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comparison editDB.py @ 1:6e3a843b6304 draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:53:18 +0000
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0:bd2ff2c7e806 1:6e3a843b6304
1 # Remove duplicate terms. As well as add any that is needed.
2
3 import explodeJSON as ej
4 from explodeJSON import save_dict_to_json
5
6
7 ### create new key
8 def add_new_key(db, add_key=[]):
9 """Set of keys to add to the database"""
10 for new_key in add_key:
11 db[new_key] = []
12
13 return db
14
15
16 ### Add values to dbase:
17 def add_value_to_term(index_val, db, add_value=[]):
18 """index value, put in value"""
19 for val in add_value:
20 db[index_val].append(val)
21
22 return db
23
24
25 ### Remove values from dbase:
26 def remove_value_from_term(index_val, db, remove_value=[]):
27 """remove values from list"""
28 for val in remove_value:
29 db[index_val].remove(val)
30
31 return db
32
33
34 ### Terms to add from a file
35 def add_from_file(input_file, index_val, db, sep="\n"):
36 """input file, new line separated currently, and append files to correct key, return is altered dictionary"""
37 terms = open(input_file).read().splitlines()
38 db = add_value_to_term(index_val, db, terms)
39 return db
40
41
42 if __name__ == "__main__":
43
44 lysis_json = "data/lysis-family-v1.0.2.json" # insert json of choice
45 db = ej.explodeJSON(lysis_json)
46 db = db.readJSON()
47 # revise_db = add_new_key(db=db,add_key=["spanins"])
48 # files = ["data/term_additions/200505_holin_domains.txt","data/term_additions/200505_Spanin_Domains.txt"]
49 terms = [
50 "DUF2570",
51 "PF10828",
52 "IPR022538",
53 "DUF2514",
54 "PF10721",
55 "IPR019659",
56 "DUF2681",
57 "PF10883",
58 "IPR020274",
59 ]
60 # revise_db = add_from_file(files[0],"holin_domains",revise_db)
61 # revise_db = add_from_file(files[1],"spanin_domains",revise_db)
62 revise_db = add_value_to_term("spanin_domains", db, add_value=terms)
63 save_dict_to_json(obj=revise_db, filename="data/lysis-family-v1.0.3.json")