snvannotators 0.0.3
SNV annotation
Requires Python: >=3.6

# `snvannotators` - SNV annotation

The package annotates SNVs.

## Example

KRAS p.A18V

```python
from pyoncokb.oncokbapi import OncokbApi
from snvannotators.cpraannotators.cpragrch37annotator import CpraGrch37Annotator
from snvannotators.snvannotation.snvannotationtodictconverter import SnvAnnotationToDictConverter
from snvmodels.cpra import Cpra
from tests.testconfig import TestConfig

# Create a Cpra object of a SNV
cpra = Cpra(chrom="chr12", pos=25398266, ref="G", alt="A")
# Get OncoKB API
config = TestConfig()
oncokb_auth = config.get_oncokb_authorization()
oncokb_api = OncokbApi(auth=oncokb_auth)
# Annotate
cpra_annotator = CpraGrch37Annotator(
    cpra=cpra,
    oncokb_api=oncokb_api,
    alt_aln_method="splign",
    tss_upstream_limit=20000,
    uncertain=False,
    promoter_tss_upstream_offset=1500,
)
snv_annotation = cpra_annotator.annotate()
```

`snv_annotation` is an object of `SnvAnnotation` class, which itself consists of objects of many other classes:

```python
from pprint import pprint
pprint(snv_annotation.__annotations__)
```

```python
{'hgvs_annotation': <class 'snvannotators.hgvsplus.annotators.hgvsannotation.HgvsAnnotation'>,
 'indicator_query_resp': typing.Optional[pyoncokb.models.indicatorqueryresp.IndicatorQueryResp],
 'knowledgebase_items': typing.Optional[typing.List[snvannotators.snvannotation.knowledgebaseitem.KnowledgebaseItem]],
 'meta': typing.Any,
 'myvariant_annotation': <class 'snvannotators.myvariant.annotation.myvariantannotation.MyvariantAnnotation'>,
 'snv': typing.Union[snvmodels.spra.cspra.Cspra, snvmodels.cpra.cpra.Cpra, snvmodels.spra.spra.Spra, hgvs.sequencevariant.SequenceVariant, str],
 'transcript_feature_range_annotations': typing.Optional[typing.List[transcriptfeatures.annotators.rangeannotators.transcriptfeaturerangeannotation.TranscriptFeatureRangeAnnotation]]}
```

Below shows the full data:

```python
SnvAnnotationToDictConverter().convert(snv_annotation=snv_annotation)
```

```python
{
    "snv": {
        "ac": "NC_000012.11",
        "pos": 25398266,
        "ref": "G",
        "alt": "A",
        "chrom": "chr12",
    },
    "hgvs_annotation": {
        "hgvs_g": "NC_000012.11:g.25398266G>A",
        "hgvs_g_normalized": "NC_000012.11:g.25398266G>A",
        "hgvs_tp_annotations": [
            {
                "tx_ac": "NM_001369787.1",
                "hgvs_t": "NM_001369787.1(KRAS):c.53C>T",
                "hgvs_p": "NP_001356716.1:p.Ala18Val",
            },
            {
                "tx_ac": "NM_033360.2",
                "hgvs_t": "NM_033360.2(KRAS):c.53C>T",
                "hgvs_p": "NP_203524.1:p.Ala18Val",
            },
            {
                "tx_ac": "NM_001369786.1",
                "hgvs_t": "NM_001369786.1(KRAS):c.53C>T",
                "hgvs_p": "NP_001356715.1:p.Ala18Val",
            },
            {
                "tx_ac": "NM_033360.3",
                "hgvs_t": "NM_033360.3(KRAS):c.53C>T",
                "hgvs_p": "NP_203524.1:p.Ala18Val",
            },
            {
                "tx_ac": "NM_004985.4",
                "hgvs_t": "NM_004985.4(KRAS):c.53C>T",
                "hgvs_p": "NP_004976.2:p.Ala18Val",
            },
            {
                "tx_ac": "NM_033360.4",
                "hgvs_t": "NM_033360.4(KRAS):c.53C>T",
                "hgvs_p": "NP_203524.1:p.Ala18Val",
            },
            {
                "tx_ac": "NM_004985.5",
                "hgvs_t": "NM_004985.5(KRAS):c.53C>T",
                "hgvs_p": "NP_004976.2:p.Ala18Val",
            },
            {
                "tx_ac": "NM_004985.3",
                "hgvs_t": "NM_004985.3(KRAS):c.53C>T",
                "hgvs_p": "NP_004976.2:p.Ala18Val",
            },
        ],
    },
    "myvariant_annotation": {
        "hgvs_chr": "chr12:g.25398266G>A",
        "raw": {
            "_id": "chr12:g.25398266G>A",
            "_version": 2,
            "cadd": {
                "_license": "http://bit.ly/2TIuab9",
                "alt": "A",
                "anc": "G",
                "annotype": "CodingTranscript",
                "bstatistic": 696,
                "chmm": {
                    "bivflnk": 0.0,
                    "enh": 0.0,
                    "enhbiv": 0.0,
                    "het": 0.0,
                    "quies": 0.079,
                    "reprpc": 0.0,
                    "reprpcwk": 0.0,
                    "tssa": 0.0,
                    "tssaflnk": 0.0,
