Mercurial > repos > stevecassidy > nltktools
annotate g_chart_parser.py @ 3:0df72a8ab095 draft default tip
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit f2432aaedd36ae7662873623d8861d0982dffdd2
| author | stevecassidy |
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| date | Mon, 20 Nov 2017 22:52:11 -0500 |
| parents | a47980ef2b96 |
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| rev | line source |
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1 import sys |
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2 import nltk |
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3 import argparse |
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a47980ef2b96
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
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4 |
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5 |
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6 def arguments(): |
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7 parser = argparse.ArgumentParser(description="run NER on a text") |
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e991d4e60c17
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8 parser.add_argument('--input', required=True, action="store", type=str, help="input text file") |
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a47980ef2b96
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
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9 parser.add_argument('--grammar', required=True, action="store", type=str, help="grammar file") |
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a47980ef2b96
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
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10 parser.add_argument('--output', required=True, action="store", type=str, help="output file path") |
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a47980ef2b96
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
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11 return parser.parse_args() |
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12 |
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13 |
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e991d4e60c17
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14 def chart_parse(in_file, grammar_file, out_file): |
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15 with open(in_file, 'r') as fd: |
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fb617586f4b2
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16 text = fd.read() |
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17 |
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fb617586f4b2
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18 with open(grammar_file, 'r') as fd: |
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19 grammar_string = fd.read() |
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20 |
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21 try: |
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22 grammar = nltk.CFG.fromstring(grammar_string) |
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23 parser = nltk.ChartParser(grammar) |
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24 sentences = nltk.sent_tokenize(text) |
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25 with open(out_file, 'w') as output: |
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fb617586f4b2
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26 for sentence in sentences: |
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fb617586f4b2
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27 words = nltk.word_tokenize(sentence) |
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28 trees = parser.parse(words) |
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fb617586f4b2
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29 for t in trees: |
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fb617586f4b2
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30 output.write(t.pformat()) |
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fb617586f4b2
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31 output.write('\n') |
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fb617586f4b2
planemo upload commit a81826fe44f09a3710a35c183aa88b745aeec064-dirty
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32 |
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fb617586f4b2
planemo upload commit a81826fe44f09a3710a35c183aa88b745aeec064-dirty
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33 except Exception as e: |
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a47980ef2b96
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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34 message = """Error with parsing. Check the input files are correct |
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a47980ef2b96
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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35 and the grammar contains every word in the input sequence. \n----\n""" + str(e) + "\n" |
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36 sys.stderr.write(message) |
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37 sys.exit() |
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38 output.close() |
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39 |
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a47980ef2b96
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
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40 |
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41 if __name__ == '__main__': |
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42 args = arguments() |
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43 chart_parse(args.input, args.grammar, args.output) |