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February 6, 2019 22:05
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Download and parses html entries from the CAZy Database (www.cazy.org). Use this instead: https://doi.org/10.1093/nar/gkx894
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#!/usr/bin/python | |
import csv, os, glob | |
import pickle | |
from BeautifulSoup import BeautifulSoup | |
cazy_dict = {} | |
os.chdir('data/html') | |
for filename in glob.iglob('*.html'): | |
print filename | |
fam_list = [] | |
fh = open(filename, 'rb') | |
fh_out_str = '/media/haldane/trab/data/cazy/data/csv/' + filename.strip('.html') + '.xls' | |
fh_out = open(fh_out_str, 'wb') | |
soup = BeautifulSoup(fh) | |
# Get the organism name, taxid, and lineage. Initialize the org container | |
org_info = soup.find('div', {'class' : 'org'}) | |
try: | |
org_name = org_info.find('font', {'class' : 'titre_cazome'}).renderContents() | |
taxid = org_info.find('a', {'target' : 'ncbitaxid'}).renderContents() | |
lineage_string = str(org_info).split(":")[-1].split('<')[0].strip() | |
fam_list = [('Organism', org_name), ("NCBI_TaxID", taxid), ('Org_Lin', | |
lineage_string)] | |
except AttributeError: | |
continue | |
# Parse the tables, skipping the final protein list | |
t = soup.findAll('table') | |
for table in t[0:-1]: | |
head = table.findAll('th') | |
family_name = head[0].findAll('div',{'class':"titre_famille"})[0].renderContents() | |
rows = table.findAll('tr') | |
for tr in rows: | |
cols = tr.findAll('td') | |
for col in cols: | |
# """ | |
# descend into each table column and try to pick out the data by | |
# CSS class. | |
# E.g: '<td class="classe" id="navigationtab2"><a | |
# href="http://www.cazy.org/CE1.html" class="nav2"><div | |
# class="famille">1</div></a><div class="nombre_de">2</div></td>' | |
# """ | |
family = col.find("div", {"class" : "famille"}).renderContents() | |
count = col.find("div", {"class" : "nombre_de"}).renderContents() | |
link_out = col.find("a",{"class" : "nav2"}, href=True)['href'] | |
family_abbrv = link_out.split('/')[-1].strip('.html') | |
fam_list.append((family_abbrv , count)) | |
# Write the dict to a new csv filename | |
cazy_dict[org_name] = dict(fam_list) | |
first_keys = ['Organism', 'NCBI_TaxID', 'Org_Lin'] # cazy_dict[org_name].keys() | |
last_keys = [k for k in cazy_dict[org_name].keys() if k not in first_keys] | |
last_keys.sort() | |
[first_keys.append(k) for k in last_keys] | |
dict_writer = csv.DictWriter(fh_out, first_keys, dialect = 'excel-tab', | |
extrasaction = 'ignore') | |
dict_writer.writer.writerow(first_keys) | |
dict_writer.writerow(cazy_dict[org_name]) | |
fh_out.close() | |
with open('/media/haldane/trab/data/cazy/data/output_cazy.pkl', 'wb') as cazy_dict_out: | |
pickle.dump(cazy_dict, cazy_dict_out) |
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#!/bin/bash | |
for i in $(echo {A..W}) | |
do | |
wget -r -l 1 --random-wait -A b[0-9]*.html http://www.cazy.org/b$i.html | |
done |
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