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 listsSupport
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:
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 : stringprogram_dir
Title : program_dir
Usage : $assembler->program_dir()
Function: get/set the program dir
Returns: string
Args : stringout_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 : $pobj->set_parameters(%params);
Function: sets the parameters listed in the hash or array
Returns : true on success
Args : [optional] hash or array of parameter/values. reset_parameters()
Title : reset_parameters
Usage : resets values
Function: resets parameters to either undef or value in passed hash
Returns : none
Args : [optional] hash of parameter-value pairsparameters_changed()
Title : parameters_changed
Usage : if ($pobj->parameters_changed) {...}
Function: Returns boolean true (1) if parameters have changed
Returns : Boolean (0 or 1)
Args : [optional] Booleanavailable_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