DENOFO Converter

The DENOFO Converter is a tool for converting the denofo annotation format between different file formats (e.g., *.dngf to *.gff or *.fasta).

There are two interfaces for the converter: a command-line interface (CLI) and a graphical user interface (GUI).

Command-line interface (CLI)

denofo.converter.converter_cli.main(): The main function of the program including argument parsing.

Graphical user interface (GUI)

class denofo.converter.converter_gui.DngfConverterGUI

closeEvent(self, a0: QCloseEvent | None)

Converter logic implementation

denofo.converter.convert.annotate_fasta(dnga_model: DeNovoGeneAnnotation, fasta_file: Path, outf: Path | None = None, identifiers: set[str] | None = None) → str

Annotate a FASTA file with the model short string representation.

Parameters:

dnga_model (DeNovoGeneAnnotation) – DeNovoGeneAnnotation model to annotate with
fasta_file (Path) – additional input file path
outf (Path, optional) – output file path, defaults to None
identifiers (set[str], optional) – identifiers to filter, defaults to None

Returns:

annotated FASTA string, if outf is None

Return type:

str

denofo.converter.convert.annotate_gff(dnga_model: DeNovoGeneAnnotation, gff_file: Path, outf: Path | None = None, feature: str = 'gene', identifiers: set[str] | None = None) → str

Annotate a GFF file with the model short string representation.

Parameters:

dnga_model (DeNovoGeneAnnotation) – DeNovoGeneAnnotation model to annotate with
gff_file (Path) – GFF file path
outf (Path, optional) – output file path, defaults to None
feature (str, optional) – feature to annotate, defaults to “gene”
identifiers (set[str], optional) – identifiers to filter, defaults to None

Returns:

annotated GFF string, if outf is None

Return type:

str

denofo.converter.convert.convert_to_json(dnga_model: DeNovoGeneAnnotation, outf: Path | None = None) → str

Convert a DeNovoGeneAnnotation model to a JSON file.

Parameters:

dnga_model (DeNovoGeneAnnotation) – DeNovoGeneAnnotation model to convert
outf (Path, optional) – output file path, defaults to None

Returns:

JSON string

Return type:

str

denofo.converter.convert.convert_to_pickle(dnga_model: DeNovoGeneAnnotation, outf: Path | None = None) → bytes

Convert a DeNovoGeneAnnotation model to a pickle file.

Parameters:

dnga_model (DeNovoGeneAnnotation) – DeNovoGeneAnnotation model to convert
outf (Path, optional) – output file path, defaults to None

Returns:

pickled model

Return type:

bytes

denofo.converter.convert.decode_short_str(short_str: str) → DeNovoGeneAnnotation

Decode a short representation string into a DeNovoGeneAnnotation model.

Parameters:: short_str (str) – short representation string
Returns:: DeNovoGeneAnnotation model
Return type:: DeNovoGeneAnnotation

denofo.converter.convert.encode_short_str(dnga_model: DeNovoGeneAnnotation) → str

Encode a DeNovoGeneAnnotation model as a short representation string.

Parameters:: dnga_model (DeNovoGeneAnnotation) – DeNovoGeneAnnotation model to encode
Returns:: short representation string
Return type:: str

denofo.converter.convert.load_from_fasta(fasta_file: Path, identifiers: set[str] | None = None) → DeNovoGeneAnnotation

Load a DeNovoGeneAnnotation model from a FASTA file.

Parameters:

fasta_file (Path) – FASTA file path
identifiers (set[str], optional) – identifiers to filter, defaults to None

Returns:

DeNovoGeneAnnotation model

Return type:

DeNovoGeneAnnotation

denofo.converter.convert.load_from_gff(gff_file: Path, feature: str = 'gene', identifiers: set[str] | None = None) → DeNovoGeneAnnotation

Load a DeNovoGeneAnnotation model from a GFF file.

Parameters:

gff_file (Path) – GFF file path
feature (str, optional) – feature to load, defaults to “gene”
identifiers (set[str], optional) – identifiers to filter, defaults to None

Returns:

DeNovoGeneAnnotation model

Return type:

DeNovoGeneAnnotation

denofo.converter.convert.load_from_json(json_file: Path) → DeNovoGeneAnnotation

Load a DeNovoGeneAnnotation model from a JSON file.

Parameters:: json_file (Path) – JSON file path
Returns:: DeNovoGeneAnnotation model
Return type:: DeNovoGeneAnnotation

denofo.converter.convert.load_from_pickle(pkl_file: Path) → DeNovoGeneAnnotation

Load a DeNovoGeneAnnotation model from a pickle file.

Parameters:: pkl_file (Path) – pickle file path
Returns:: DeNovoGeneAnnotation model
Return type:: DeNovoGeneAnnotation