Outputs

cmuts writes HDF5 files with a consistent schema, containing output reactivity values, statistical errors, and coverage statistics.

File Attributes

Every file records what produced it, on the root group. These are attributes and not datasets, so h5py reads them from f.attrs.

Attribute	Description
program	The name of the program that produced this file.
version	The version of cmuts that produced this file.

with h5py.File("output.h5") as f:
    print(f.attrs["program"], f.attrs["version"])

Output Datasets

Which datasets a file holds depends on what wrote it, and so does what the numbers in them mean. Each program’s page lists the datasets it writes and describes them as they stand in its own output.

Mixed-Length Libraries

For the datasets whose size depends on the reference lengths, the size is always chosen to be the length of the longest reference. For libraries with mixed-length sequences, the rows in the reactivity, error, and coverage datasets are padded with NaN beyond the length of that row’s reference.

Warning

NaNs also appear at low-depth bases in the reactivity and error datasets.

Reading Outputs

import h5py
import numpy as np

with h5py.File("output.h5") as f:
    reactivity = f["reactivity"][:]
    error = f["error"][:]

Signal-To-Noise

snr = reactivity / error                     # per-base
snr = np.mean(reactivity / error, axis=-1)   # per-reference