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/

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)

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