                    "tssbiv": 0.0,
                    "tx": 0.189,
                    "txflnk": 0.0,
                    "txwk": 0.701,
                    "znfrpts": 0.0,
                },
                "chrom": 12,
                "consdetail": "missense",
                "consequence": "NON_SYNONYMOUS",
                "consscore": 7,
                "cpg": 0.04,
                "dna": {
                    "helt": -1.75,
                    "mgw": -0.21,
                    "prot": 0.91,
                    "roll": -1.16,
                },
                "encode": {
                    "exp": 238.03,
                    "h3k27ac": 3.0,
                    "h3k4me1": 12.28,
                    "h3k4me3": 5.08,
                    "nucleo": 0.8,
                },
                "exon": "2/6",
                "fitcons": 0.723164,
                "gc": 0.37,
                "gene": {
                    "ccds_id": "CCDS8703.1",
                    "cds": {
                        "cdna_pos": 117,
                        "cds_pos": 53,
                        "rel_cdna_pos": 0.1,
                        "rel_cds_pos": 0.09,
                    },
                    "feature_id": "ENST00000256078",
                    "gene_id": "ENSG00000133703",
                    "genename": "KRAS",
                    "prot": {
                        "domain": "ndomain",
                        "protpos": 18,
                        "rel_prot_pos": 0.1,
                    },
                },
                "gerp": {
                    "n": 5.68,
                    "rs": 662.8,
                    "rs_pval": 7.10496e-183,
                    "s": 5.68,
                },
                "grantham": 64,
                "isderived": "TRUE",
                "isknownvariant": "FALSE",
                "istv": "FALSE",
                "length": 0,
                "mapability": {"20bp": 1, "35bp": 1},
                "min_dist_tse": 11513,
                "min_dist_tss": 5472,
                "mutindex": 28,
                "naa": "V",
                "oaa": "A",
                "phast_cons": {
                    "mammalian": 1.0,
                    "primate": 0.998,
                    "vertebrate": 1.0,
                },
                "phred": 32,
                "phylop": {
                    "mammalian": 2.664,
                    "primate": 0.559,
                    "vertebrate": 5.859,
                },
                "polyphen": {"cat": "probably_damaging", "val": 0.985},
                "pos": 25398266,
                "rawscore": 6.801703,
                "ref": "G",
                "segway": "R4",
                "sift": {"cat": "deleterious", "val": 0},
                "type": "SNV",
            },
            "chrom": "12",
            "clinvar": {
                "_license": "http://bit.ly/2SQdcI0",
                "allele_id": 1687832,
                "alt": "A",
                "chrom": "12",
                "cytogenic": "12p12.1",
                "gene": {"id": "3845", "symbol": "KRAS"},
                "hg19": {"end": 25398266, "start": 25398266},
                "hg38": {"end": 25245332, "start": 25245332},
                "hgvs": {
                    "coding": [
                        "LRG_344t1:c.53C>T",
                        "LRG_344t2:c.53C>T",
                        "NM_001369786.1:c.53C>T",
                        "NM_001369787.1:c.53C>T",
                        "NM_004985.5:c.53C>T",
                        "NM_033360.4:c.53C>T",
                    ],
                    "genomic": [
                        "LRG_344:g.10672C>T",
                        "NC_000012.11:g.25398266G>A",
                        "NC_000012.12:g.25245332G>A",
                        "NG_007524.2:g.10672C>T",
                    ],
                    "protein": [
                        "LRG_344p1:p.Ala18Val",
                        "LRG_344p2:p.Ala18Val",
                        "NP_001356715.1:p.Ala18Val",
                        "NP_001356716.1:p.Ala18Val",
                        "NP_004976.2:p.Ala18Val",
                        "NP_203524.1:p.Ala18Val",
                    ],
                },
                "rcv": {
                    "accession": "RCV002264903",
                    "clinical_significance": "Pathogenic",
                    "conditions": {
                        "identifiers": {
                            "medgen": "C1860991",
                            "mondo": "MONDO:0012371",
