scout/parse/panel.py
def get_omim_panel_genes(genemap2_lines, mim2gene_lines, alias_genes):
    """Return all genes that should be included in the OMIM-AUTO panel
    Return the hgnc symbols
    
    Genes that have at least one 'established' or 'provisional' phenotype connection
    are included in the gene panel
    
    Args:
        genemap2_lines(iterable)
        mim2gene_lines(iterable)
        alias_genes(dict): A dictionary that maps hgnc_symbol to hgnc_id
    
    Yields:
        hgnc_symbol(str)
    """
    parsed_genes = get_mim_genes(genemap2_lines, mim2gene_lines)
    
    STATUS_TO_ADD = set(['established', 'provisional'])
    
    for hgnc_symbol in parsed_genes:
        try:
            gene = parsed_genes[hgnc_symbol]
            keep = False
            for phenotype_info in gene.get('phenotypes',[]):
                if phenotype_info['status'] in STATUS_TO_ADD:
                    keep = True
                    break
            if keep:
                hgnc_id_info = alias_genes.get(hgnc_symbol)
                if not hgnc_id_info:
                    for symbol in gene.get('hgnc_symbols', []):
                        if symbol in alias_genes:
                            hgnc_id_info = alias_genes[symbol]
                            break

                if hgnc_id_info:
                    yield {
                    'hgnc_id': hgnc_id_info['true'],
                    'hgnc_symbol': hgnc_symbol,
                    }
                else:
                    LOG.warning("Gene symbol %s does not exist", hgnc_symbol)
                    
        except KeyError:
            pass
def get_omim_panel_genes(genemap2_lines, mim2gene_lines, alias_genes):
    """Return all genes that should be included in the OMIM-AUTO panel
    Return the hgnc symbols
    
    Genes that have at least one 'established' or 'provisional' phenotype connection
    are included in the gene panel
    
    Args:
        genemap2_lines(iterable)
        mim2gene_lines(iterable)
        alias_genes(dict): A dictionary that maps hgnc_symbol to hgnc_id
    
    Yields:
        hgnc_symbol(str)
    """
    parsed_genes = get_mim_genes(genemap2_lines, mim2gene_lines)
    
    STATUS_TO_ADD = set(['established', 'provisional'])
    
    for hgnc_symbol in parsed_genes:
        try:
            gene = parsed_genes[hgnc_symbol]
            keep = False
            for phenotype_info in gene.get('phenotypes',[]):
                if phenotype_info['status'] in STATUS_TO_ADD:
                    keep = True
                    break
            if keep:
                hgnc_id_info = alias_genes.get(hgnc_symbol)
                if not hgnc_id_info:
                    for symbol in gene.get('hgnc_symbols', []):
                        if symbol in alias_genes:
                            hgnc_id_info = alias_genes[symbol]
                            break

                if hgnc_id_info:
                    yield {
                    'hgnc_id': hgnc_id_info['true'],
                    'hgnc_symbol': hgnc_symbol,
                    }
                else:
                    LOG.warning("Gene symbol %s does not exist", hgnc_symbol)
                    
        except KeyError:
            pass
def get_omim_panel_genes ( genemap2_lines , mim2gene_lines , alias_genes ) : parsed_genes = get_mim_genes ( genemap2_lines , mim2gene_lines ) STATUS_TO_ADD = set ( [ 'established' , 'provisional' ] ) for hgnc_symbol in parsed_genes : try : gene = parsed_genes [ hgnc_symbol ] keep = False for phenotype_info in gene . get ( 'phenotypes' , [ ] ) : if phenotype_info [ 'status' ] in STATUS_TO_ADD : keep = True break if keep : hgnc_id_info = alias_genes . get ( hgnc_symbol ) if not hgnc_id_info : for symbol in gene . get ( 'hgnc_symbols' , [ ] ) : if symbol in alias_genes : hgnc_id_info = alias_genes [ symbol ] break if hgnc_id_info : yield { 'hgnc_id' : hgnc_id_info [ 'true' ] , 'hgnc_symbol' : hgnc_symbol , } else : LOG . warning ( "Gene symbol %s does not exist" , hgnc_symbol ) except KeyError : pass
Return all genes that should be included in the OMIM-AUTO panel
    Return the hgnc symbols
    
    Genes that have at least one 'established' or 'provisional' phenotype connection
    are included in the gene panel
    
    Args:
        genemap2_lines(iterable)
        mim2gene_lines(iterable)
        alias_genes(dict): A dictionary that maps hgnc_symbol to hgnc_id
    
    Yields:
        hgnc_symbol(str)
Return all genes that should be included in the OMIM - AUTO panel Return the hgnc symbols Genes that have at least one established or provisional phenotype connection are included in the gene panel Args : genemap2_lines ( iterable ) mim2gene_lines ( iterable ) alias_genes ( dict ) : A dictionary that maps hgnc_symbol to hgnc_id Yields : hgnc_symbol ( str )