::Tools::Run::WrapperBase to make it relatively easy to create run wrappers around suites of related programs, like "samtools" or "blast+".

Some definitions:

  • program

    The program is the command-line frontend application. "samtools", for example, is run from the command line as follows:

     $ samtools view -bS in.bam > out.sam
     $ samtools faidx
  • command

    The command is the specific component of a suite run by executing the program. In the example above, "view" and "faidx" are commands.

  • command prefix

    The command prefix is an abbreviation of the command name used internally by "CommandExts" method, and sometimes by the user of the factory for specifying command line parameters to subcommands of composite commands.

  • composite command

    A composite command is a pipeline or script representing a series of separate executions of different commands. Composite commands can be specified by configuring "CommandExts" appropriately; the composite command can be run by the user from a factory in the same way as ordinary commands.

  • options, parameters, switches and filespecs

    An option is any command-line option; i.e., a specification set off by a command-line by a specifier (like "-v" or "--outfile"). Parameters are command-line options that accept a value ("-title mydb"); switches are boolean flags ("--no-filter"). Filespecs are barewords at the end of the command line that usually indicate input or output files. In this module, this includes files that capture STDIN, STDOUT, or STDERR via redirection.

  • pseudo-program

    A ``pseudo-program'' is a way to refer to a collection of related applications that are run independently from the command line, rather than via a frontend program. The "blast+" suite of programs is an example: "blastn", "makeblastdb", etc. "CommandExts" can be configured to create a single factory for a suite of related, independent programs that treats each independent program as a ``pseudo-program'' command.

This module essentially adds the non-assembler-specific wrapper machinery of fangly's Bio::Tools::Run::AssemblerBase to the Bio::Tools::Run::WrapperBase namespace, adding the general command-handling capability of Bio::Tools::Run::BWA. It creates run factories that are automatically Bio::ParameterBaseI compliant, meaning that "available_parameters()", "set_parameters()", "get_parameters", "reset_parameters()", and "parameters_changed()" are available.


"CommandExts" is currently set up to read particular package globals which define the program, the commands available, command-line options for those commands, and human-readable aliases for those options.

The easiest way to use "CommandExts" is probably to create two modules:


The package globals should be defined in the "Config" module, and the run package itself should begin with the following mantra:

 use YourRunPkg::Config;
 use Bio::Tools::Run::WrapperBase;
 use Bio::Tools::Run::WrapperBase::CommandExts;
 sub new {
     my $class = shift;
     my @args = @_;
     my $self = $class->SUPER::new(@args);
     return $self;

The following globals can/should be defined in the "Config" module:


See ``Config Globals'' for detailed descriptions.

The work of creating a run wrapper with "CommandExts" lies mainly in setting up the globals. The key methods for the developer interface are:

  • program_dir($path_to_programs)

    Set this to point the factory to the executables.

  • _run(@file_args)

    Runs an instantiated factory with the given file args. Use in the
     "run()" method override.

  • _create_factory_set()

    Returns a hash of instantiated factories for each true command from a composite command factory. The hash keys are the true command names, so you could do

     $cmds = $composite_fac->_create_factory_set;
     for (@true_commands) {
  • executables($cmd,[$fullpath])

    For pseudo-programs, this gets/sets the full path to the executable of the true program corresponding to the command $cmd.

Implementing Composite Commands

Implementing Pseudo-programs

To indicate that a package wraps disparate programs under a single pseudo program, use an asterisk before the program name:

 package Bio::Tools::Run::YourPkg::Config;
 our $program_name = '*blast+';

and "_run" will know what to do. Specify the rest of the globals as if the desired programs were commands. Use the basename of the programs for the command names.

If all the programs can be found in a single directory, just specify that directory in "program_dir()". If not, use "executables()" to set the paths to each program explicitly:

 foreach (keys %cmdpaths) {
    $self->executables($_, $cmdpaths{$_});

Config Globals

Here is an example config file. Further details in prose are below.

 package Dummy::Config;
 use strict;
 use warnings;
 no warnings qw(qw);
 use Exporter;
 push @ISA, 'Exporter';
 @EXPORT = qw(
 our $program_name = '*flurb';
 our $program_dir = 'C:\cygwin\usr\local\bin';
 our $use_dash = 'mixed';
 our $join = ' ';
 our @program_commands = qw(
 our %command_prefixes = (
     blastp => 'blp',
     tblastn => 'tbn',
     goob => 'g',
     blorb => 'b',
     multiglob => 'm'
 our @program_params = qw(
 our @program_switches = qw(
 our %param_translation = (
     'g|narf'     => 'n',
     'g|schlurb'  => 'schlurb',
     'g|freen'    => 'f',
     'b|scroob'   => 's',
     'b|frelb'    => 'frelb'
 our %command_files = (
     'goob'       => [qw( fas faq )],
 our %composite_commands = (
     'multiglob' => [qw( blorb goob )]

$use_dash can be one of "single", "double", or "mixed". See Bio::Tools::Run::WrapperBase.

