Source code for bioutils.cytobands

``./sbin/ucsc-cytoband-to-json cytoband-hg38.txt.gz | gzip -c >bioutils/_data/cytobands/ucsc-hg38.json.gz``

import gzip
import json

import pkg_resources

_data_dir = "_data/cytobands"
_data_path_fmt = _data_dir + "/" + "{name}.json.gz"

[docs]def get_cytoband_names(): """Retrieves available cytobands from the ``_data/cytobands`` directory. Returns: list of str: The names of the available cytobands. Examples: >>> sorted(get_cytoband_names()) ['ucsc-hg19', 'ucsc-hg38'] """ return [ n.replace(".json.gz", "") for n in pkg_resources.resource_listdir(__name__, _data_dir) if n.endswith(".json.gz") ]
[docs]def get_cytoband_map(name): """Retrives a cytoband by name. Args: name (str): The name of the cytoband to retrieve. Returns: dict: A dictionary of the cytoband data. Examples: >>> map = get_cytoband_map("ucsc-hg38") >>> map["1"]["p32.2"] [55600000, 58500000, 'gpos50'] """ fn = pkg_resources.resource_filename(__name__, _data_path_fmt.format(name=name)) return json.load(, mode="rt", encoding="utf-8"))
[docs]def get_cytoband_maps(names=[]): """Retrieves data from multiple cytobands. If cytobands are not specified, retrieves data from all available ones. Args: names (list of str, optional): The names of cytobands to retrieve data for. Returns: dict: A dictionary of the form ``{cytoband_name, cytoband_data}``. Examples: >>> maps = get_cytoband_maps() >>> maps["ucsc-hg38"]["1"]["p32.2"] [55600000, 58500000, 'gpos50'] >>> maps["ucsc-hg19"]["1"]["p32.2"] [56100000, 59000000, 'gpos50'] """ if names == []: names = get_cytoband_names() return {name: get_cytoband_map(name) for name in names}