                            "omim": "609942",
                            "orphanet": "648",
                        },
                        "name": "Noonan syndrome 3 (NS3)",
                        "synonyms": ["KRAS gene related Noonan syndrome"],
                    },
                    "number_submitters": 1,
                    "origin": "de novo",
                    "preferred_name": "NM_004985.5(KRAS):c.53C>T (p.Ala18Val)",
                    "review_status": "criteria provided, single submitter",
                },
                "ref": "G",
                "rsid": "rs2135806030",
                "type": "single nucleotide variant",
                "variant_id": 1695421,
            },
            "dbnsfp": {
                "_license": "http://bit.ly/2VLnQBz",
                "aa": {
                    "alt": "V",
                    "codon_degeneracy": [0, 0, 0, 0],
                    "codonpos": [2, 2, 2, 2],
                    "pos": [18, 18, 18, 18],
                    "ref": "A",
                    "refcodon": ["GCC", "GCC", "GCC", "GCC"],
                },
                "alphamissense": {
                    "pred": ["P", "P", "P", "P"],
                    "rankscore": 0.95577,
                    "score": [0.9951, 0.9862, 0.9951, 0.7008],
                },
                "alt": "A",
                "ancestral_allele": "G",
                "appris": ["alternative1", "principal4"],
                "bayesdel": {
                    "add_af": {
                        "pred": "D",
                        "rankscore": 0.91206,
                        "score": 0.42359,
                    },
                    "no_af": {
                        "pred": "D",
                        "rankscore": 0.91097,
                        "score": 0.370681,
                    },
                },
                "bstatistic": {
                    "converted_rankscore": 0.57054,
                    "score": 707.0,
                },
                "chrom": "12",
                "clinpred": {
                    "pred": "D",
                    "rankscore": 0.81922,
                    "score": 0.991609394550323,
                },
                "clinvar": {
                    "clinvar_id": "1695421",
                    "clnsig": "Pathogenic",
                    "hgvs": "NC_000012.12:g.25245332G>A",
                    "medgen": "C1860991",
                    "omim": "609942",
                    "orphanet": "648",
                    "review": "criteria_provided,_single_submitter",
                    "trait": "Noonan_syndrome_3",
                },
                "dann": {"rankscore": 0.98518, "score": 0.999173161627483},
                "deogen2": {
                    "pred": "D",
                    "rankscore": 0.97794,
                    "score": 0.891291,
                },
                "eigen": {
                    "phred_coding": 14.91392,
                    "raw_coding": 1.03070516408223,
                    "raw_coding_rankscore": 0.96612,
                },
                "eigen-pc": {
                    "phred_coding": 17.52826,
                    "raw_coding": 0.97751439147273,
                    "raw_coding_rankscore": 0.98143,
                },
                "ensembl": {
                    "geneid": [
                        "ENSG00000133703",
                        "ENSG00000133703",
                        "ENSG00000133703",
                        "ENSG00000133703",
                    ],
                    "proteinid": [
                        "ENSP00000308495",
                        "ENSP00000452512",
                        "ENSP00000256078",
                        "ENSP00000451856",
                    ],
                    "transcriptid": [
                        "ENST00000311936",
                        "ENST00000557334",
                        "ENST00000256078",
                        "ENST00000556131",
                    ],
                },
                "esm1b": {
                    "pred": ["D", "D"],
                    "rankscore": 0.98564,
                    "score": [-16.632, -16.115],
                },
                "eve": {
                    "class10_pred": "U",
                    "class20_pred": "U",
                    "class25_pred": "U",
                    "class30_pred": "U",
                    "class40_pred": "U",
                    "class50_pred": "U",
                    "class60_pred": "U",
