Mercurial > repos > dcouvin > resfinder4

comparison resfinder/cge/out/test.py @ 0:55051a9bc58d draft default tip

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author dcouvin
date Mon, 10 Jan 2022 20:06:07 +0000
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-1:000000000000 0:55051a9bc58d
1 #!/usr/bin/env python3
2
3 import json
4 import os.path
5
6 from result import Result
7 from exceptions import CGECoreOutTypeError, CGECoreOutInputError
8 from template import CGEOutTemplate
9 from translate import Translate
10
11
12 try:
13 CGEOutTemplate("nonsense")
14 except CGECoreOutTypeError:
15 print("Caught expected template error.")
16
17 soft_dict = CGEOutTemplate("software_result")
18 soft_dict["software_name"] = "ResFinder"
19 soft_dict["key"] = "soft_dict key"
20 soft_dict["version"] = "3.2.0"
21
22 soft_result = Result(**soft_dict)
23
24 test_gene = {
25 "type": "gene",
26 "key": "some_gene_key",
27 "name": "gen_name",
28 "identity": "187",
29 "alignment_length": "800",
30 "ref_gene_lenght": "800",
31 "coverage": "89",
32 "ref_id": "some_ref_id"
33 }
34
35 soft_result.add_class(cl="genes", **test_gene)
36
37 test_dict = {
38 "type": "software_result",
39 "software_name": "ResFinder",
40 "software_version": "4.0",
41 "run_date": "20200214",
42 "key": "software_key"
43 }
44
45 result = Result(result_type="software_result", **test_dict)
46 result.add_class(cl="genes", **test_gene)
47
48 test_trans_table = {
49 "primary": "key",
50 "gene": "name",
51 "id": "identity",
52 "alignment": "alignment_length",
53 "gene_lenght": "ref_gene_lenght",
54 "cov": "coverage"
55 }
56
57 translator = Translate("gene", test_trans_table)
58
59 test_gene2 = {
60 "primary": "some_gene_key2",
61 "gene": "gen_name2",
62 "id": "97",
63 "alignment": "800",
64 "gene_lenght": "800",
65 "cov": "99"
66 }
67
68 result.add_class(cl="genes", result_type="gene",
69 **translator.translate(test_gene2))
70
71 try:
72 result.check_results()
73 soft_result.check_results()
74 except CGECoreOutInputError as e:
75 print("Error dict:\n{}".format(e.errors))
76
77 print(json.dumps(result))
78 print(json.dumps(soft_result))