Skip to content

VariantValidator

Check and Encode HGVS string

The default mRNA transcript for the HGVS strings should be added in the constructor byt can be overridden in the encode_hgvs method.

Parameters:

Name Type Description Default
genome_build str

The genome assembly, one of "GRCh37", "GRCh38", "hg19", "hg38"

 required
transcript str

An mRNA transcript that is the reference for the HGVS string, opt

 None
Source code in pyphetools/creation/variant_validator.py 
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
class VariantValidator:
    """
    Check and Encode HGVS string

    The default mRNA transcript for the HGVS strings should be added in the constructor byt can be overridden in the
    encode_hgvs method.

    :param genome_build: The genome assembly, one of "GRCh37", "GRCh38", "hg19", "hg38"
    :type genome_build: str
    :param transcript: An mRNA transcript that is the reference for the HGVS string, opt
    :type transcript: str
    """

    def __init__(self, genome_build, transcript=None):
        """
        Constructor
        """
        if genome_build not in ACCEPTABLE_GENOMES:
            raise ValueError(f"genome_build \"{genome_build}\" not recognized")
        self._genome_assembly = genome_build
        self._transcript = transcript

    def encode_hgvs(self, hgvs, custom_transcript=None):
        """
        Encode an HGVS string as a pyphetools Variant object

        :param hgvs: Human Genome Variation Society (HGVS) representation of a variant, e.g., c.36613706dup
        :type hgvs: str
        :param custom_transcript: a transcript (e.g., NM_001848.2), if different from the default transcript, optional
        :type custom_transcript: str
        :returns: pyphetools Variant object
        :rtype: HgvsVariant
        """
        if custom_transcript is not None:
            transcript = custom_transcript
        elif self._transcript is not None:
            transcript = self._transcript
        else:
            raise ValueError("Cannot run variant validator without transcript")
        api_url = URL_SCHEME % (self._genome_assembly, transcript, hgvs, transcript)
        #f"https://rest.variantvalidator.org/VariantValidator/variantvalidator/{self._genome_assembly}/{transcript}%3A{hgvs}/{transcript}"
        #
        print(api_url)
        response = requests.get(api_url)
        # We expect to get a dictionary with three keys. The first is the name of the variant, e.g., ACC:HGVS, then we
        # get flag and metadata
        vv_dict = response.json()
        if 'flag' in vv_dict:
            if vv_dict['flag'] != 'gene_variant':
                flag = vv_dict['flag']
                raise ValueError(f"Expecting to get a gene_variant from Variant Validator but got {flag}")
        # This is the easiest way to get the variant key, which may contain difficult characters
        variant_key = [k for k in vv_dict.keys() if k not in {'flag', 'metadata'}][0]
        var = vv_dict[variant_key]
        hgnc = None
        if 'gene_ids' in var and 'hgnc_id' in var['gene_ids']:
            hgnc = var['gene_ids']['hgnc_id']
        symbol = None
        if 'gene_symbol' in var:
            symbol = var['gene_symbol']
        assemblies = var['primary_assembly_loci']
        if not self._genome_assembly in assemblies:
            raise ValueError(f"Could not identified {self._genome_assembly} in Variant Validator response")
        assembly = assemblies[self._genome_assembly]
        hgvs_transcript_var = var.get('hgvs_transcript_variant', None)
        genomic_hgvs = assembly.get('hgvs_genomic_description', None)
        reference_sequence_records = var.get('reference_sequence_records', None)
        if reference_sequence_records is not None:
            transcript = reference_sequence_records['transcript']
            if transcript.startswith('https://www.ncbi.nlm.nih.gov/nuccore/'):
                transcript = transcript[37:]
        else:
            transcript = None
        # 'vcf': {'alt': 'C', 'chr': '16', 'pos': '1756403', 'ref': 'CG'}},
        if not 'vcf' in assembly:
            raise ValueError(f"Could not identify vcf element in Variant Validator genome assembly response")
        return HgvsVariant(assembly=self._genome_assembly, vcf_d=assembly['vcf'], symbol=symbol,
                        hgnc=hgnc, transcript=transcript, hgvs=hgvs_transcript_var, g_hgvs=genomic_hgvs)

