Mercurial > repos > dcouvin > resfinder4
diff resfinder/cge/out/beone.json @ 0:55051a9bc58d draft default tip
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author | dcouvin |
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date | Mon, 10 Jan 2022 20:06:07 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/resfinder/cge/out/beone.json Mon Jan 10 20:06:07 2022 +0000 @@ -0,0 +1,95 @@ +{ +"software_result": { + "type": "software_result", + "key": "string*", + "software_name": "string*", + "software_version": "string*", + "software_branch": "string", + "software_commit": "string", + "software_log": "string", + "run_id": "string", + "run_date": "date", + "databases": "dict database:class", + "genes": "dict gene:class", + "seq_variations": "dict seq_variation:class", + "phenotypes": "dict phenotype:class" + }, +"database": { + "type": "database", + "key": "string*", + "database_name": "string*", + "database_version": "string", + "database_branch": "string", + "database_commit": "string", + "checksum_sha256": "char64" + }, +"gene": { + "type": "gene", + "key": "string*", + "name": "string*", + "identity": "percentage", + "alignment_length": "integer", + "ref_gene_lenght": "integer", + "coverage": "percentage", + "depth": "float", + "ref_id": "string*", + "ref_acc": "string", + "ref_start_pos": "integer", + "ref_end_pos": "integer", + "query_id": "string", + "query_start_pos": "integer", + "query_end_pos": "integer", + "phenotypes": "array phenotype.key", + "ref_database": "database.key" + }, +"seq_region": { + "type": "seq_region", + "key": "string*", + "name": "string*", + "gene": "bool_or_unknown", + "identity": "percentage", + "alignment_length": "integer", + "ref_gene_lenght": "integer", + "coverage": "percentage", + "depth": "float", + "ref_id": "string*", + "ref_acc": "string", + "ref_start_pos": "integer", + "ref_end_pos": "integer", + "query_id": "string", + "query_start_pos": "integer", + "query_end_pos": "integer", + "phenotypes": "array phenotype.key", + "ref_database": "database.key" + }, +"seq_variation": { + "type": "seq_variation", + "key": "string*", + "ref_id": "string*", + "seq_var": "seq_var_string", + "codon_change": "codon_change_string", + "ref_codon": "nucleotides", + "var_codon": "nucleotides", + "ref_aa": "aminoacid_1_char", + "var_aa": "aminoacid_1_char", + "ref_start_pos": "integer", + "ref_end_pos": "integer", + "substitution": "bool", + "insertion": "bool", + "deletion": "bool", + "ref_database": "database.key", + "genes": "array gene.key", + "phenotypes": "array phenotype.key" + }, +"phenotype": { + "type": "phenotype", + "key": "string*", + "category": "vocabulary*", + "amr_classes": "array vocabulary", + "amr_resistance": "vocabulary", + "amr_resistant": "bool_or_unknown", + "genes": "array gene.key", + "seq_variations": "array seq_variation.key", + "ref_database": "database.key" + } +}