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       Bio::Tools::Run::WrapperBase::CommandExts - Extensions to WrapperBase for handling
       programs with commands *ALPHA*


       Devs, see "DEVELOPER INTERFACE".  Users, see "USER INTERFACE".


       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

       ·   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


       "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;
        our (@ISA, @EXPORT, @EXPORT_OK);
        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.
                  - General discussion  - About the mailing lists

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

       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

perl v5.24.1                                2017-01Bio::Tools::Run::WrapperBase::CommandExts(3pm)