utils

utils

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() (syntactic sugar)

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]

fetch_genbank_by_accid

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

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
TextIOWrapper	Genbank data

Examples:

>>> gbk_text = fetch_genbank_by_accid("NC_013600")
>>> gbk = Genbank(gbk_text)

load_example_fasta_dataset

load_example_fasta_dataset(
    name: GenbankDatasetName,
    *,
    cache_dir: str | Path | None = None,
    overwrite_cache: bool = False,
    quiet: bool = True
) -> list[Path]

Load pygenomeviz example fasta dataset

Load genbank datasets from https://github.com/moshi4/pygenomeviz-data-v1 and convert genbank to fasta format. Cache datasets in local directory (Default: ~/.cache/pygenomeviz/).

List of dataset name

• acinetobacter_phage (4 species)
• yersinia_phage (4 species)
• enterobacteria_phage (6 species)
• mycoplasma_mycoides (4 species)
• escherichia_coli (4 species, gzip compressed)
• saccharomyces (3 species, gzip compressed)

PARAMETER	DESCRIPTION
name	Dataset name (e.g. enterobacteria_phage) TYPE: str
cache_dir	Output cache directory (Default: ~/.cache/pygenomeviz/) TYPE: str | Path | None DEFAULT: None
overwrite_cache	If True, overwrite cached dataset TYPE: bool DEFAULT: False
quiet	If True, no print log on screen. TYPE: bool DEFAULT: True

RETURNS	DESCRIPTION
fasta_files	Fasta files TYPE: list[Path]

load_example_genbank_dataset

load_example_genbank_dataset(
    name: GenbankDatasetName,
    *,
    cache_dir: str | Path | None = None,
    overwrite_cache: bool = False,
    quiet: bool = True
) -> list[Path]

Load pygenomeviz example genbank dataset

Load genbank datasets from https://github.com/moshi4/pygenomeviz-data-v1 and cache datasets in local directory (Default: ~/.cache/pygenomeviz/).

List of dataset name

• acinetobacter_phage (4 species)
• yersinia_phage (4 species)
• enterobacteria_phage (6 species)
• mycoplasma_mycoides (4 species)
• escherichia_coli (4 species, gzip compressed)
• saccharomyces (3 species, gzip compressed)

PARAMETER	DESCRIPTION
name	Dataset name (e.g. enterobacteria_phage) TYPE: str
cache_dir	Output cache directory (Default: ~/.cache/pygenomeviz/) TYPE: str | Path | None DEFAULT: None
overwrite_cache	If True, overwrite cached dataset TYPE: bool DEFAULT: False
quiet	If True, no print log on screen. TYPE: bool DEFAULT: True

RETURNS	DESCRIPTION
gbk_files	Genbank files TYPE: list[Path]

load_example_gff_file

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

Load pygenomeviz example GFF file

Load example GFF file from https://github.com/moshi4/pygenomeviz-data-v1/ and cache GFF file in local directory (Default: ~/.cache/pygenomeviz/).

List of example GFF filename

• enterobacteria_phage.gff
• mycoplasma_mycoides.gff
• escherichia_coli.gff.gz
• saccharomyces_cerevisiae.gff.gz

PARAMETER	DESCRIPTION
filename	GFF filename (e.g. enterobacteria_phage.gff) TYPE: str
cache_dir	Output cache directory (Default: ~/.cache/pygenomeviz/) TYPE: str | Path | None DEFAULT: None
overwrite_cache	If True, overwrite cached GFF file TYPE: bool DEFAULT: False

RETURNS	DESCRIPTION
gff_file	GFF file TYPE: Path

extract_features_within_range

extract_features_within_range(
    features: list[SeqFeature], *, target_range: tuple[int, int]
) -> list[SeqFeature]

Extract features by target range

PARAMETER	DESCRIPTION
features	Features to be extracted TYPE: list[SeqFeature]
target_range	Target range TYPE: tuple[int, int]

RETURNS	DESCRIPTION
range_features	Features within target range TYPE: list[SeqFeature]

interpolate_color

interpolate_color(base_color: str, v: float, vmin: float = 0, vmax: float = 100) -> str

Interpolate the base color between vmin and vmax

vmin[nearly white] <= v <= vmax[base_color]

PARAMETER	DESCRIPTION
base_color	Base color for interpolation TYPE: str
v	Interpolation value TYPE: float
vmin	Min value TYPE: float DEFAULT: 0
vmax	Max value TYPE: float DEFAULT: 100

RETURNS	DESCRIPTION
interpolate_color	Interpolated hexcolor TYPE: str

is_pseudo_feature

is_pseudo_feature(feature: SeqFeature) -> bool

Check target feature is pseudo or not from qualifiers tag

PARAMETER	DESCRIPTION
feature	Target feature TYPE: SeqFeature

RETURNS	DESCRIPTION
check_result	pseudo check result TYPE: bool

to_stack_features

to_stack_features(features: list[SeqFeature]) -> list[list[SeqFeature]]

Convert feature list to non-overlap stack feature list of lists

PARAMETER	DESCRIPTION
features	Features TYPE: list[SeqFeature]

RETURNS	DESCRIPTION
stack_features	Stacked features TYPE: list[list[SeqFeature]]