scout/utils/link.py
def add_omim_info(genes, alias_genes, genemap_lines, mim2gene_lines):
    """Add omim information
    
    We collect information on what phenotypes that are associated with a gene,
    what inheritance models that are associated and the correct omim id.
    
    Args:
        genes(dict): Dictionary with all genes
        alias_genes(dict): Genes mapped to all aliases
        genemap_lines(iterable): Iterable with raw omim info
        mim2gene_lines(iterable): Iterable with raw omim info

    """
    LOG.info("Add omim info")
    omim_genes = get_mim_genes(genemap_lines, mim2gene_lines)
    
    for hgnc_symbol in omim_genes:
        omim_info = omim_genes[hgnc_symbol]
        inheritance = omim_info.get('inheritance', set())
        
        for hgnc_id in get_correct_ids(hgnc_symbol, alias_genes):
            gene_info = genes[hgnc_id]

            # Update the omim id to the one found in omim
            gene_info['omim_id'] = omim_info['mim_number']

            gene_info['inheritance_models'] = list(inheritance)
            gene_info['phenotypes'] = omim_info.get('phenotypes', [])
def add_omim_info(genes, alias_genes, genemap_lines, mim2gene_lines):
    """Add omim information
    
    We collect information on what phenotypes that are associated with a gene,
    what inheritance models that are associated and the correct omim id.
    
    Args:
        genes(dict): Dictionary with all genes
        alias_genes(dict): Genes mapped to all aliases
        genemap_lines(iterable): Iterable with raw omim info
        mim2gene_lines(iterable): Iterable with raw omim info

    """
    LOG.info("Add omim info")
    omim_genes = get_mim_genes(genemap_lines, mim2gene_lines)
    
    for hgnc_symbol in omim_genes:
        omim_info = omim_genes[hgnc_symbol]
        inheritance = omim_info.get('inheritance', set())
        
        for hgnc_id in get_correct_ids(hgnc_symbol, alias_genes):
            gene_info = genes[hgnc_id]

            # Update the omim id to the one found in omim
            gene_info['omim_id'] = omim_info['mim_number']

            gene_info['inheritance_models'] = list(inheritance)
            gene_info['phenotypes'] = omim_info.get('phenotypes', [])
Add omim information
    
    We collect information on what phenotypes that are associated with a gene,
    what inheritance models that are associated and the correct omim id.
    
    Args:
        genes(dict): Dictionary with all genes
        alias_genes(dict): Genes mapped to all aliases
        genemap_lines(iterable): Iterable with raw omim info
        mim2gene_lines(iterable): Iterable with raw omim info