scout/commands/view/aliases.py
def aliases(context, build, symbol):
    """Show all alias symbols and how they map to ids"""
    LOG.info("Running scout view aliases")
    adapter = context.obj['adapter']
    
    if symbol:
        alias_genes = {}
        res = adapter.gene_by_alias(symbol, build=build)
        for gene_obj in res:
            hgnc_id = gene_obj['hgnc_id']
            # Collect the true symbol given by hgnc
            hgnc_symbol = gene_obj['hgnc_symbol']
            # Loop aver all aliases
            for alias in gene_obj['aliases']:
                true_id = None
                # If the alias is the same as hgnc symbol we know the true id
                if alias == hgnc_symbol:
                    true_id = hgnc_id
                # If the alias is already in the list we add the id
                if alias in alias_genes:
                    alias_genes[alias]['ids'].add(hgnc_id)
                    if true_id:
                        alias_genes[alias]['true'] = hgnc_id
                else:
                    alias_genes[alias] = {
                        'true': hgnc_id,
                        'ids': set([hgnc_id])
                    }

    else:
        alias_genes = adapter.genes_by_alias(build=build)
    
    if len(alias_genes) == 0:
        LOG.info("No gene found for build %s", build)
        return

    click.echo("#hgnc_symbol\ttrue_id\thgnc_ids")
    for alias_symbol in alias_genes:
        info = alias_genes[alias_symbol]
        # pp(info)
        click.echo("{0}\t{1}\t{2}\t".format(
            alias_symbol,
            (alias_genes[alias_symbol]['true'] or 'None'),
            ', '.join([str(gene_id) for gene_id in alias_genes[alias_symbol]['ids']])
        )
        )
def aliases(context, build, symbol):
    """Show all alias symbols and how they map to ids"""
    LOG.info("Running scout view aliases")
    adapter = context.obj['adapter']
    
    if symbol:
        alias_genes = {}
        res = adapter.gene_by_alias(symbol, build=build)
        for gene_obj in res:
            hgnc_id = gene_obj['hgnc_id']
            # Collect the true symbol given by hgnc
            hgnc_symbol = gene_obj['hgnc_symbol']
            # Loop aver all aliases
            for alias in gene_obj['aliases']:
                true_id = None
                # If the alias is the same as hgnc symbol we know the true id
                if alias == hgnc_symbol:
                    true_id = hgnc_id
                # If the alias is already in the list we add the id
                if alias in alias_genes:
                    alias_genes[alias]['ids'].add(hgnc_id)
                    if true_id:
                        alias_genes[alias]['true'] = hgnc_id
                else:
                    alias_genes[alias] = {
                        'true': hgnc_id,
                        'ids': set([hgnc_id])
                    }

    else:
        alias_genes = adapter.genes_by_alias(build=build)
    
    if len(alias_genes) == 0:
        LOG.info("No gene found for build %s", build)
        return

    click.echo("#hgnc_symbol\ttrue_id\thgnc_ids")
    for alias_symbol in alias_genes:
        info = alias_genes[alias_symbol]
        # pp(info)
        click.echo("{0}\t{1}\t{2}\t".format(
            alias_symbol,
            (alias_genes[alias_symbol]['true'] or 'None'),
            ', '.join([str(gene_id) for gene_id in alias_genes[alias_symbol]['ids']])
        )
        )
Show all alias symbols and how they map to ids