Provided by: libbio-perl-perl_1.6.924-3_all 
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
find
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 = $factory->furshlugginer;
#...
}
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send
your comments and suggestions preferably to the Bioperl mailing list. Your participation
is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will
be able look at the problem and quickly address it. Please include a thorough description
of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Mark A. Jensen
Email maj -at- fortinbras -dot- us
Describe contact details here
CONTRIBUTORS
Dan Kortschak ( dan -dot- kortschak -at- adelaide -dot- edu -dot- au )
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are
usually preceded with a _
new()
Title : new
Usage :
Function: constructor for WrapperBase::CommandExts ;
correctly binds configuration variables
to the WrapperBase object
Returns : Bio::Tools::Run::WrapperBase object with command extensions
Args :
Note : this method subsumes the old _register_program_commands and
_set_program_options, leaving out the assembler-specific
parms ($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
perl v5.20.2 2015-10Bio::Tools::Run::WrapperBase::CommandExts(3pm)