scout/utils/link.py
def add_ensembl_info(genes, ensembl_lines):
    """Add the coordinates from ensembl
    
    Args:
        genes(dict): Dictionary with all genes
        ensembl_lines(iteable): Iteable with raw ensembl info
    """
    
    LOG.info("Adding ensembl coordinates")
    # Parse and add the ensembl gene info
    if isinstance(ensembl_lines, DataFrame):
        ensembl_genes = parse_ensembl_gene_request(ensembl_lines)
    else:
        ensembl_genes = parse_ensembl_genes(ensembl_lines)

    for ensembl_gene in ensembl_genes:
        gene_obj = genes.get(ensembl_gene['hgnc_id'])
        if not gene_obj:
            continue
        gene_obj['chromosome'] = ensembl_gene['chrom']
        gene_obj['start'] = ensembl_gene['gene_start']
        gene_obj['end'] = ensembl_gene['gene_end']
        # ensembl ids can differ between builds. There is one stated in HGNC
        # that is true for build 38. So we add information from ensembl
        gene_obj['ensembl_gene_id'] = ensembl_gene['ensembl_gene_id']
def add_ensembl_info(genes, ensembl_lines):
    """Add the coordinates from ensembl
    
    Args:
        genes(dict): Dictionary with all genes
        ensembl_lines(iteable): Iteable with raw ensembl info
    """
    
    LOG.info("Adding ensembl coordinates")
    # Parse and add the ensembl gene info
    if isinstance(ensembl_lines, DataFrame):
        ensembl_genes = parse_ensembl_gene_request(ensembl_lines)
    else:
        ensembl_genes = parse_ensembl_genes(ensembl_lines)

    for ensembl_gene in ensembl_genes:
        gene_obj = genes.get(ensembl_gene['hgnc_id'])
        if not gene_obj:
            continue
        gene_obj['chromosome'] = ensembl_gene['chrom']
        gene_obj['start'] = ensembl_gene['gene_start']
        gene_obj['end'] = ensembl_gene['gene_end']
        # ensembl ids can differ between builds. There is one stated in HGNC
        # that is true for build 38. So we add information from ensembl
        gene_obj['ensembl_gene_id'] = ensembl_gene['ensembl_gene_id']
Add the coordinates from ensembl
    
    Args:
        genes(dict): Dictionary with all genes
        ensembl_lines(iteable): Iteable with raw ensembl info