Mercurial > repos > dcouvin > resfinder
comparison resfinder/cge/out/beone.json @ 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 { | |
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 } |