Readers

Cutevariant imports variant data from an Abstract class called AbstractReader. You can inherits from it to support custom format which contains variants.

Methods to override

3 methods must be overrided :

AbstractReader.get_fields()

Yield fields as dictionnaries with the following structure:

• name (str): the field name
• category (str): the table which the field belongs to. It can be (variants,annotations, samples) #TODO rename
• description (str): The definition of the field
• type (str): Field type in Python format ( str, int, float,bool)
• constraint (str:optional): SQL constraints

{
    "name": "chr", 
     "category": "variants",    
     "description": "chromosom",    
     "type": "str",    
     "constraint": "NOT NULL",     
 }

AbstractReader.get_variants()

Yield variants as dictionnaries with the following structure:

• chr (str): chromosom name
• pos (str): chromosom name
• ref (str): chromosom name
• alt (str): chromosom name
• field n (type): n fields more returns by get_fields with category variants
• annotations (list):
  • transcript (str): Transcript name
  • gene (str): gene name
  • field n (type_): n fields more returns by get_fields with category annotations
• samples (list):
  • name (str): name of sample
  • gt (int): Genotype of variant for the sample. ( 0: homozygous wild, 1: heterozygous, 2: homozygous muted, -1: unknown)

{
"chr": "11",
 "pos": 125010,
 "ref": "T",
 "alt": "A",
 "dp": 32,
 "annotations": [
     {"transcript": "NM_234234", "gene": "CFTR", "in_exon": true, "pathogen_score": 0.2},
     {"transcript": "NM_234235", "gene": "CFTR","in_exon": false, "pathogen_score": 0.5},
 ],
 "samples": [{"name": "sacha", "gt": 1, "af": 0.4}]
}

AbstractReader.get_samples()

Return a list of samples. If you have no sample, you can avoid to override this method.

Exemple

You can get inspired by the FakeReader

from .abstractreader import AbstractReader

class FakeReader(AbstractReader):
    def __init__(self):
        super().__init__(None)

    def get_variants(self):
        yield {
            "chr": "11",
            "pos": 125010,
            "ref": "T",
            "alt": "A",
            "annotations": [
                {"transcript": "NM_234234", "gene": "CFTR"},
                {"transcript": "NM_234235", "gene": "CFTR"},
            ],
            "samples": [{"name": "sacha", "gt": 1}],
        }

        yield {
            "chr": "12",
            "pos": 125010,
            "ref": "T",
            "alt": "A",
            "annotations": [
                {"transcript": "NM_234234", "gene": "CFTR"},
                {"transcript": "NM_234235", "gene": "CFTR"},
            ],
            "samples": [{"name": "sacha", "gt": 1}],
        }

        yield {
            "chr": "13",
            "pos": 125010,
            "ref": "T",
            "alt": "A",
            "annotations": [
                {"transcript": "NM_234234", "gene": "CFTR"},
                {"transcript": "NM_234235", "gene": "CFTR"},
            ],
            "samples": [{"name": "sacha", "gt": 1}],
        }

    def get_fields(self):
        """Extract fields informations from VCF fields
        .. note:: Fields used in PRIMARY KEYS have the constraint NOT NULL.
            By default, all other fields can have NULL values.
        """

        yield {
            "name": "chr",
            "category": "variants",
            "description": "chromosom",
            "type": "str",
            "constraint": "NOT NULL",
        }
        yield {
            "name": "pos",
            "category": "variants",
            "description": "position",
            "type": "int",
            "constraint": "NOT NULL",
        }

        yield {
            "name": "ref",
            "category": "variants",
            "description": "reference base",
            "type": "str",
            "constraint": "NOT NULL",
        }
        yield {
            "name": "alt",
            "category": "variants",
            "description": "alternative base",
            "type": "str",
            "constraint": "NOT NULL",
        }

        yield {
            "name": "gt",
            "category": "samples",
            "description": "genotype",
            "type": "int",
        }

        yield {
            "name": "af",
            "category": "samples",
            "description": "allele frequency",
            "type": "float",
        }

        yield {
            "name": "gene",
            "category": "annotations",
            "description": "gene name",
            "type": "str",
        }

        yield {
            "name": "transcript",
            "category": "annotations",
            "description": "gene transcripts",
            "type": "str",
        }

    def get_samples(self):
        return ["sacha"]