scout/build/variant/gene.py
def build_gene(gene, hgncid_to_gene=None):
    """Build a gene object
        
        Has to build the transcripts for the genes to
    
    Args:
        gene(dict): Parsed information from the VCF
        hgncid_to_gene(dict): A map from hgnc_id  -> hgnc_gene objects 

    Returns:
        gene_obj(dict)
    
    gene = dict(
        # The hgnc gene id
        hgnc_id = int, # required
        hgnc_symbol = str, 
        ensembl_gene_id = str, 
        # A list of Transcript objects
        transcripts = list, # list of <transcript>
        # This is the worst functional impact of all transcripts
        functional_annotation = str, # choices=SO_TERM_KEYS
        # This is the region of the most severe functional impact
        region_annotation = str, # choices=FEATURE_TYPES
        # This is most severe sift prediction of all transcripts
        sift_prediction = str, # choices=CONSEQUENCE
        # This is most severe polyphen prediction of all transcripts
        polyphen_prediction = str, # choices=CONSEQUENCE
    )
    
    """
    hgncid_to_gene = hgncid_to_gene or {}
    gene_obj = dict()
 
    # This id is collected from the VCF
    # Typically annotated by VEP or snpEFF
    hgnc_id = int(gene['hgnc_id'])
    gene_obj['hgnc_id'] = hgnc_id

    # Get the gene information from database
    hgnc_gene = hgncid_to_gene.get(hgnc_id)
    
    inheritance = set()
    hgnc_transcripts = []
    if hgnc_gene:
        # Set the hgnc symbol etc to the one internally in Scout
        gene_obj['hgnc_symbol'] = hgnc_gene['hgnc_symbol']
        gene_obj['ensembl_id'] = hgnc_gene['ensembl_id']
        gene_obj['description'] = hgnc_gene['description']

        if hgnc_gene.get('inheritance_models'):
            gene_obj['inheritance'] = hgnc_gene['inheritance_models']
    
    transcripts = []
    for transcript in gene['transcripts']:
        transcript_obj = build_transcript(transcript)
        transcripts.append(transcript_obj)
    gene_obj['transcripts'] = transcripts

    functional_annotation = gene.get('most_severe_consequence')
    if functional_annotation:
        if not functional_annotation in SO_TERM_KEYS:
            LOG.warning("Invalid functional annotation %s", functional_annotation)
        else:
            gene_obj['functional_annotation'] = functional_annotation
    
    region_annotation = gene.get('region_annotation')
    if region_annotation:
        if not region_annotation in FEATURE_TYPES:
            LOG.warning("Invalid region annotation %s", region_annotation)
        else:
            gene_obj['region_annotation'] = region_annotation
 
    sift_prediction = gene.get('most_severe_sift')
    if sift_prediction:
        if not sift_prediction in CONSEQUENCE:
            LOG.warning("Invalid sift prediction %s", sift_prediction)
        else:
            gene_obj['sift_prediction'] = sift_prediction

    polyphen_prediction = gene.get('most_severe_polyphen')
    if polyphen_prediction:
        if not polyphen_prediction in CONSEQUENCE:
            LOG.warning("Invalid polyphen prediction %s", polyphen_prediction)
        else:
            gene_obj['polyphen_prediction'] = polyphen_prediction
    
    gene_obj['hgvs_identifier'] = gene['hgvs_identifier']
    gene_obj['canonical_transcript'] = gene['canonical_transcript']
    gene_obj['exon'] = gene['exon']
    
    return gene_obj
def build_gene(gene, hgncid_to_gene=None):
    """Build a gene object
        
        Has to build the transcripts for the genes to
    
    Args:
        gene(dict): Parsed information from the VCF
        hgncid_to_gene(dict): A map from hgnc_id  -> hgnc_gene objects 

