Genbank Class

Genbank

Genbank(
    gbk_source: str | Path | TextIOWrapper,
    name: str | None = None,
    reverse: bool = False,
    min_range: int | None = None,
    max_range: int | 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`
`name`	name (If None, `file name` or `record name` is set) TYPE: `str \| None` DEFAULT: `None`
`reverse`	If True, reverse complement genome is used TYPE: `bool` DEFAULT: `False`
`min_range`	Min range to be extracted (Default: `0`) TYPE: `int \| None` DEFAULT: `None`
`max_range`	Max range to be extracted (Default: `genome length`) TYPE: `int \| None` DEFAULT: `None`

name `property`

name: str

Name

records `property`

records: list[SeqRecord]

Genbank records

full_genome_length `property`

full_genome_length: int

Full genome sequence length

genome_length `property`

genome_length: int

Range genome sequence length (Same as range_size)

range_size `property`

range_size: int

Range size (max_range - min_range)

full_genome_seq `property`

full_genome_seq: str

Full genome sequence

genome_seq `property`

genome_seq: str

Range genome sequence

calc_genome_gc_content

calc_genome_gc_content() -> float

Calculate genome GC content

calc_gc_skew

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

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
`gc_skew_result_tuple`	Position list & GC skew list TYPE: `tuple[ndarray, ndarray]`

calc_gc_content

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

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 GCskew calculation (Default: `self.genome_seq`) TYPE: `str \| None` DEFAULT: `None`

RETURNS	DESCRIPTION
`gc_content_result_tuple`	Position list & GC content list TYPE: `tuple[ndarray, ndarray]`

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, int]`

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 | None = "CDS",
    target_strand: int | None = None,
    pseudogene: bool | None = False,
) -> 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 \| None` DEFAULT: `'CDS'`
`target_strand`	Extract target strand. If None, extract regardless of strand. TYPE: `int \| None` DEFAULT: `None`
`pseudogene`	If True, `pseudo=`, `pseudogene=` tagged record only extract. If False, `pseudo=`, `pseudogene=` not tagged record only extract. If None, extract regardless of pseudogene tag. TYPE: `bool \| None` DEFAULT: `False`

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

extract_features

extract_features(
    feature_type: str = "CDS",
    target_strand: int | None = None,
    fix_position: bool = False,
    allow_partial: bool = False,
    pseudogene: bool = False,
) -> list[SeqFeature]

Extract features within min-max range

PARAMETER	DESCRIPTION
`feature_type`	Extract feature type TYPE: `str` DEFAULT: `'CDS'`
`target_strand`	Extract target strand TYPE: `int \| None` DEFAULT: `None`
`fix_position`	If True, fix feature start & end position by specified min_range parameter (fixed_start = start - min_range, fixed_end = end - min_range) TYPE: `bool` DEFAULT: `False`
`allow_partial`	If True, allow extraction of features that are partially included in range TYPE: `bool` DEFAULT: `False`
`pseudogene`	If True and `feature_type='CDS'`, only extract CDS features with `/pseudo` or `/pseudogene` qualifiers. TYPE: `bool` DEFAULT: `False`

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

write_cds_fasta

write_cds_fasta(
    fasta_outfile: str | Path,
    seqtype: str = "protein",
    fix_position: bool = False,
    allow_partial: bool = False,
)

Write CDS protein features fasta file

PARAMETER	DESCRIPTION
`fasta_outfile`	CDS fasta file TYPE: `str \| Path`
`seqtype`	Sequence type (`protein`\|`nucleotide`) TYPE: `str` DEFAULT: `'protein'`
`fix_position`	If True, fix feature start & end position by specified min_range parameter (fixed_start = start - min_range, fixed_end = end - min_range) TYPE: `bool` DEFAULT: `False`
`allow_partial`	If True, features that are partially included in range are also extracted TYPE: `bool` DEFAULT: `False`

write_genome_fasta

write_genome_fasta(outfile: str | Path) -> None

Write genome fasta file

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