def gene(context, pretty, gene): """Calculate stats for a given gene.""" query = context.obj['db'].gene_metrics(*gene) columns = ['sample_id'] + STAT_COLUMNS + ['gene_id'] for result in query: row = {column: value for column, value in zip(columns, result)} click.echo(dump_json(row, pretty=pretty))
def mean(context, sample, pretty): """Calculate mean statistics.""" query = context.obj['db'].mean(sample_ids=sample) columns = ['sample_id'] + STAT_COLUMNS for result in query: row = {column: value for column, value in zip(columns, result)} click.echo(dump_json(row, pretty=pretty))
def extra_fields(columns): """Parse additional, chanjo specific fields. Contains transcript and gene ids. Args: columns (List[str]): list of two columns with related element ids Returns: List[tuple]: list of tuples with paired elements """ try: transcripts = columns[0].split(',') genes = columns[1].split(',') except IndexError: return [] return zip(transcripts, genes)
def extra_fields(columns): """Parse additional, chanjo specific fields. Contains transcript and gene ids. Args: columns (List[str]): list of two columns with related element ids Returns: List[tuple]: list of tuples with paired elements """ try: transcripts = columns[0].split(",") genes = columns[1].split(",") except IndexError: return [] return zip(transcripts, genes)