Mercurial > repos > dcouvin > resfinder

comparison resfinder/cge/out/beone.json @ 0:a16d245332d6 draft default tip

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author dcouvin
date Wed, 08 Dec 2021 01:46:07 +0000
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-1:000000000000 0:a16d245332d6
1 {
2 "software_result": {
3 "type": "software_result",
4 "key": "string*",
5 "software_name": "string*",
6 "software_version": "string*",
7 "software_branch": "string",
8 "software_commit": "string",
9 "software_log": "string",
10 "run_id": "string",
11 "run_date": "date",
12 "databases": "dict database:class",
13 "genes": "dict gene:class",
14 "seq_variations": "dict seq_variation:class",
15 "phenotypes": "dict phenotype:class"
16 },
17 "database": {
18 "type": "database",
19 "key": "string*",
20 "database_name": "string*",
21 "database_version": "string",
22 "database_branch": "string",
23 "database_commit": "string",
24 "checksum_sha256": "char64"
25 },
26 "gene": {
27 "type": "gene",
28 "key": "string*",
29 "name": "string*",
30 "identity": "percentage",
31 "alignment_length": "integer",
32 "ref_gene_lenght": "integer",
33 "coverage": "percentage",
34 "depth": "float",
35 "ref_id": "string*",
36 "ref_acc": "string",
37 "ref_start_pos": "integer",
38 "ref_end_pos": "integer",
39 "query_id": "string",
40 "query_start_pos": "integer",
41 "query_end_pos": "integer",
42 "phenotypes": "array phenotype.key",
43 "ref_database": "database.key"
44 },
45 "seq_region": {
46 "type": "seq_region",
47 "key": "string*",
48 "name": "string*",
49 "gene": "bool_or_unknown",
50 "identity": "percentage",
51 "alignment_length": "integer",
52 "ref_gene_lenght": "integer",
53 "coverage": "percentage",
54 "depth": "float",
55 "ref_id": "string*",
56 "ref_acc": "string",
57 "ref_start_pos": "integer",
58 "ref_end_pos": "integer",
59 "query_id": "string",
60 "query_start_pos": "integer",
61 "query_end_pos": "integer",
62 "phenotypes": "array phenotype.key",
63 "ref_database": "database.key"
64 },
65 "seq_variation": {
66 "type": "seq_variation",
67 "key": "string*",
68 "ref_id": "string*",
69 "seq_var": "seq_var_string",
70 "codon_change": "codon_change_string",
71 "ref_codon": "nucleotides",
72 "var_codon": "nucleotides",
73 "ref_aa": "aminoacid_1_char",
74 "var_aa": "aminoacid_1_char",
75 "ref_start_pos": "integer",
76 "ref_end_pos": "integer",
77 "substitution": "bool",
78 "insertion": "bool",
79 "deletion": "bool",
80 "ref_database": "database.key",
81 "genes": "array gene.key",
82 "phenotypes": "array phenotype.key"
83 },
84 "phenotype": {
85 "type": "phenotype",
86 "key": "string*",
87 "category": "vocabulary*",
88 "amr_classes": "array vocabulary",
89 "amr_resistance": "vocabulary",
90 "amr_resistant": "bool_or_unknown",
91 "genes": "array gene.key",
92 "seq_variations": "array seq_variation.key",
93 "ref_database": "database.key"
94 }
95 }