                    "class70_pred": "U",
                    "class75_pred": "P",
                    "class80_pred": "P",
                    "class90_pred": "P",
                    "rankscore": 0.72008,
                    "score": 0.6483115419004939,
                },
                "fathmm": {
                    "converted_rankscore": 0.80387,
                    "pred": ["T", "T", "T", "T"],
                    "score": [-1.39, -0.53, -0.53, -0.53],
                },
                "fathmm-mkl": {
                    "coding_group": "AEFBI",
                    "coding_pred": "D",
                    "coding_rankscore": 0.88157,
                    "coding_score": 0.98885,
                },
                "fathmm-xf": {
                    "coding_pred": "D",
                    "coding_rankscore": 0.85047,
                    "coding_score": 0.902509,
                },
                "fitcons": {
                    "gm12878": {
                        "confidence_value": 0,
                        "rankscore": 0.81188,
                        "score": 0.709663,
                    },
                    "h1-hesc": {
                        "confidence_value": 0,
                        "rankscore": 0.96076,
                        "score": 0.743671,
                    },
                    "huvec": {
                        "confidence_value": 0,
                        "rankscore": 0.4955,
                        "score": 0.631631,
                    },
                    "integrated": {
                        "confidence_value": 0,
                        "rankscore": 0.92422,
                        "score": 0.732398,
                    },
                },
                "gencode_basic": ["Y", "Y", "Y", "Y"],
                "genename": ["KRAS", "KRAS", "KRAS", "KRAS"],
                "genocanyon": {"rankscore": 0.98316, "score": 1.0},
                "gerp++": {"nr": 5.68, "rs": 5.68, "rs_rankscore": 0.88021},
                "gmvp": {"rankscore": 0.96401, "score": 0.9641457346713307},
                "hg18": {"end": 25289533, "start": 25289533},
                "hg19": {"end": 25398266, "start": 25398266},
                "hg38": {"end": 25245332, "start": 25245332},
                "hgvsc": "c.53C>T",
                "hgvsp": ["p.Ala18Val", "p.A18V"],
                "interpro": {
                    "domain": [
                        "Small GTP-binding protein domain",
                        "Small GTP-binding protein domain",
                    ]
                },
                "list-s2": {
                    "pred": ["D", "D", "D", "D"],
                    "rankscore": 0.94559,
                    "score": [0.979335, 0.981385, 0.979335, 0.984002],
                },
                "lrt": {
                    "converted_rankscore": 0.8433,
                    "omega": 0.0,
                    "pred": "D",
                    "score": 0.0,
                },
                "m-cap": {
                    "pred": "D",
                    "rankscore": 0.88087,
                    "score": 0.227357,
                },
                "metalr": {
                    "pred": "D",
                    "rankscore": 0.91865,
                    "score": 0.7611,
                },
                "metarnn": {
                    "pred": ["D", "D", "D", "D"],
                    "rankscore": 0.90261,
                    "score": [0.9089627, 0.9089627, 0.9089627, 0.9089627],
                },
                "metasvm": {
                    "pred": "D",
                    "rankscore": 0.93471,
                    "score": 0.7239,
                },
                "mpc": {"rankscore": 0.985, "score": 2.6732094712},
                "mutationassessor": {
                    "pred": ["M", "M"],
                    "rankscore": 0.76484,
                    "score": [2.615, 2.615],
                },
                "mutationtaster": {
                    "aae": ["A18V", "A18V", "A18V", "A18V"],
                    "converted_rankscore": 0.81001,
                    "model": [
                        "simple_aae",
                        "simple_aae",
                        "simple_aae",
                        "simple_aae",
                    ],
                    "pred": ["D", "D", "D", "D"],
                    "score": [1.0, 1.0, 1.0, 1.0],
                },
                "mutpred": {
                    "aa_change": ["A18V", "A18V", "A18V", "A18V"],
