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MUSIALvDictSchema.json
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{
"$schema": "MUSIALvDict",
"title": "MUSIAL Variants Dictionary",
"description": "Storage of (coding gene) features located on a single locus, their nucleotide variants, the induced amino acid mutations and information about the protein product of the respective feature.",
"type": "object",
"properties": {
"parameters": {
"description": "Parameters used to infer nucleotide variants, i.e. all stored variants comply with the parameters in at least one sample.",
"type": "object",
"properties": {
"minCoverage": {
"description": "The minimal depth of coverage wrt. reads of a variant to be accepted.",
"type": "number",
"minimum": 0.0
},
"minFrequency": {
"description": "The minimal frequency wrt. reads supporting a homozygous allele call for a variant to be accepted.",
"type": "number",
"minimum": 0.0,
"maximum": 1.0
},
"minHetFrequency": {
"description": "The minimal frequency wrt. reads supporting a heterozygous allele call for a variant to be accepted.",
"type": "number",
"minimum": 0.0,
"maximum": 1.0
},
"maxHetFrequency": {
"description": "The maximal frequency wrt. reads supporting a heterozygous allele call for a variant to be accepted.",
"type": "number",
"minimum": 0.0,
"maximum": 1.0
},
"minQuality": {
"description": "The minimal call quality for a variant to be accepted.",
"type": "number",
"minimum": 0.0
}
},
"required": [
"minCoverage",
"minFrequency",
"minHetFrequency",
"maxHetFrequency",
"minQuality"
]
},
"features": {
"description": "Stores pattern properties associated with a single (coding gene) feature. The key of each feature defines the internal gene name and stores an object.",
"type": "object",
"patternProperties": {
"^.+$": {
"description": "Information about a single (coding gene) feature stored as `object`.",
"type": "object",
"properties": {
"name": {
"description": "The internal gene name; has to be equal to the key at which this object is stored.",
"type": "string"
},
"nucleotideSequence": {
"description": "The nucleotide sequence of the (coding gene) feature.",
"type": "string",
"pattern": "^[ATGCN]+$"
},
"chromosome": {
"description": "The name of the locus this feature is located on. Should equal the value of `chromosome` of the parent object of this feature.",
"type": "string"
},
"start": {
"description": "The 1-based start position of the (coding gene) feature on its locus",
"type": "integer",
"minimum": 1
},
"end": {
"description": "The 1-based end position of the (coding gene) feature on its locus",
"type": "integer"
},
"isSense": {
"description": "Whether the (coding gene) feature is encoded on the sense or antisense strand.",
"type": "boolean"
},
"allocatedProtein": {
"description": "Information about the protein product of this feature and how it is affected by recorded variants.",
"type": "object",
"properties": {
"name": {
"description": "The internal name of the protein.",
"type": "string"
},
"pdb": {
"description": "File content of a `pdb` format file of the allocated proteins structure.",
"type": "string"
},
"chainSequences": {
"description": "The reference amino acid sequence of protein per chain.",
"type": "object",
"patternProperties": {
"^[A-Z]{1}$": {
"description": "Reference amino acid sequence of a single chain. Lower case substrings are translated from the genes sequence but were not included in the `pdb` format file.",
"type": "string",
"pattern": "^[ARNDCEQGHILKMFPSTWYVX*arndceqghilkmfpstwyvx]+$"
}
}
},
"proteoforms": {
"description": "Proteoforms with respect to the translated (coding gene) feature nucleotide sequence. Keys used to store proteoforms represent a hash encoding of the proteoforms sequence concatenated with `x` and the percentage of alternate positions wrt. the reference.",
"type": "object",
"patternProperties": {
"^[-]?[0-9]+x[0-1]{1}\\.[0-9]{2}$": {
"description": "Information about a single proteoform allocated to exactly one (coding gene) feature stored as `object`.",
"type": "object",
"properties": {
"name": {
"description": "The internal proteoform name; has to be equal to the key at which this object is stored.",
"type": "string"
},
"annotations": {
"description": "Any `string` type key/value pairs yielding meta-information about the feature.",
"type": "object",
"properties": {
"vSwab": {
"description": "String representation of all variants occuring in this proteoform.",
"type": "string",
"pattern": "(^$)|(^[ARNDCEQGHILKMFPSTWYVX*-]+@[0-9]+(-|\\+)[0-9](\\|[ARNDCEQGHILKMFPSTWYVX*-]+@[0-9]+(-|\\+)[0-9])*$)"
}
},
"additionalProperties": {
"description": "Additional meta-information about the proteoform.",
"type": "string"
},
"required": [
"vSwab"
]
},
"samples": {
"description": "List of all samples names that cause this proteoform.",
"type": "array",
"items": [
{
"description": "Items have to match keys of the `samples` property.",
"type": "string"
}
]
}
},
"required": [
"name",
"annotations",
"samples"
]
}
}
},
"variants": {
