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#!/usr/bin/env python3
import regex
# Parse TXTREE from Catalogue of Life
# https://www.catalogueoflife.org/data/download
# To use this script:
# - Manually remove all non-animal species (not too hard since animalia is the 1st kingdom)
# - Save that as animalia.txtree
# - Run script, ignoring all the warnings about weird lines so long as there aren't too many.
# - Get output in taxa.txt
high_taxon_regex = regex.compile(r'^[A-Z](-|\p{L})+$')
species_regex = regex.compile(r"^(\p{Ll}|\p{Nd})(-|\p{L}|\p{Nd}|\.|')*$", flags=regex.U)
parenthetical_regex = regex.compile(r' \((\w|\.)+\) ')
with open('animalia.txtree') as animalia, open('taxa.txt', 'w') as taxa:
for line in animalia:
line = line.strip().lstrip('=').replace('†', '').replace(' [sensu lato] ', ' ')
line = parenthetical_regex.sub(' ', line)
if '[species]' in line:
words = line.split()
if len(words) < 2 or \
not high_taxon_regex.match(words[0]) or \
not species_regex.match(words[1]):
print('Weird line:',line)
continue
taxa.write(words[0] + ' ' + words[1] + '\n')
elif (i := line.find(' ')) > 0 and high_taxon_regex.match(taxon := line[:i]):
taxa.write(taxon + '\n')
else:
print('Weird line:', line)
continue
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