Exemple #1
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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))
Exemple #2
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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))
Exemple #3
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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)
Exemple #4
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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)