There is a syntax for the %command_files specification. The token matching "[a-zA-Z0-9_]+" in each element of each arrayref becomes the named filespec parameter for the "_run()" method in the wrapper class. Additional symbols surrounding this token indicate how this argument should be handled. Some examples:

 >out  : stdout is redirected into the file 
         specified by (..., -out => $file,... )
 <in   : stdin is accepted from the file 
         specified by (..., -in => $file,... )
 2>log : stderr is redirected into the file
         specified by (..., -log => $file,... )
 #opt  : this filespec argument is optional
         (no throw if -opt => $option is missing)
 2>#log: if -log is not specified in the arguments, the stderr() 
         method will capture stderr
 *lst  : this filespec can take multiple arguments,
         specify using an arrayref (..., -lst => [$file1, $file2], ...)
 *#lst : an optional list

The tokens above are examples; they can be anything matching the above regexp.


Using a wrapper created with "Bio::Tools::Run::WrapperBase::CommandExts":
  • Getting a list of available commands, parameters, and filespecs:

    To get a list of commands, simply:

     @commands = Bio::Tools::Run::ThePkg->available_commands;

    The wrapper will generally have human-readable aliases for each of the command-line options for the wrapped program and commands. To obtain a list of the parameters and switches available for a particular command, do

     $factory = Bio::Tools::Run::ThePkg->new( -command => 'glurb' );
     @params = $factory->available_parameters('params');
     @switches = $factory->available_parameters('switches');
     @filespec = $factory->available_parameters('filespec');
     @filespec = $factory->filespec; # alias
  • Create factories

    The factory is a handle on the program and command you wish to run. Create a factory using "new" to set command-line parameters:

     $factory = Bio::Tools::Run::ThePkg->new( -command => 'glurb', 
                                              -freen => 1,
                                              -furschlugginer => 'vreeble' );

    A shorthand for this is:

     $factory = Bio::Tools::Run::ThePkg->new_glurb( 
                                           -freen => 1, 
                                           -furschlugginer => 'vreeble' );
  • Running programs

    To run the program, use the "run" method, providing filespecs as arguments

     $factory = Bio::Tools::Run::ThePkg->new_assemble( -min_qual => 63 );
     $factory->run( -faq1 => 'read1.fq', -faq2 => 'read2.fq', 
                    -ref => 'refseq.fas', -out => 'new.sam' );
     # do another
     $factory->run( -faq1 => 'read-old1.fq', -faq2 => 'read-old2.fq', 
                    -ref => 'refseq.fas', -out => 'old.sam' );

    Messages on STDOUT and STDERR are dumped into their respective attributes:

     $stdout = $factory->stdout;
     $stderr = $factory->stderr;

    unless STDOUT and/or STDERR are part of the named files in the filespec.

  • Setting/getting/resetting/polling parameters.

    A "CommandExts"-based factory is always Bio::ParameterBaseI compliant. That means that you may set, get, and reset parameters using "set_parameters()", "get_parameters()", and "reset_parameters". You can ask whether parameters have changed since they were last accessed by using the predicate "parameters_changed". See Bio::ParameterBaseI for more details.

    Once set, parameters become attributes of the factory. Thus, you can get their values as follows:

     if ($factory->freen) { 
        $furs = $factory->furshlugginer;


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  - About the mailing lists


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:

AUTHOR - Mark A. Jensen

Email maj -at- fortinbras -dot- us

Describe contact details here


Dan Kortschak ( dan -dot- kortschak -at- adelaide -dot- edu -dot- au )


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


 Title   : new
 Usage   : 
 Function: constructor for WrapperBase::CommandExts ; 
           correctly binds configuration variables
           to the WrapperBase object
 Returns : Bio::Tools::Run::WrapperBase object with command extensions
 Args    : 
 Note    : this method subsumes the old _register_program_commands and
           _set_program_options, leaving out the assembler-specific
           parms ($qual_param and out_type())


 Title   : program_name
 Usage   : $factory->program_name($name)
 Function: get/set the executable name
 Returns:  string
 Args    : string


 Title   : program_dir
 Usage   : $factory->program_dir($dir)
 Function: get/set the program dir
 Returns:  string
 Args    : string


 Title   : _register_program_commands
 Usage   : $factory->_register_program_commands( \@commands, \%prefixes )
 Function: Register the commands a program accepts (for programs that act
           as frontends for a set of commands, each command having its own
           set of params/switches)
 Returns : true on success
 Args    : arrayref to a list of commands (scalar strings),
           hashref to a translation table of the form
           { $prefix1 => $command1, ... } [optional]
 Note    : To implement a program with this kind of calling structure, 
           include a parameter called 'command' in the 
           @program_params global
 Note    : The translation table is used to associate parameters and 
           switches specified in _set_program_options with the correct
           program command. In the globals @program_params and
           @program_switches, specify elements as 'prefix1|param' and 
           'prefix1|switch', etc.


