scout/utils/link.py
def add_exac_info(genes, alias_genes, exac_lines):
    """Add information from the exac genes
    
    Currently we only add the pLi score on gene level
    
    The exac resource only use HGNC symbol to identify genes so we need
    our alias mapping.
    
    Args:
        genes(dict): Dictionary with all genes
        alias_genes(dict): Genes mapped to all aliases
        ensembl_lines(iteable): Iteable with raw ensembl info
        
    """
    LOG.info("Add exac pli scores")
    for exac_gene in parse_exac_genes(exac_lines):
        hgnc_symbol = exac_gene['hgnc_symbol'].upper()
        pli_score = exac_gene['pli_score']
        
        for hgnc_id in get_correct_ids(hgnc_symbol, alias_genes):
            genes[hgnc_id]['pli_score'] = pli_score
def add_exac_info(genes, alias_genes, exac_lines):
    """Add information from the exac genes
    
    Currently we only add the pLi score on gene level
    
    The exac resource only use HGNC symbol to identify genes so we need
    our alias mapping.
    
    Args:
        genes(dict): Dictionary with all genes
        alias_genes(dict): Genes mapped to all aliases
        ensembl_lines(iteable): Iteable with raw ensembl info
        
    """
    LOG.info("Add exac pli scores")
    for exac_gene in parse_exac_genes(exac_lines):
        hgnc_symbol = exac_gene['hgnc_symbol'].upper()
        pli_score = exac_gene['pli_score']
        
        for hgnc_id in get_correct_ids(hgnc_symbol, alias_genes):
            genes[hgnc_id]['pli_score'] = pli_score
def add_exac_info ( genes , alias_genes , exac_lines ) : LOG . info ( "Add exac pli scores" ) for exac_gene in parse_exac_genes ( exac_lines ) : hgnc_symbol = exac_gene [ 'hgnc_symbol' ] . upper ( ) pli_score = exac_gene [ 'pli_score' ] for hgnc_id in get_correct_ids ( hgnc_symbol , alias_genes ) : genes [ hgnc_id ] [ 'pli_score' ] = pli_score
Add information from the exac genes
    
    Currently we only add the pLi score on gene level
    
    The exac resource only use HGNC symbol to identify genes so we need
    our alias mapping.
    
    Args:
        genes(dict): Dictionary with all genes
        alias_genes(dict): Genes mapped to all aliases
        ensembl_lines(iteable): Iteable with raw ensembl info
Add information from the exac genes Currently we only add the pLi score on gene level The exac resource only use HGNC symbol to identify genes so we need our alias mapping . Args : genes ( dict ) : Dictionary with all genes alias_genes ( dict ) : Genes mapped to all aliases ensembl_lines ( iteable ) : Iteable with raw ensembl info