GenomeTypeObject

NAME

GenomeTypeObject - a helper class for manipulating GenomeAnnotation service genome objects.

SYNOPSIS

$obj = GenomeTypeObject->new()

$obj = GenomeTypeObject->initialize($raw_genome_object)

DESCRIPTION

The GenomeTypeObject class wraps a number of common operations to be performed against the genome object as defined in the KBase GenomeAnnotation service.

To use the methods here it is sufficient to just bless the JSON object containing the genome data into the GenomeTypeObject class, but it is more efficient to initialize it using the initialize method:

$obj = GenomeTypeObject->initialize($raw_json)

Doing this will create internal indexes on the feature and contig data structures to accelerate access to individual data items.

Before using the genome object as a raw JSON object again, however, you must invoke the prepare_for_return() method which strips these indexes out of the data object.

$obj = GenomeTypeObject->new()

Create a new empty genome object.

$obj = GenomeTypeObject->create_from_file($filename)

Load the given file, assumed to contain the JSON form of a genome object, and return as a GenomeTypeObject instance.

The resulting object has not had the initialize method invoked on it.

$obj->destroy_to_file($filename)

Write the given object in JSON form to the specified file. The object will be rendered unusable (i.e., unblessed)

$obj->set_metadata({ … });

Set the metadata fields on this genome object based on a metadata object as defined in the GenomeAnnotation typespec:

typedef structure
{
 genome_id id;
 string scientific_name;
 string domain;
 int genetic_code;
 string source;
 string source_id;
 int ncbi_taxonomy_id;
 string taxonomy;
 string owner;
} genome_metadata

$obj->add_contigs($contigs)

Add the given set of contigs to this genome object. $contigs is a list of contig objects, which we add to the genome object without further inspection.

$obj->add_features_from_list($features)

Add the given features to the genome. Features here are instances of the compact_tuple type:

typedef tuple <string id, string location, string feature_type, string function, string aliases> compact_feature;

used in the importation of features from an external source via a tab-separated text file.

We create an event for this import so that the source of the features so added is tracked.

Returns a hash mapping from the feature ID in the list to the allocated feature ID.

$obj->add_feature($params)

Add a new feature. The details of the feature are defined in the parameters hash. It has the following keys:

-id Identifier for this feature. If not provided, a new identifier will be created based on the genome id, the type of the feature and the current largest identifier for that feature type.

$obj->write_protein_translations_to_file($filename)

Write the protein translations to a FASTA file.

$obj->write_contigs_to_file($filename)

Write the contigs to a FASTA file.

metrics

my $metricHash = $gto->metrics();

Return a hash of metrics about this GTO. The metrics returned will include N50, N70, N90, total DNA length, and probable completeness.

RETURN

Returns a reference to a hash with the following keys.

N50

The N50 of the contig lengths (see /n_metric).

N70

The N70 of the contig lengths.

N90

The N90 of the contig lengths.

totlen

The total DNA length.

complete

1 if the genome is mostly complete, else 0.

n_metric

my $length = $gto->n_metric($thresh);

Compute the NXX metric for the contig lengths, where XX is a percentage (usually 50, 70, or 90). A higher value for the metric indicates a higher-quality assembly. The N70 metric is the length of the shortest contig in the set of longest contigs comprising 70% of the total contig lengths. Similarly, the N50 metric is the length of the shortest contig in the set of longest contigs comprising 50% of the total contig lengths.

thresh

The threshold to use for the desired metric. For example, specify 70 for an N70 metric.

RETURN

Returns the length of the contig at the desired metric level.