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)
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 = '' ) : 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'
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