scrap.py

# -*- coding: utf-8 -*-
"""Untitled3.ipynb

Automatically generated by Colaboratory.

Original file is located at
    https://colab.research.google.com/drive/1OPk27uLuoRSbYWcNdKG0Qtq0Ffb9RrcT
"""

import requests
import pandas as pd

urls = ['https://nascent.colorado.edu/samples/all_samples','https://nascent.colorado.edu/datasets']

for url in urls:
  html = requests.get(url).content
  dfs = pd.read_html(html)
  # Make the first line header and string
  dfs[0].columns = dfs[0].iloc[0]
  dfs[0] = dfs[0].iloc[1:].astype(str)
  # pretty print dfs
  for i, df in enumerate(dfs):
    print(f"{i}: {df.shape}")
    print(df.head())
  # Write to parquet file
  dfs[0].to_parquet(f"{url.split('/')[-1]}.parquet")
  # Make a csv version while we're here
  dfs[0].to_csv(f"{url.split('/')[-1]}.csv")

# Scrap this website
# https://nascent.colorado.edu/
# TODO once we pick out some samples of interest
import requests
from bs4 import BeautifulSoup

response = requests.get('https://nascent.colorado.edu/samples/SRZ7741175')
soup = BeautifulSoup(response.content, 'html.parser')

bed_files = soup.find_all('a', href=re.compile('.bed$'))

for bed_file in bed_files:
  print(bed_file['href'])