 Title   : _set_program_options
 Usage   : $factory->_set_program_options( \@ args );
 Function: Register the parameters and flags that an assembler takes.
 Returns : 1 for success
 Args    : - arguments passed by the user
           - parameters that the program accepts, optional (default: none)
           - switches that the program accepts, optional (default: none)
           - parameter translation, optional (default: no translation occurs)
           - dash option for the program parameters, [1|single|double|mixed],
             optional (default: yes, use single dashes only)
           - join, optional (default: ' ')


 Title   : _translate_params
 Usage   : @options = $assembler->_translate_params( );
 Function: Translate the Bioperl arguments into the arguments to pass to the
           program on the command line
 Returns : Arrayref of arguments
 Args    : none


 Title   : executable
 Usage   : 
 Function: find the full path to the main executable,
           or to the command executable for pseudo-programs
 Returns : full path, if found
 Args    : [optional] explicit path to the executable
           (will set the appropriate command exec if
           [optional] boolean flag whether or not to warn when exe no found
 Note    : overrides


 Title   : executables
 Usage   : 
 Function: find the full path to a command's executable
 Returns : full path (scalar string)
 Args    : command (scalar string), 
           [optional] explicit path to this command exe
           [optional] boolean flag whether or not to warn when exe no found


 Title   : _find_executable
 Usage   : my $exe_path = $fac->_find_executable($exe, $warn);
 Function: find the full path to a named executable,
 Returns : full path, if found
 Args    : name of executable to find
           [optional] boolean flag whether or not to warn when exe no found
 Note    : differs from executable and executables in not
           setting any object attributes


 Title   : _register_composite_commands
 Usage   : 
 Function: adds subcomand params and switches for composite commands
 Returns : true on success
 Args    : \%composite_commands,


 Title   : _create_factory_set
 Usage   : @facs = $self->_create_factory_set
 Function: instantiate a set of individual command factories for
           a given composite command
           Factories will have the correct parameter fields set for
           their own subcommand
 Returns : hash of factories: ( $subcmd_prefix => $subcmd_factory, ... )
 Args    : none


 Title   : _collate_subcmd_args
 Usage   : $args_hash = $self->_collate_subcmd_args
 Function: collate parameters and switches into command-specific
           arg lists for passing to new()
 Returns : hash of named argument lists
 Args    : [optional] composite cmd prefix (scalar string) 
           [default is 'run']


 Title   : _run
 Usage   : $fac->_run( @file_args )
 Function: Run a command as specified during object contruction
 Returns : true on success
 Args    : a specification of the files to operate on according
           to the filespec


 Title   : no_throw_on_crash
 Usage   : 
 Function: prevent throw on execution error
 Returns : 
 Args    : [optional] boolean


 Title   : last_execution
 Usage   : 
 Function: return the last executed command with options
 Returns : string of command line sent to IPC::Run
 Args    :


 Title   : _dash_switch
 Usage   : $version = $fac->_dash_switch( $switch )
 Function: Returns an appropriately dashed switch for the executable
 Args    : A string containing a switch without dashes
 Returns : string containing an appropriately dashed switch for the current executable


 Title   : stdout
 Usage   : $fac->stdout()
 Function: store the output from STDOUT for the run, 
           if no file specified in _run arguments
 Example : 
 Returns : scalar string
 Args    : on set, new value (a scalar or undef, optional)


 Title   : stderr
 Usage   : $fac->stderr()
 Function: store the output from STDERR for the run, 
           if no file is specified in _run arguments
 Example : 
 Returns : scalar string
 Args    : on set, new value (a scalar or undef, optional)


 Title   : is_pseudo
 Usage   : $obj->is_pseudo($newval)
 Function: returns true if this factory represents
           a pseudo-program
 Example : 
 Returns : value of is_pseudo (boolean)
 Args    : on set, new value (a scalar or undef, optional)


AUTOLOAD permits


as an alias for

 $class->new( -command => 'yourcommand', @args );

Bio:ParameterBaseI compliance


 Title   : set_parameters
 Usage   : $pobj->set_parameters(%params);
 Function: sets the parameters listed in the hash or array
 Returns : true on success
 Args    : [optional] hash or array of parameter/values.


 Title   : reset_parameters
 Usage   : resets values
 Function: resets parameters to either undef or value in passed hash
 Returns : none
 Args    : [optional] hash of parameter-value pairs


 Title   : parameters_changed
 Usage   : if ($pobj->parameters_changed) {...}
 Function: Returns boolean true (1) if parameters have changed
 Returns : Boolean (0 or 1)
 Args    : [optional] Boolean


 Title   : available_parameters
 Usage   : @params = $pobj->available_parameters()
 Function: Returns a list of the available parameters
 Returns : Array of parameters
 Args    : 'params' for settable program parameters
           'switches' for boolean program switches
           default: all


 Title   : get_parameters
 Usage   : %params = $pobj->get_parameters;
 Function: Returns list of key-value pairs of parameter => value
 Returns : List of key-value pairs
 Args    : [optional] A string is allowed if subsets are wanted or (if a
           parameter subset is default) 'all' to return all parameters