alexlenail

from IPython.display import display, Javascript

def beep():
    display(Javascript('''(function() {
        var context = new (window.AudioContext || window.webkitAudioContext)();
        var oscillator = context.createOscillator();
        oscillator.type = 'sine';
        oscillator.frequency.setValueAtTime(440, context.currentTime); // Frequency in Hz (440 is a standard 'A' note)
        oscillator.connect(context.destination);
        oscillator.start();

alexlenail

import pprint
from termcolor import colored

def inspect_object(obj, _indent=0):
    """Recursively prints the attributes of an object with condensed and colored output."""
    indent = ' ' * _indent
    if isinstance(obj, dict):
        for key, value in obj.items():
            if isinstance(value, (dict, list)) or hasattr(value, '__dict__'):
                print(f"{indent}{colored(key, 'green')}:")

alexlenail

import colorsys

def darken_and_vivid_hex_color(hex_color, darken_factor=0.2, vivid_factor=0.2):
    # Remove the hash at the start if it's there
    hex_color = hex_color.lstrip('#')

    # Convert hex to RGB
    rgb = tuple(int(hex_color[i:i+2], 16) for i in (0, 2, 4))
    
    # Normalize RGB values to the range [0, 1]

alexlenail

import numpy as np
import pandas as pd

import matplotlib
import matplotlib.pyplot as plt

plt.rcParams['figure.figsize'] = [8, 8]
plt.rcParams['figure.dpi'] = 240
plt.rcParams['svg.fonttype'] = 'none'
plt.rcParams['pdf.use14corefonts'] = True

alexlenail

import mygene

def gene_annotations(names, map_from=['symbol', 'alias'], fields=['ensembl.gene','name','summary'], species='human'):

    names = pd.Series(names)

    print(f"passed {len(names)} symbols")

    names_stripped = names.str.strip()
    if any(names_stripped != names):

alexlenail

from gprofiler import GProfiler
gp = GProfiler(return_dataframe=True)

def gprofiler_orthologs(query, human_to_mouse=False, mouse_to_human=False, organism='mmusculus', target='hsapiens', returnall=False):

    if isinstance(query, pd.Index): query = query.tolist()
    elif isinstance(query, pd.Series): query = query.values.tolist()

    q = [x for x in np.unique(query).tolist() if str(x) != 'nan']
    if len(q) != len(query): print(f'{len(q)} unique of {len(query)}')

alexlenail

def pseudobulk_adata(adata, obs_vars):
    
    return pd.DataFrame({index: np.squeeze(np.asarray(adata[cell_indices].X.sum(0))) for index, cell_indices in dict(adata.obs.groupby(obs_vars).groups).items()}, index=adata.var.index).T

def flat(mtx): return np.squeeze(np.asarray(mtx))

def pseudobulks(adata, by_column, do_pseudobulks_per=[], op='sum'):

    # check that all the entries in for_each are really columns in adata
    assert all([col in adata.obs.columns for col in do_pseudobulks_per])

alexlenail

def pct(floatt): return '{:.1%}'.format(floatt)

alexlenail

import os
os.system("printf '\a'") # or '\7'

alexlenail

import h5py
import numpy as np

def read_h5_to_dict(h5_path):
    
    out_dict = {}

    def add_h5_node_to_dict(name, node, out_dict=out_dict):

        fullname = node.name