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annotate g_collocation.py @ 3:0df72a8ab095 draft default tip

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planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit f2432aaedd36ae7662873623d8861d0982dffdd2
author stevecassidy
date Mon, 20 Nov 2017 22:52:11 -0500
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1 import nltk
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2 from nltk.collocations import BigramCollocationFinder, BigramAssocMeasures
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3 from nltk.collocations import TrigramCollocationFinder, TrigramAssocMeasures
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4 import argparse
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6 nltk.download('punkt', quiet=True)
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9 def Parser():
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10 the_parser = argparse.ArgumentParser(description="Parse the sentence using Chart Parser and a supplied grammar")
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11 the_parser.add_argument('--input', required=True, action="store", type=str, help="input text file")
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12 the_parser.add_argument('--output', required=True, action="store", type=str, help="output file path")
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13 the_parser.add_argument('--freq_filter', required=True, action="store", type=str, help="The minimum number of required occurrences in the corpus")
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14 the_parser.add_argument('--results', required=True, action="store", type=str, help="The maximum number of collocations to show in the results")
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15 the_parser.add_argument('--coll_type', required=True, action="store", type=str, help="Type of collocations to find")
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16 the_parser.add_argument('--pos', required=True, action="store", type=str, help="Data input is a set of POS tags")
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18 return the_parser.parse_args()
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21 def collocation(inp, outp, freq_filter, results, coll_type, pos):
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22 pos = bool(pos == 'true')
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23 with open(inp, 'r') as fd:
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24 i = fd.read()
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25
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26 all_words = []
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27 if pos:
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28 text = i.split(' ')[:-1]
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29 all_words = [x[0:x.index('/')] if x != '\n' else x for x in text]
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30 all_words = [x.strip(' ').strip('\n') for x in all_words]
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31 else:
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32 sents = nltk.sent_tokenize(i)
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33 for sent in sents:
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34 all_words += nltk.word_tokenize(sent)
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35 if coll_type == 'bigram':
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36 measures = BigramAssocMeasures()
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37 finder = BigramCollocationFinder.from_words(all_words)
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38 else:
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39 measures = TrigramAssocMeasures()
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40 finder = TrigramCollocationFinder.from_words(all_words)
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41 finder.apply_freq_filter(int(freq_filter))
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42 # score the ngrams and get the first N
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43 colls = finder.score_ngrams(measures.pmi)[:int(results)]
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44 with open(outp, 'w') as output:
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45 for coll in colls:
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46 (a, b), score = coll
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47 output.write("%s\t%s\n" % (a, b))
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50 if __name__ == '__main__':
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51 args = Parser()
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52
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53 collocation(args.input, args.output, args.freq_filter, args.results, args.coll_type, args.pos)