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NAME

Smash::Analyses::GenePredictor::MetaGene - Implementation of MetaGene gene prediction software pipeline

SYNOPSIS

        my $instance = Smash::Analyses::GenePredictor::MetaGene->new
                                (
                                        'NAME'        => $label,
                                        'OUTPUT_DIR'  => $output_dir,
                                        'PREDICTOR'   => 'MetaGene',
                                        'FASTA_FILE'  => $fasta,
                                        'SELF_TRAIN'  => 0,
                                        'VERSION'     => "2008-08-19"
                                );
        $instance->run();

DESCRIPTION

This module implements the wrapper around the MetaGeneAnnotator program. MGA will treat multiple sequences to be from the same species when "-s" is given. Otherwise, each sequence is treated individually.

FUNCTIONS

Smash has switched to the MetaGeneAnnotator program from the original MetaGene program.

MetaGene specific functions

program

Find the correct version of the software. Smash first gets the architecture of the host and then looks for the right version. Since most 64bit linux versions can also execute 32bit code, it will fall back to 32bit versions if the 64bit version is not available on a 64bit machine.

Mandatory and conditionally mandatory functions

is_trainable

returns 1.

train_min

returns 200000.

parameter_settings

describes the rule based creation of parameter set for commandline.

create_multifasta_gene_gff

parses the output from MetaGene and creates a GFF file containing gene coordinates.

Suggested functions

min_length

returns 41.

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