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#!/usr/bin/env python

"""
Get a GEO series matrix file describing an experiment and
parse it into project level and sample level data.
"""

import os
from typing import Tuple, Union
import tempfile

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#! python3.7

import argparse
import os
import numpy as np
import speech_recognition as sr
import whisper
import torch

from datetime import datetime, timedelta

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#!/bin/bash

# Terminate on first error
set -e

# Check if input file is provided
if [ -z "$1" ]; then
  echo "Usage: $0 <input_file.pdf>"
  exit 1
fi

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"""
Re-analyze GeoMx data from Rendeiro et al. 2021 doi:s41586-021-03475-6

Requirements (Python 3.10+):
pip install \
    "anndata" \
    "matplotlib>=3.8.3" \
    "numpy>=1.26.4" \
    "pandas>=2.1.0" \
    "scanpy" \

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from pathlib import Path

import parmap
import requests


def update(gsll):
    return [g for g in gsll if not (output_dir / (g + ".gmt")).exists()]

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"""
Download file from Google Drive URL
"""
import os
import time

import click
from selenium import webdriver
from selenium.webdriver.common.by import By
from selenium.webdriver.firefox.options import Options as FirefoxOptions

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"""
Use dataloaders with nuclei coordinates for training.
"""

from functools import partial

import requests
import h5py
from tqdm import tqdm
import numpy as np

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Introduction to linux command line/ipython/git/R for bioinformatics:

• https://github.com/biom262/biom262-2016
• https://github.com/ricket-sjtu/bi028
• https://github.com/YeoLab/single-cell-bioinformatics/
• https://github.com/YeoLab/single-cell-bioinformatics/tree/master/notebooks
• https://github.com/ltminty/Bioinformatics-and-R/blob/master/Rbioinformatics.ipynb

RNA-seq:

• https://github.com/Caroldm/RNA-Seq-Tutorial---Jupyter-notebook/blob/master/RNAseq%20tutorial.ipynb