scout/load/hgnc_gene.py
def load_hgnc(adapter, genes=None, ensembl_lines=None, hgnc_lines=None, exac_lines=None, mim2gene_lines=None,
              genemap_lines=None, hpo_lines=None, transcripts_lines=None, build='37', omim_api_key=''):
    """Load Genes and transcripts into the database
              
    If no resources are provided the correct ones will be fetched.
    
    Args:
        adapter(scout.adapter.MongoAdapter)
        genes(dict): If genes are already parsed
        ensembl_lines(iterable(str)): Lines formated with ensembl gene information
        hgnc_lines(iterable(str)): Lines with gene information from genenames.org
        exac_lines(iterable(str)): Lines with information pLi-scores from ExAC
        mim2gene(iterable(str)): Lines with map from omim id to gene symbol
        genemap_lines(iterable(str)): Lines with information of omim entries
        hpo_lines(iterable(str)): Lines information about map from hpo terms to genes
        transcripts_lines(iterable): iterable with ensembl transcript lines
        build(str): What build to use. Defaults to '37'

    """
    gene_objs = load_hgnc_genes(
        adapter=adapter, 
        genes = genes, 
        ensembl_lines=ensembl_lines, 
        hgnc_lines=hgnc_lines, 
        exac_lines=exac_lines, 
        mim2gene_lines=mim2gene_lines,
        genemap_lines=genemap_lines, 
        hpo_lines=hpo_lines, 
        build=build, 
        omim_api_key=omim_api_key,
    )
    
    ensembl_genes = {}
    for gene_obj in gene_objs:
        ensembl_genes[gene_obj['ensembl_id']] = gene_obj
    
    transcript_objs = load_transcripts(
        adapter=adapter, 
        transcripts_lines=transcripts_lines, 
        build=build, 
        ensembl_genes=ensembl_genes)
def load_hgnc(adapter, genes=None, ensembl_lines=None, hgnc_lines=None, exac_lines=None, mim2gene_lines=None,
              genemap_lines=None, hpo_lines=None, transcripts_lines=None, build='37', omim_api_key=''):
    """Load Genes and transcripts into the database
              
    If no resources are provided the correct ones will be fetched.
    
    Args:
        adapter(scout.adapter.MongoAdapter)
        genes(dict): If genes are already parsed
        ensembl_lines(iterable(str)): Lines formated with ensembl gene information
        hgnc_lines(iterable(str)): Lines with gene information from genenames.org
        exac_lines(iterable(str)): Lines with information pLi-scores from ExAC
        mim2gene(iterable(str)): Lines with map from omim id to gene symbol
        genemap_lines(iterable(str)): Lines with information of omim entries
        hpo_lines(iterable(str)): Lines information about map from hpo terms to genes
        transcripts_lines(iterable): iterable with ensembl transcript lines
        build(str): What build to use. Defaults to '37'

    """
    gene_objs = load_hgnc_genes(
        adapter=adapter, 
        genes = genes, 
        ensembl_lines=ensembl_lines, 
        hgnc_lines=hgnc_lines, 
        exac_lines=exac_lines, 
        mim2gene_lines=mim2gene_lines,
        genemap_lines=genemap_lines, 
        hpo_lines=hpo_lines, 
        build=build, 
        omim_api_key=omim_api_key,
    )
    
    ensembl_genes = {}
    for gene_obj in gene_objs:
        ensembl_genes[gene_obj['ensembl_id']] = gene_obj
    
    transcript_objs = load_transcripts(
        adapter=adapter, 
        transcripts_lines=transcripts_lines, 
        build=build, 
        ensembl_genes=ensembl_genes)
Load Genes and transcripts into the database
              
    If no resources are provided the correct ones will be fetched.
    
    Args:
        adapter(scout.adapter.MongoAdapter)
        genes(dict): If genes are already parsed
        ensembl_lines(iterable(str)): Lines formated with ensembl gene information
        hgnc_lines(iterable(str)): Lines with gene information from genenames.org
        exac_lines(iterable(str)): Lines with information pLi-scores from ExAC
        mim2gene(iterable(str)): Lines with map from omim id to gene symbol
        genemap_lines(iterable(str)): Lines with information of omim entries
        hpo_lines(iterable(str)): Lines information about map from hpo terms to genes
        transcripts_lines(iterable): iterable with ensembl transcript lines
        build(str): What build to use. Defaults to '37'