Provided by: libbio-perl-run-perl_1.7.1-3_all bug

NAME

       Bio::Tools::Run::AssemblerBase - base class for wrapping external assemblers

SYNOPSIS

       Give standard usage here

DESCRIPTION

       Describe the object here # use of globals for configuration...  # I've created the
       separate Config.pm module, and 'use'd it in the # main module, for instance...  # other
       configuration globals: # $use_dash = [1|single|double|mixed]

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:

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

AUTHOR - Florent Angly

       Email florent dot angly at gmail dot com

CONTRIBUTORS

       Mark A. Jensen - maj -at- fortinbras -dot- us

APPENDIX

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

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

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

   out_type
        Title   : out_type
        Usage   : $assembler->out_type('Bio::Assembly::ScaffoldI')
        Function: get/set the desired type of output
        Returns : The type of results to return
        Args    : Type of results to return (optional):
                        'Bio::Assembly::IO' object
                        'Bio::Assembly::ScaffoldI' object (default)
                        The name of a file to save the results in

   _assembly_format
        Title   : _assembly_format
        Usage   : $assembler->_assembly_format('ace')
        Function: get/set the driver to use to parse the assembly results
        Returns : the driver to use to parse the assembly results
        Args    : the driver to use to parse the assembly results (optional)

   _assembly_variant
        Title   : _assembly_variant
        Usage   : $assembler->_assembly_variant('454')
        Function: get/set the driver variant to use to parse the assembly results. For
                  example, the ACE format has the ACE-454 and the ACE-consed variants
        Returns : the driver variant to use to parse the assembly results
        Args    : the driver variant to use to parse the assembly results (optional)

   _check_executable
        Title   : _check_executable
        Usage   : $assembler->_check_executable()
        Function: Verifies that the program executable can be found, or throw an error.
        Returns:  1 for success
        Args    : -

   _check_sequence_input
        Title   : _check_sequence_input
        Usage   : $assembler->_check_sequence_input($seqs)
        Function: Check that the sequence input is a valid file, or an arrayref of
                    sequence objects (Bio::PrimarySeqI or Bio::SeqI). If not, an
                    exception is thrown.
        Returns : 1 if the check passed
        Args    : sequence input

   _check_optional_quality_input
        Title   : _check_optional_quality_input
        Usage   : $assembler->_check_optional_quality_input($quals)
        Function: If a quality score input is provided, check that it is either a
                    valid file or an arrayref of quality score objects (Bio::Seq::
                    QualI or Bio::Seq::Quality). If not, an exception is thrown.
        Returns : 1 if the check passed (or quality score input was provided)
        Args    : quality score input

   _prepare_input_file
        Title   : _prepare_input_file
        Usage   : ($fasta_file, $qual_file) =  $assembler->_prepare_input_file(\@seqs, \@quals);
        Function: Create the input FASTA and QUAL files as needed. If the input
                  sequences are provided in a (FASTA) file, the optional input quality
                  scores are also expected to be in a (QUAL) file. If the input
                  sequences are an arrayref of bioperl sequence objects, the optional
                  input quality scores are expected to be an arrayref of bioperl
                  quality score objects, in the same order as the sequence objects.
        Returns : - input filehandle
                  - input filename
        Args    : - sequence input (FASTA file or sequence object arrayref)
                  - optional quality score input (QUAL file or quality score object
                      arrayref)

   _write_seq_file
        Title   :   _write_seq_file
        Usage   :   ($fasta_file, $qual_file) = $assembler->_write_seq_file(\@seqs, \@quals)
        Function:   Write temporary FASTA and QUAL files on disk
        Returns :   name of FASTA file
                    name of QUAL file (undef if no quality scoress)
        Args    :   - arrayref of sequence objects
                    - optional arrayref of quality score objects

   _prepare_output_file
        Title   : _prepare_output_file
        Usage   : ($out_fh, $out_file) =  $assembler->_prepare_output_file( );
        Function: Prepare the output file
        Returns : - output filehandle
                  - output filename
        Args    : none

   _export_results
        Title   : _export_results
        Usage   : $results = $assembler->_export_results($asm_file);
        Function: Export the assembly results
        Returns : Exported assembly (file or IO object or assembly object)
        Args    : -Name of the file containing an assembly
                  - -keep_asm => boolean (if true, do not unlink $asm_file)
                  -[optional] additional named args required by the B:A:IO object

   _register_program_commands()
        Title   : _register_program_commands
        Usage   : $assembler->_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   : $assembler->_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
                    assembler on the command line
        Returns : Arrayref of arguments
        Args    : none

   _prepare_input_sequences
        Title   : _prepare_input_sequences
        Usage   : ($seqs, $quals) = $assembler->_prepare_input_sequences(\@seqs, \@quals);
        Function: Do something to the input sequence and qual objects. By default,
                  nothing happens. Overload this method in the specific assembly module
                  if processing of the sequences is needed (e.g. as in the
                  TigrAssembler module).
        Returns : - sequence input
                  - optional quality score input
        Args    : - sequence input (FASTA file or sequence object arrayref)
                  - optional quality score input (QUAL file or quality score object
                      arrayref)

   _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   : $assembly = $assembler->run(\@seqs, \@quals);
                    or
                  $assembly = $assembler->run($fasta_file, $qual_file);
        Function: Run the assembler. The specific assembler wrapper needs to provide
                    the $assembler->_run() method.
        Returns : Assembly results (file, IO object or Assembly object)
        Args    : - sequence input (FASTA file or sequence object arrayref)
                  - optional quality score input (QUAL file or quality score object
                      arrayref)

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