scout/commands/update/genes.py
def genes(context, build, api_key):
    """
    Load the hgnc aliases to the mongo database.
    """
    LOG.info("Running scout update genes")
    adapter = context.obj['adapter']

    # Fetch the omim information
    api_key = api_key or context.obj.get('omim_api_key')
    if not api_key:
        LOG.warning("Please provide a omim api key to load the omim gene panel")
        context.abort()

    try:
        mim_files = fetch_mim_files(api_key, mim2genes=True, morbidmap=True, genemap2=True)
    except Exception as err:
        LOG.warning(err)
        context.abort()

    LOG.warning("Dropping all gene information")
    adapter.drop_genes(build)
    LOG.info("Genes dropped")
    LOG.warning("Dropping all transcript information")
    adapter.drop_transcripts(build)
    LOG.info("transcripts dropped")

    hpo_genes = fetch_hpo_genes()
    
    if build:
        builds = [build]
    else:
        builds = ['37', '38']
    
    hgnc_lines = fetch_hgnc()
    exac_lines = fetch_exac_constraint()
    
    
    for build in builds:
        ensembl_genes = fetch_ensembl_genes(build=build)
        
        # load the genes
        hgnc_genes = load_hgnc_genes(
            adapter=adapter,
            ensembl_lines=ensembl_genes,
            hgnc_lines=hgnc_lines,
            exac_lines=exac_lines,
            mim2gene_lines=mim_files['mim2genes'],
            genemap_lines=mim_files['genemap2'],
            hpo_lines=hpo_genes,
            build=build,
        )

        ensembl_genes = {}
        for gene_obj in hgnc_genes:
            ensembl_id = gene_obj['ensembl_id']
            ensembl_genes[ensembl_id] = gene_obj

        # Fetch the transcripts from ensembl
        ensembl_transcripts = fetch_ensembl_transcripts(build=build)
        
        transcripts = load_transcripts(adapter, ensembl_transcripts, build, ensembl_genes)

    adapter.update_indexes()
        
    LOG.info("Genes, transcripts and Exons loaded")
def genes(context, build, api_key):
    """
    Load the hgnc aliases to the mongo database.
    """
    LOG.info("Running scout update genes")
    adapter = context.obj['adapter']

    # Fetch the omim information
    api_key = api_key or context.obj.get('omim_api_key')
    if not api_key:
        LOG.warning("Please provide a omim api key to load the omim gene panel")
        context.abort()

    try:
        mim_files = fetch_mim_files(api_key, mim2genes=True, morbidmap=True, genemap2=True)
    except Exception as err:
        LOG.warning(err)
        context.abort()

    LOG.warning("Dropping all gene information")
    adapter.drop_genes(build)
    LOG.info("Genes dropped")
    LOG.warning("Dropping all transcript information")
    adapter.drop_transcripts(build)
    LOG.info("transcripts dropped")

    hpo_genes = fetch_hpo_genes()
    
    if build:
        builds = [build]
    else:
        builds = ['37', '38']
    
    hgnc_lines = fetch_hgnc()
    exac_lines = fetch_exac_constraint()
    
    
    for build in builds:
        ensembl_genes = fetch_ensembl_genes(build=build)
        
        # load the genes
        hgnc_genes = load_hgnc_genes(
            adapter=adapter,
            ensembl_lines=ensembl_genes,
            hgnc_lines=hgnc_lines,
            exac_lines=exac_lines,
            mim2gene_lines=mim_files['mim2genes'],
            genemap_lines=mim_files['genemap2'],
            hpo_lines=hpo_genes,
            build=build,
        )

        ensembl_genes = {}
        for gene_obj in hgnc_genes:
            ensembl_id = gene_obj['ensembl_id']
            ensembl_genes[ensembl_id] = gene_obj

        # Fetch the transcripts from ensembl
        ensembl_transcripts = fetch_ensembl_transcripts(build=build)
        
        transcripts = load_transcripts(adapter, ensembl_transcripts, build, ensembl_genes)

    adapter.update_indexes()
        
    LOG.info("Genes, transcripts and Exons loaded")
Load the hgnc aliases to the mongo database.