__init__(genome_build, transcript=None)

Constructor

Source code in pyphetools/creation/variant_validator.py 
23
24
25
26
27
28
29
30
def __init__(self, genome_build, transcript=None):
    """
    Constructor
    """
    if genome_build not in ACCEPTABLE_GENOMES:
        raise ValueError(f"genome_build \"{genome_build}\" not recognized")
    self._genome_assembly = genome_build
    self._transcript = transcript

encode_hgvs(hgvs, custom_transcript=None)

Encode an HGVS string as a pyphetools Variant object

Parameters:

Name Type Description Default
hgvs str

Human Genome Variation Society (HGVS) representation of a variant, e.g., c.36613706dup

 required
custom_transcript str

a transcript (e.g., NM_001848.2), if different from the default transcript, optional

 None

Returns:

Type Description
HgvsVariant

pyphetools Variant object
Source code in pyphetools/creation/variant_validator.py 
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
def encode_hgvs(self, hgvs, custom_transcript=None):
    """
    Encode an HGVS string as a pyphetools Variant object

    :param hgvs: Human Genome Variation Society (HGVS) representation of a variant, e.g., c.36613706dup
    :type hgvs: str
    :param custom_transcript: a transcript (e.g., NM_001848.2), if different from the default transcript, optional
    :type custom_transcript: str
    :returns: pyphetools Variant object
    :rtype: HgvsVariant
    """
    if custom_transcript is not None:
        transcript = custom_transcript
    elif self._transcript is not None:
        transcript = self._transcript
    else:
        raise ValueError("Cannot run variant validator without transcript")
    api_url = URL_SCHEME % (self._genome_assembly, transcript, hgvs, transcript)
    #f"https://rest.variantvalidator.org/VariantValidator/variantvalidator/{self._genome_assembly}/{transcript}%3A{hgvs}/{transcript}"
    #
    print(api_url)
    response = requests.get(api_url)
    # We expect to get a dictionary with three keys. The first is the name of the variant, e.g., ACC:HGVS, then we
    # get flag and metadata
    vv_dict = response.json()
    if 'flag' in vv_dict:
        if vv_dict['flag'] != 'gene_variant':
            flag = vv_dict['flag']
            raise ValueError(f"Expecting to get a gene_variant from Variant Validator but got {flag}")
    # This is the easiest way to get the variant key, which may contain difficult characters
    variant_key = [k for k in vv_dict.keys() if k not in {'flag', 'metadata'}][0]
    var = vv_dict[variant_key]
    hgnc = None
    if 'gene_ids' in var and 'hgnc_id' in var['gene_ids']:
        hgnc = var['gene_ids']['hgnc_id']
    symbol = None
    if 'gene_symbol' in var:
        symbol = var['gene_symbol']
    assemblies = var['primary_assembly_loci']
    if not self._genome_assembly in assemblies:
        raise ValueError(f"Could not identified {self._genome_assembly} in Variant Validator response")
    assembly = assemblies[self._genome_assembly]
    hgvs_transcript_var = var.get('hgvs_transcript_variant', None)
    genomic_hgvs = assembly.get('hgvs_genomic_description', None)
    reference_sequence_records = var.get('reference_sequence_records', None)
    if reference_sequence_records is not None:
        transcript = reference_sequence_records['transcript']
        if transcript.startswith('https://www.ncbi.nlm.nih.gov/nuccore/'):
            transcript = transcript[37:]
    else:
        transcript = None
    # 'vcf': {'alt': 'C', 'chr': '16', 'pos': '1756403', 'ref': 'CG'}},
    if not 'vcf' in assembly:
        raise ValueError(f"Could not identify vcf element in Variant Validator genome assembly response")
    return HgvsVariant(assembly=self._genome_assembly, vcf_d=assembly['vcf'], symbol=symbol,
                    hgnc=hgnc, transcript=transcript, hgvs=hgvs_transcript_var, g_hgvs=genomic_hgvs)