"description": "Information about amino acid variants stored in a nested object structure.",
"type": "object",
"patternProperties": {
"^[0-9]+(\\+|-)[0.9]+$": {
"description": "The position of the variant/mutation on the protein sequence concatenated with how many positions are added (+) or removed (-) by this mutation.",
"type": "object",
"patternProperties": {
"^[ARNDCEQGHILKMFPSTWYVX*]+$": {
"description": "The alternate amino acid sequence of the variant. May include `-` for gaps and stores the content of the `position` inclusively.",
"type": "object",
"properties": {
"annotations": {
"description": "Any `string` type key/value pairs yielding meta-information about the variant.",
"type": "object",
"properties": {
"cause": {
"description": "String representation of all nucleotide variants that cause this amino acid mutation(s).",
"type": "string",
"pattern": "^[ACGTN-]+@[0-9]+(\\|[ACGTN-]+@[0-9]+)*$"
}
},
"additionalProperties": {
"description": "Additional meta-information about the proteoform.",
"type": "string"
},
"required": [ ]
},
"occurrence": {
"description": "List of all proteoforms names that yield this variant.",
"type": "array",
"items": [
{
"description": "Items have to match keys of the `proteoforms` property.",
"type": "string"
}
]
}
},
"required": [
"annotations",
"occurrence"
]
}
}
}
}
}
},
"required": [
"name",
"pdb",
"chainSequences",
"proteoforms",
"variants"
]
},
"annotations": {
"description": "Any `string` type key/value pairs yielding meta-information about the feature.",
"type": "object",
"patternProperties": {
"^.+$": {
"description": "Meta-information about the feature. The property `geneName` (the value of the `name` attribute of the feature in the used `GFF` file of the parent locus).",
"type": "string"
}
},
"required": [
"geneName"
]
}
},
"required": [
"name",
"nucleotideSequence",
"chromosome",
"start",
"end",
"isSense",
"annotations"
]
}
}
},
"samples": {
"description": "Information about samples, i.e. possibly deviating genotypes of any of the stored features.",
"type": "object",
"patternProperties": {
"^.+$": {
"description": "Information about a single sample stored as `object`.",
"type": "object",
"properties": {
"name": {
"description": "The internal sample name; has to be equal to the key at which this object is stored.",
"type": "string"
},
"annotations": {
"description": "Any `string` type key/value pairs yielding meta-information about the sample.",
"type": "object",
"patternProperties": {
"^.+vSwab$": {
"description": "String representation of all variants occuring in this sample. Keys have to match #vSwab where # is the internal name of any stored feature.",
"type": "string",
"pattern": "(^$)|(^[ACGTN-]+@[0-9]+(\\|[ACGTN-]+@[0-9]+)*$)"
}
},
"additionalProperties": {
"description": "Additional meta-information about the sample.",
"type": "string"
}
}
},
"required": [
"name",
"annotations"
]
}
}
},
"software": {
"description": "The software with which the variants dictionary was computed.",
"type": "string"
},
"date": {
"description": "The date at which the variants dictionary was computed.",
"type": "string"
},
"chromosome": {
"description": "The locus/chromosome on which all stored (coding gene) features are located at.",
"type": "string"
},
"variants": {
"description": "Information about nucleotide variants stored in a nested object structure.",
"type": "object",
"patternProperties": {
"^[0-9]+$": {
"description": "The position of the variant on the parent locus.",
"type": "object",
"patternProperties": {
"^[ACGTN-]+$": {
"description": "The alternate nucleotide sequence of the variant. May include `-` for gaps and stores the content of the `position` inclusively.",
"type": "object",
"properties": {
"annotations": {
"description": "Any `string` type key/value pairs yielding meta-information about the variant.",
"type": "object",
"patternProperties": {
"^.+_EFF$": {
"description": "Special annotation property reflecting the `|` separated fields Annotation, Putative_impact, and HGVS.p coding of a SnpEff annotation. Keys have to match #_EFF where # is the value of a `annotations`/`geneName` property of any stored feature.",
"type": "string",
"pattern": "^.+\\|(HIGH|MODERATE|LOW|MODIFIER)\\|p\\..*$"
}
},
"additionalProperties": {
"description": "Additional meta-information about the variant.",
"type": "string"
}
},
"occurrence": {
"description": "Yields key/value pairs indicating the occurence of this variant in a specific sample as well as meta-information of this occurence. Each key should be equal to exactly one key in `samples`.",
"type": "object",
"patternProperties": {
"^.+$": {
"description": "`|` separated values indicating `rejected`, `primary`, `quality`, `frequency` and `coverage`.",
"type": "string",
"pattern": "^(true|false)\\|(true|false)\\|[0-9]+\\.[0-9]{1,2}\\|(0|1)\\.[0-9]{1,2}\\|[0-9]+\\.[0-9]{1}$"
}
}
}
},
"required": [
"annotations",
"occurrence"
]
}
}
}
}
}
},
"required": [
"parameters",
"features",
"samples",
"software",
"date",
"chromosome",
"variants"
]
}