                    "accession": ["P01116", "P01116", "P01116", "P01116"],
                    "pred": [
                        {
                            "mechanism": "Gain of catalytic residue at S17",
                            "p_val": 0.0,
                        },
                        {
                            "mechanism": "Gain of catalytic residue at S17",
                            "p_val": 0.0,
                        },
                        {
                            "mechanism": "Gain of catalytic residue at S17",
                            "p_val": 0.0,
                        },
                        {
                            "mechanism": "Gain of catalytic residue at S17",
                            "p_val": 0.0,
                        },
                    ],
                    "rankscore": 0.87821,
                    "score": [0.747, 0.747, 0.747, 0.747],
                },
                "mvp": {
                    "rankscore": 0.98622,
                    "score": [
                        0.986379006677,
                        0.986379006677,
                        0.986379006677,
                        0.986379006677,
                    ],
                },
                "phastcons": {
                    "100way_vertebrate": {
                        "rankscore": 0.71638,
                        "score": 1.0,
                    },
                    "17way_primate": {"rankscore": 0.97212, "score": 1.0},
                    "470way_mammalian": {
                        "rankscore": 0.68203,
                        "score": 1.0,
                    },
                },
                "phylop": {
                    "100way_vertebrate": {
                        "rankscore": 0.99183,
                        "score": 9.985,
                    },
                    "17way_primate": {"rankscore": 0.53741, "score": 0.654},
                    "470way_mammalian": {
                        "rankscore": 0.98601,
                        "score": 11.872,
                    },
                },
                "polyphen2": {
                    "hdiv": {
                        "pred": ["D", "D"],
                        "rankscore": 0.90584,
                        "score": [0.999, 1.0],
                    },
                    "hvar": {
                        "pred": ["P", "D"],
                        "rankscore": 0.74104,
                        "score": [0.893, 0.978],
                    },
                },
                "primateai": {
                    "pred": "D",
                    "rankscore": 0.94572,
                    "score": 0.884602069855,
                },
                "provean": {
                    "converted_rankscore": 0.7224,
                    "pred": ["D", "D", "D", "D"],
                    "score": [-3.31, -3.84, -3.21, -3.81],
                },
                "ref": "G",
                "reliability_index": 10,
                "revel": {
                    "rankscore": 0.94989,
                    "score": [0.84, 0.84, 0.84, 0.84],
                },
                "rsid": "rs2135806030",
                "sift": {
                    "converted_rankscore": 0.7849,
                    "pred": ["D", "D", "D", "D"],
                    "score": [0.001, 0.001, 0.001, 0.001],
                },
                "sift4g": {
                    "converted_rankscore": 0.83351,
                    "pred": ["D", "D", "D", "D"],
                    "score": [0.001, 0.001, 0.001, 0.001],
                },
                "siphy_29way": {
                    "logodds_rankscore": 0.90353,
                    "logodds_score": 18.3719,
                    "pi": {"a": 0.0, "c": 0.0, "g": 1.0, "t": 0.0},
                },
                "tsl": [1, 5, 1, 1],
                "uniprot": [
                    {"acc": "P01116-2", "entry": "RASK_HUMAN"},
                    {"acc": "G3V5T7", "entry": "G3V5T7_HUMAN"},
                    {"acc": "P01116", "entry": "RASK_HUMAN"},
                    {"acc": "G3V4K2", "entry": "G3V4K2_HUMAN"},
                ],
                "varity": {
                    "er": {"rankscore": 0.99266, "score": 0.96570957},
                    "er_loo": {"rankscore": 0.99266, "score": 0.96570957},
                    "r": {"rankscore": 0.99706, "score": 0.98890454},
                    "r_loo": {"rankscore": 0.99706, "score": 0.98890454},
                },
                "vep_canonical": "YES",
