Carlos-Francisco Méndez-Cruz / conditional-random-fields

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Carlos-Francisco Méndez-Cruz
8c2b229a 1 parent 90224aa9

Prepare abstracts

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Showing 1 changed file with 11 additions and 1 deletions
...@@ -22,6 +22,8 @@ __author__ = 'CMendezC' ...@@ -22,6 +22,8 @@ __author__ = 'CMendezC'
22 # --inputPath /export/space1/users/compu2/bionlp/conditional-random-fields/data-sets 22 # --inputPath /export/space1/users/compu2/bionlp/conditional-random-fields/data-sets
23 # --inputFile text-annotated-abstracts-original.txt 23 # --inputFile text-annotated-abstracts-original.txt
24 # --outputPath /export/space1/users/compu2/bionlp/conditional-random-fields/data-sets/original 24 # --outputPath /export/space1/users/compu2/bionlp/conditional-random-fields/data-sets/original
25 +# --dicPath /export/space1/users/compu2/bionlp/nlp-preprocessing-pipeline/dictionaries
26 +# --dicFile genes.txt
25 # python3 prepare-abstracts.py --inputPath /export/space1/users/compu2/bionlp/conditional-random-fields/data-sets --inputFile text-annotated-abstracts-original.txt --outputPath /export/space1/users/compu2/bionlp/conditional-random-fields/data-sets/original 27 # python3 prepare-abstracts.py --inputPath /export/space1/users/compu2/bionlp/conditional-random-fields/data-sets --inputFile text-annotated-abstracts-original.txt --outputPath /export/space1/users/compu2/bionlp/conditional-random-fields/data-sets/original
26 28
27 if __name__ == "__main__": 29 if __name__ == "__main__":
...@@ -33,6 +35,10 @@ if __name__ == "__main__": ...@@ -33,6 +35,10 @@ if __name__ == "__main__":
33 help="Input file", metavar="FILE") 35 help="Input file", metavar="FILE")
34 parser.add_option("--outputPath", dest="outputPath", 36 parser.add_option("--outputPath", dest="outputPath",
35 help="Output path", metavar="PATH") 37 help="Output path", metavar="PATH")
38 + parser.add_option("--dicPath", dest="dicPath",
39 + help="Dictionary path", metavar="PATH")
40 + parser.add_option("--dicFile", dest="dicFile",
41 + help="Dictionary file", metavar="FILE")
36 42
37 (options, args) = parser.parse_args() 43 (options, args) = parser.parse_args()
38 if len(args) > 0: 44 if len(args) > 0:
...@@ -44,6 +50,8 @@ if __name__ == "__main__": ...@@ -44,6 +50,8 @@ if __name__ == "__main__":
44 print("Input path: " + str(options.inputPath)) 50 print("Input path: " + str(options.inputPath))
45 print("Input file", str(options.inputFile)) 51 print("Input file", str(options.inputFile))
46 print("Output path: " + str(options.outputPath)) 52 print("Output path: " + str(options.outputPath))
53 + print("Dictionary path: " + str(options.dicPath))
54 + print("Dictionary file", str(options.dicFile))
47 55
48 filesWritten = 0 56 filesWritten = 0
49 t0 = time() 57 t0 = time()
...@@ -69,6 +77,8 @@ if __name__ == "__main__": ...@@ -69,6 +77,8 @@ if __name__ == "__main__":
69 oFile.write(line) 77 oFile.write(line)
70 else: 78 else:
71 print("Warning: line without PMID") 79 print("Warning: line without PMID")
72 - 80 + with open(os.path.join(options.dicPath, options.dicFile), "w", encoding="utf-8", errors="replace") as dFile:
81 + for gene in hashGenes.keys():
82 + dFile.write("{}\n".format(gene))
73 83
74 84
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