NAME

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

SYNOPSIS

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

DESCRIPTION

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.

DEVELOPER INTERFACE

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:

Bio::Tools::Run::YourRunPkg
Bio::Tools::Run::YourRunPkg::Config

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:

$program_name
$program_dir
$use_dash
$join
@program_commands 
%command_prefixes
@program_params
@program_switches 
%param_translation
%composite_commands
%command_files

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) {
   $cmds->{$_}->_run(@file_args);
}
```
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(
             $program_name
             $program_dir
             $use_dash
             $join
             @program_commands
             %command_prefixes
             @program_params
             @program_switches
             %param_translation
             %command_files
             %composite_commands
            );

our $program_name = '*flurb';
our $program_dir = 'C:\cygwin\usr\local\bin';
our $use_dash = 'mixed';
our $join = ' ';

our @program_commands = qw(
 rpsblast
 cat
 goob
 blorb
 multiglob
  );

our %command_prefixes = (
    blastp => 'blp',
    tblastn => 'tbn',
    goob => 'g',
    blorb => 'b',
    multiglob => 'm'
    );

our @program_params = qw(
    command
    g|narf
    g|schlurb
    b|scroob
    b|frelb
    m|trud
);

our @program_switches = qw(
    g|freen
    b|klep
);

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 )]
    );
1;

$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.

USER INTERFACE

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;
   #...
}
```

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:

https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Mark A. Jensen

Email maj -at- fortinbras -dot- us

Describe contact details here

CONTRIBUTORS

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

APPENDIX

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

new()

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())

program_name

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

program_dir

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

_register_program_commands()

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.

_set_program_options

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: ' ')

_translate_params

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

executable()

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
           applicable)
          [optional] boolean flag whether or not to warn when exe no found
Note    : overrides WrapperBase.pm

executables()

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

_find_executable()

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

_register_composite_commands()

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

_create_factory_set()

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

_collate_subcmd_args()

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']

_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

no_throw_on_crash()

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

last_execution()

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

_dash_switch()

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

stdout()

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)

stderr()

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)

is_pseudo()

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

AUTOLOAD permits

$class->new_yourcommand(@args);

as an alias for

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

Bio:ParameterBaseI compliance

set_parameters()

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.

reset_parameters()

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

parameters_changed()

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

available_parameters()

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

get_parameters()

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

To install Bio::Seq, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Bio::Seq

CPAN shell

perl -MCPAN -e shell
install Bio::Seq

For more information on module installation, please visit the detailed CPAN module installation guide.

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