                "vest4": {
                    "rankscore": 0.93959,
                    "score": [0.906, 0.89, 0.934, 0.906],
                },
            },
            "dbsnp": {
                "_license": "http://bit.ly/2AqoLOc",
                "alt": "A",
                "chrom": "12",
                "dbsnp_build": 156,
                "gene": {
                    "geneid": 3845,
                    "is_pseudo": False,
                    "name": "KRAS proto-oncogene, GTPase",
                    "rnas": [
                        {
                            "codon_aligned_transcript_change": {
                                "deleted_sequence": "GCC",
                                "inserted_sequence": "GCC",
                                "position": 228,
                                "seq_id": "NM_001369786.1",
                            },
                            "hgvs": "NM_001369786.1:c.53=",
                            "protein": {
                                "variant": {
                                    "spdi": {
                                        "deleted_sequence": "A",
                                        "inserted_sequence": "A",
                                        "position": 17,
                                        "seq_id": "NP_001356715.1",
                                    }
                                }
                            },
                            "protein_product": {"refseq": "NP_001356715.1"},
                            "refseq": "NM_001369786.1",
                            "so": [
                                {
                                    "accession": "SO:0001580",
                                    "name": "coding_sequence_variant",
                                }
                            ],
                        },
                        {
                            "codon_aligned_transcript_change": {
                                "deleted_sequence": "GCC",
                                "inserted_sequence": "GCC",
                                "position": 228,
                                "seq_id": "NM_001369787.1",
                            },
                            "hgvs": "NM_001369787.1:c.53=",
                            "protein": {
                                "variant": {
                                    "spdi": {
                                        "deleted_sequence": "A",
                                        "inserted_sequence": "A",
                                        "position": 17,
                                        "seq_id": "NP_001356716.1",
                                    }
                                }
                            },
                            "protein_product": {"refseq": "NP_001356716.1"},
                            "refseq": "NM_001369787.1",
                            "so": [
                                {
                                    "accession": "SO:0001580",
                                    "name": "coding_sequence_variant",
                                }
                            ],
                        },
                        {
                            "codon_aligned_transcript_change": {
                                "deleted_sequence": "GCC",
                                "inserted_sequence": "GCC",
                                "position": 241,
                                "seq_id": "NM_004985.5",
                            },
                            "hgvs": "NM_004985.5:c.53=",
                            "protein": {
                                "variant": {
                                    "spdi": {
                                        "deleted_sequence": "A",
                                        "inserted_sequence": "A",
                                        "position": 17,
                                        "seq_id": "NP_004976.2",
                                    }
                                }
                            },
                            "protein_product": {"refseq": "NP_004976.2"},
                            "refseq": "NM_004985.5",
                            "so": [
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                "rsid": "rs2135806030",
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            "hg19": {"end": 25398266, "start": 25398266},
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