Mercurial > repos > dcouvin > resfinder
comparison resfinder/cge/out/test.py @ 0:a16d245332d6 draft default tip
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author | dcouvin |
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date | Wed, 08 Dec 2021 01:46:07 +0000 |
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-1:000000000000 | 0:a16d245332d6 |
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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)) |