Training Info¶

class pyrodigal.TrainingInfo¶

A collection of parameters obtained after training.

New in version 0.5.0.

__init__(*args, **kwargs)¶

dump(fp)¶

Write a training info to a file-like handle.

Parameters: fp (file-like object) – An file-like handle opened in binary mode, into which the training info should be written.

Danger

This method is not safe to use across different machines. The internal binary structure will be dumped as-is, and because the C types can change in size and representation between CPUs and OS, the file will not portable. This method is only provided to offer the same kind of features as the Prodigal binary. For a safe way of storing and sharing a TrainingInfo, use the pickle module.

New in version 0.6.4.

load(fp)¶

Load a training info from a file-like handle.

Parameters: fp (file-like object) – An file-like handle opened in binary mode, from which to read the training info.
Returns: TrainingInfo – The deserialized training info.

Danger

Raises: EOFError – When less bytes than expected could be read from the source file handle.

New in version 0.6.4.

bias¶

The GC frame bias for each of the 3 positions.

Type: tuple of float

gc¶

The GC content of the training sequence.

Type: float

start_weight¶

The start score weight to use for the training sequence.

Type: float

translation_table¶

The translation table used during training.

Type: int

type_weights¶

The weights for ATG, GTG and TTG.

Type: tuple of float

uses_sd¶

True if the sequence uses a Shine/Dalgarno motif.

Type: bool

class pyrodigal.MetagenomicBin¶

A pre-trained collection used to find genes in metagenomic mode.

training_info¶

The training info for this metagenomic bin.

Type: TrainingInfo

description¶

A condensed text description for this metagenomic bin.

Type: str

index¶

The index of this metagenomic bin.

Type: int