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80 lines
2.8 KiB
Python
80 lines
2.8 KiB
Python
import os
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from pathlib import Path
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'''
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Written by Elinor 1/26, updated 2/12
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Input: text file of taxonomies. make sure each taxonomic level is separated with '; ' (semicolon space) or the
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script will not parse the names right
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This cuts off the genus (and species if there is one), uniquifies the list and writes them out to files by the first
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word of the taxonomy
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WARNING: if you run the script multiple times, DELETE THE PREVIOUS OUTPUT. this is because it appends lines to the
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end of files so you will have many duplicates
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'''
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Path(f'unique_taxon_lists').mkdir(parents=True, exist_ok=True)#makes output folder
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with open ('all_taxa.txt') as t:
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names = t.readlines()
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to_uniquify = []
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skipped = []
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for name in names: #iterate through each line of txt file
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#Adding short names to keep
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if len(name.split('; ')) <= 2:
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if ';' in name:#this removes things that are only one word (ex 'no taxID')
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to_uniquify.append(name)#add short taxonomies to list to uniquify because we don't want to remove any taxonomic information
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#for names over 2 parts
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else:
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if ' ' in name.split('; ')[-1]:#check if it has a species name
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if len(name.split('; ')) > 3:#remove sp and genus from taxonomies with over 3 parts
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short_tax = name.split('; ')[:-2]
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to_uniquify.append('; '.join(short_tax))
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#if short, only remove -1
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if len(name.split('; ')) < 4:#remove sp only from taxa with 3 or fewer parts
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short_tax = name.split('; ')[:-1]
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to_uniquify.append('; '.join(short_tax))
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#for names without species names
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else: #if there is no species name, remove genus only
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if len(name.split('; ')) > 3:#remove sp and genus from taxonomies with over 3 parts
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short_tax = name.split('; ')[:-1]
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to_uniquify.append('; '.join(short_tax))
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else:
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to_uniquify.append(name)
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unique_taxonomies = {}#initialize dictionary
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count = 0
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for i in to_uniquify:#iterate through names that have species removed
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item = i.split('; ')#divide up each word in the line of the taxonomy
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for name in item:#iterate through words in each
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count+=1#count number of words total
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unique_taxonomies.update({name.strip(): item[0]})#write to dictionary with key as word (so they automatically get uniquified) and value = MC
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print(f'You have {len(unique_taxonomies)} unique taxonomies\n\n')
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#write to csvs by major clade
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for taxa, mc in unique_taxonomies.items():
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file = open(f'unique_taxon_lists/{mc.strip()}.csv', 'a+')#open/create a file with the name of the major clade of each taxonomy
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file.write(f'{taxa}\n')#write each taxonomy to the file named by its major clade
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file.close#close the file i dont know what happens if you dont do this but its probably bad
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with open('unique_taxon_lists/all_unique_terms.csv', 'w') as o:
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for taxa, mc in unique_taxonomies.items():
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o.write(f'{taxa}\n')
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