Genbank Class

Genbank

Genbank(
    gbk_source: str | Path | TextIOWrapper | list[SeqRecord], *, name: str | None = None
)

Genbank Parser Class

PARAMETER	DESCRIPTION
`gbk_source`	Genbank file or source (`.gz`, `.bz2`, `.zip` compressed file can be readable) TYPE:* `str \| Path \| TextIOWrapper \| list[SeqRecord]`
`name`	name (If None, `file name` or `record name` is set) TYPE: `str \| None` DEFAULT: `None`

name `property`

name: str

Name

records `property`

records: list[SeqRecord]

Genbank records

genome_seq `property`

genome_seq: str

Genome sequence (only first record)

genome_length `property`

genome_length: int

Genome length (only first record)

full_genome_seq `property`

full_genome_seq: str

Full genome sequence (concatenate all records)

full_genome_length `property`

full_genome_length: int

Full genome length (concatenate all records)

calc_genome_gc_content

calc_genome_gc_content(seq: str | None = None) -> float

Calculate genome GC content

PARAMETER	DESCRIPTION
`seq`	Sequence for GC content calculation (Default: `self.genome_seq`) TYPE: `str \| None` DEFAULT: `None`

RETURNS	DESCRIPTION
`gc_content`	GC content TYPE: `float`

calc_gc_skew

calc_gc_skew(
    window_size: int | None = None,
    step_size: int | None = None,
    *,
    seq: str | None = None
) -> tuple[NDArray[np.int64], NDArray[np.float64]]

Calculate GC skew in sliding window

PARAMETER	DESCRIPTION
`window_size`	Window size (Default: `genome_size / 500`) TYPE: `int \| None` DEFAULT: `None`
`step_size`	Step size (Default: `genome_size / 1000`) TYPE: `int \| None` DEFAULT: `None`
`seq`	Sequence for GCskew calculation (Default: `self.genome_seq`) TYPE: `str \| None` DEFAULT: `None`

RETURNS	DESCRIPTION
`pos_list`	Position list TYPE: `NDArray[int64]`
`gc_skew_list`	GC skew list TYPE: `NDArray[float64]`

calc_gc_content

calc_gc_content(
    window_size: int | None = None,
    step_size: int | None = None,
    *,
    seq: str | None = None
) -> tuple[NDArray[np.int64], NDArray[np.float64]]

Calculate GC content in sliding window

PARAMETER	DESCRIPTION
`window_size`	Window size (Default: `genome_size / 500`) TYPE: `int \| None` DEFAULT: `None`
`step_size`	Step size (Default: `genome_size / 1000`) TYPE: `int \| None` DEFAULT: `None`
`seq`	Sequence for GC content calculation (Default: `self.genome_seq`) TYPE: `str \| None` DEFAULT: `None`

RETURNS	DESCRIPTION
`pos_list`	Position list TYPE: `NDArray[int64]`
`gc_content_list`	GC content list TYPE: `NDArray[float64]`

get_seqid2seq

get_seqid2seq() -> dict[str, str]

Get seqid & complete/contig/scaffold genome sequence dict

RETURNS	DESCRIPTION
`seqid2seq`	seqid & genome sequence dict TYPE: `dict[str, str]`

get_seqid2size

get_seqid2size() -> dict[str, int]

Get seqid & complete/contig/scaffold genome size dict

RETURNS	DESCRIPTION
`seqid2size`	seqid & genome size dict TYPE: `dict[str, int]`

get_seqid2features

get_seqid2features(
    feature_type: str | list[str] | None = "CDS", target_strand: int | None = None
) -> dict[str, list[SeqFeature]]

Get seqid & features in target seqid genome dict

PARAMETER	DESCRIPTION
`feature_type`	Feature type (`CDS`, `gene`, `mRNA`, etc...) If None, extract regardless of feature type. TYPE: `str \| list[str] \| None` DEFAULT: `'CDS'`
`target_strand`	Extract target strand. If None, extract regardless of strand. TYPE: `int \| None` DEFAULT: `None`

RETURNS	DESCRIPTION
`seqid2features`	seqid & features dict TYPE: `dict[str, list[SeqFeature]]`

extract_features

extract_features(
    feature_type: str | list[str] | None = "CDS",
    *,
    target_strand: int | None = None,
    target_range: tuple[int, int] | None = None
) -> list[SeqFeature]

Extract features (only first record)

PARAMETER	DESCRIPTION
`feature_type`	Feature type (`CDS`, `gene`, `mRNA`, etc...) If None, extract regardless of feature type. TYPE: `str \| list[str] \| None` DEFAULT: `'CDS'`
`target_strand`	Extract target strand. If None, extract regardless of strand. TYPE: `int \| None` DEFAULT: `None`
`target_range`	Extract target range. If None, extract regardless of range. TYPE: `tuple[int, int] \| None` DEFAULT: `None`

RETURNS	DESCRIPTION
`features`	Extracted features TYPE: `list[SeqFeature]`

write_cds_fasta

write_cds_fasta(outfile: str | Path) -> None

Write CDS fasta file

PARAMETER	DESCRIPTION
`outfile`	Output CDS fasta file TYPE: `str \| Path`

write_genome_fasta

write_genome_fasta(outfile: str | Path) -> None

Write genome fasta file

PARAMETER	DESCRIPTION
`outfile`	Output genome fasta file TYPE: `str \| Path`