Utility Class

load_prokaryote_example_file

load_prokaryote_example_file(
    filename: str, cache_dir: str | Path | None = None, overwrite_cache: bool = False
) -> Path

Load pycirclize example Genbank or GFF file

Load example file from https://github.com/moshi4/pycirclize-data/ and cache file in local directory (Default: ~/.cache/pycirclize/).

List of example Genbank or GFF filename

enterobacteria_phage.[gbk|gff]
mycoplasma_alvi.[gbk|gff]
escherichia_coli.[gbk|gff].gz

PARAMETER	DESCRIPTION
`filename`	Genbank or GFF filename (e.g. `enterobacteria_phage.gff`) TYPE: `str`
`cache_dir`	Output cache directory (Default: `~/.cache/pycirclize/`) TYPE: `str \| Path \| None` DEFAULT: `None`
`overwrite_cache`	If True, overwrite cache file. Assumed to be used when cache file is corrupt. TYPE: `bool` DEFAULT: `False`

RETURNS	DESCRIPTION
`file_path`	Genbank or GFF file TYPE: `Path`

load_eukaryote_example_dataset

load_eukaryote_example_dataset(
    name: str = "hg38",
    cache_dir: str | Path | None = None,
    overwrite_cache: bool = False,
) -> tuple[Path, Path, list[ChrLink]]

Load pycirclize eukaryote example dataset

Load example file from https://github.com/moshi4/pycirclize-data/ and cache file in local directory (Default: ~/.cache/pycirclize/).

List of dataset contents (download from UCSC)

Chromosome BED file (e.g. chr1 0 248956422)
Cytoband file (e.g. chr1 0 2300000 p36.33 gneg)
Chromosome links (e.g. chr1 1000 4321 chr3 8000 5600)

PARAMETER	DESCRIPTION
`name`	Dataset name (`hg38`\|`hs1`\|`mm10`\|`mm39`) TYPE: `str` DEFAULT: `'hg38'`
`cache_dir`	Output cache directory (Default: `~/.cache/pycirclize/`) TYPE: `str \| Path \| None` DEFAULT: `None`
`overwrite_cache`	If True, overwrite cache dataset. Assumed to be used when cache dataset is corrupt. TYPE: `bool` DEFAULT: `False`

RETURNS	DESCRIPTION
`chr_bed_file`	BED file TYPE: `Path`
`cytoband_file`	Cytoband file TYPE: `Path`
`chr_links`	Chromosome links TYPE: `list[ChrLink]`

load_example_tree_file

load_example_tree_file(filename: str) -> Path

Load example phylogenetic tree file

List of example tree filename

small_example.nwk (7 species)
medium_example.nwk (21 species)
large_example.nwk (190 species)
alphabet.nwk (26 species)

PARAMETER	DESCRIPTION
`filename`	Target filename TYPE: `str`

RETURNS	DESCRIPTION
`tree_file`	Tree file (Newick format) TYPE: `Path`

load_example_image_file

load_example_image_file(filename: str) -> Path

Load example image file from local package data

e.g. python_logo.png

PARAMETER	DESCRIPTION
`filename`	Image file name TYPE: `str`

RETURNS	DESCRIPTION
`image_file_path`	Image file path TYPE: `Path`

fetch_genbank_by_accid

fetch_genbank_by_accid(
    accid: str, gbk_outfile: str | Path | None = None, email: str | None = None
) -> StringIO

Fetch genbank text by Accession ID

PARAMETER	DESCRIPTION
`accid`	Accession ID TYPE: `str`
`gbk_outfile`	If file path is set, write fetch data to file TYPE: `str \| Path \| None` DEFAULT: `None`
`email`	Email address to notify download limitation (Required for bulk download) TYPE: `str \| None` DEFAULT: `None`

RETURNS	DESCRIPTION
`gbk_str_io`	Genbank data TYPE: `StringIO`

Examples:

>>> gbk_fetch_data = fetch_genbank_by_accid("NC_002483")
>>> gbk = Genbank(gbk_fetch_data)

calc_group_spaces

calc_group_spaces(
    groups: list[int],
    *,
    space_bw_group: float = 15,
    space_in_group: float = 2,
    endspace: bool = True
) -> list[float]

Calculate spaces between/within groups

This function can be used to easily calculate the space size when data is separated into multiple groups for display. For example, to set up a space to divide [A, B, C, D, E, F, G, H, I, J] into three groups such as [(A, B, C, D), (E, F, G), (H, I, J)], set groups=[4, 3, 3].

PARAMETER	DESCRIPTION
`groups`	List of each group number (e.g. `[4, 3, 3]`) TYPE: `list[int]`
`space_bw_group`	Space size between group TYPE: `float` DEFAULT: `15`
`space_in_group`	Space size within group TYPE: `float` DEFAULT: `2`
`endspace`	If True, insert space after the end group TYPE: `bool` DEFAULT: `True`

RETURNS	DESCRIPTION
`spaces`	Spaces between/within groups TYPE: `list[float]`

ColorCycler

Color Cycler Class

new

__new__(n: int | None = None) -> str

Get hexcolor cyclically from cmap by counter or user specified number

ColorCycler() works same as ColorCycler.get_color()

PARAMETER	DESCRIPTION
`n`	Number for color cycle. If None, counter class variable is used. TYPE: `int \| None` DEFAULT: `None`

RETURNS	DESCRIPTION
`hexcolor`	Cyclic hexcolor string TYPE: `str`

reset_cycle `classmethod`

reset_cycle() -> None

Reset cycle counter

set_cmap `classmethod`

set_cmap(name: str) -> None

Set colormap (Default: tab10)

get_color `classmethod`

get_color(n: int | None = None) -> str

Get hexcolor cyclically from cmap by counter or user specified number

PARAMETER	DESCRIPTION
`n`	Number for color cycle. If None, counter class variable is used. TYPE: `int \| None` DEFAULT: `None`

RETURNS	DESCRIPTION
`hexcolor`	Cyclic hexcolor string TYPE: `str`

get_color_list `classmethod`

get_color_list(n: int | None = None) -> list[str]

Get hexcolor list of colormap

PARAMETER	DESCRIPTION
`n`	If n is None, all(=cmap.N) hexcolors are extracted from colormap. If n is specified, hexcolors are extracted from n equally divided colormap. TYPE: `int \| None` DEFAULT: `None`

RETURNS	DESCRIPTION
`hexcolor_list`	Hexcolor list TYPE: `list[str]`