    Returns:
        gene_obj(dict)
    
    gene = dict(
        # The hgnc gene id
        hgnc_id = int, # required
        hgnc_symbol = str, 
        ensembl_gene_id = str, 
        # A list of Transcript objects
        transcripts = list, # list of <transcript>
        # This is the worst functional impact of all transcripts
        functional_annotation = str, # choices=SO_TERM_KEYS
        # This is the region of the most severe functional impact
        region_annotation = str, # choices=FEATURE_TYPES
        # This is most severe sift prediction of all transcripts
        sift_prediction = str, # choices=CONSEQUENCE
        # This is most severe polyphen prediction of all transcripts
        polyphen_prediction = str, # choices=CONSEQUENCE
    )
    
    """
    hgncid_to_gene = hgncid_to_gene or {}
    gene_obj = dict()
 
    # This id is collected from the VCF
    # Typically annotated by VEP or snpEFF
    hgnc_id = int(gene['hgnc_id'])
    gene_obj['hgnc_id'] = hgnc_id

    # Get the gene information from database
    hgnc_gene = hgncid_to_gene.get(hgnc_id)
    
    inheritance = set()
    hgnc_transcripts = []
    if hgnc_gene:
        # Set the hgnc symbol etc to the one internally in Scout
        gene_obj['hgnc_symbol'] = hgnc_gene['hgnc_symbol']
        gene_obj['ensembl_id'] = hgnc_gene['ensembl_id']
        gene_obj['description'] = hgnc_gene['description']

        if hgnc_gene.get('inheritance_models'):
            gene_obj['inheritance'] = hgnc_gene['inheritance_models']
    
    transcripts = []
    for transcript in gene['transcripts']:
        transcript_obj = build_transcript(transcript)
        transcripts.append(transcript_obj)
    gene_obj['transcripts'] = transcripts

    functional_annotation = gene.get('most_severe_consequence')
    if functional_annotation:
        if not functional_annotation in SO_TERM_KEYS:
            LOG.warning("Invalid functional annotation %s", functional_annotation)
        else:
            gene_obj['functional_annotation'] = functional_annotation
    
    region_annotation = gene.get('region_annotation')
    if region_annotation:
        if not region_annotation in FEATURE_TYPES:
            LOG.warning("Invalid region annotation %s", region_annotation)
        else:
            gene_obj['region_annotation'] = region_annotation
 
    sift_prediction = gene.get('most_severe_sift')
    if sift_prediction:
        if not sift_prediction in CONSEQUENCE:
            LOG.warning("Invalid sift prediction %s", sift_prediction)
        else:
            gene_obj['sift_prediction'] = sift_prediction

    polyphen_prediction = gene.get('most_severe_polyphen')
    if polyphen_prediction:
        if not polyphen_prediction in CONSEQUENCE:
            LOG.warning("Invalid polyphen prediction %s", polyphen_prediction)
        else:
            gene_obj['polyphen_prediction'] = polyphen_prediction
    
    gene_obj['hgvs_identifier'] = gene['hgvs_identifier']
    gene_obj['canonical_transcript'] = gene['canonical_transcript']
    gene_obj['exon'] = gene['exon']
    
    return gene_obj
Build a gene object
        
        Has to build the transcripts for the genes to
    
    Args:
        gene(dict): Parsed information from the VCF
        hgncid_to_gene(dict): A map from hgnc_id  -> hgnc_gene objects 

    Returns:
        gene_obj(dict)
    
    gene = dict(
        # The hgnc gene id
        hgnc_id = int, # required
        hgnc_symbol = str, 
        ensembl_gene_id = str, 
        # A list of Transcript objects
        transcripts = list, # list of <transcript>
        # This is the worst functional impact of all transcripts
        functional_annotation = str, # choices=SO_TERM_KEYS
        # This is the region of the most severe functional impact
        region_annotation = str, # choices=FEATURE_TYPES
        # This is most severe sift prediction of all transcripts
        sift_prediction = str, # choices=CONSEQUENCE
        # This is most severe polyphen prediction of all transcripts
        polyphen_prediction = str, # choices=CONSEQUENCE
    )