import pandas as pd
from matplotlib.collections import BrokenBarHCollection
from coolbox.utilities import (
get_logger,
GenomeRange,
file_to_intervaltree,
hex2rgb,
to_gr,
)
from .base import Track
log = get_logger(__name__)
class Ideogram(Track):
"""
The chromosome ideograme track.
Parameters
----------
file_ : str
Path to chromosome ideogram txt file,
ideogram file is download from the UCSC Table Browser CytoBandIdeo table (in "all table" group).
see: http://genome.ucsc.edu/cgi-bin/hgTables?hgta_group=allTables&hgta_table=cytoBandIdeo
color_scheme : dict, optional
Color scheme of ideogram, default: Ideogram.DEFAULT_COLOR_SCHEME
show_name : bool, optional
Show band name or not. default True.
import os
import os.path as osp
import subprocess as subp
from typing import Tuple
import runpy
import fire
import nbformat as nbf
import coolbox
from coolbox.utilities import get_logger
from coolbox.utilities.genome import GenomeRange
from coolbox.api import *
log = get_logger("CoolBox CLI")
def get_element_type_by_str(elem_str):
import coolbox.api
try:
elem_tp = eval("coolbox.api." + elem_str)
except NameError:
log.error(
f"No element type name as {elem_tp}, all elements type see: " +
"https://gangcaolab.github.io/CoolBox/api.html")
return elem_tp
def get_compose_code(elem_str, args, kwargs):
compose_code = elem_str + "("
compose_code += ", ".join([repr(arg) for arg in args] +