shapToBigwig

Help Info

Take an hdf5-format file generated by the flat shap script and render it to a bigwig.

usage: shapToBigwig [-h] [--h5 H5] [--bw BW] [--verbose]

Named Arguments

--h5

The name of the hdf5-format file to be read in.

--bw

The name of the bigwig file that should be written.

--verbose

Print progress messages.

Default: False

Usage

A little script that takes an hdf5 generated by interpretFlat and renders a bigwig file.

class bpreveal.shapToBigwig.BatchedH5Reader(h5fp, batchSize)

Read in an hdf5 in chunks.

Parameters:

• batchSize (int) – The number of elements that should be read in at once

• h5fp (File) – The (open) hdf5 file object to read from.

readScore(idx)

Read in score information from the hdf5.

Parameters:

idx (int) – The index of the score that we want to read.

Returns:

An array of shape (input-length, NUM_BASES) containing hypothetical scores.

Return type:

ndarray[tuple[Any, …], dtype[float16]]

readSeq(idx)

Read in sequence information from the hdf5.

Parameters:

idx (int) – The index of the sequence to read.

Returns:

One-hot encoded sequences, shape (input-length, NUM_BASES)

Return type:

ndarray[tuple[Any, …], dtype[uint8]]

bpreveal.shapToBigwig.writeBigWig(inH5, outFname)

Write the data in the h5 file to a bigwig on disk.

Parameters:

• inH5 (File) – The (open) hdf5 file to use

• outFname (str) – The name of the bigwig to save

Return type:

None

bpreveal.shapToBigwig.getParser()

Generate (but don’t parse_args()) the parser.

Returns:

An ArgumentParser, ready to call parse_args()

Return type:

ArgumentParser

bpreveal.shapToBigwig.main()

Run the program.

Return type:

None