cmuts csv

Purpose

Converting a cmuts HDF5 file into a comma-separated table.

Requires

• A cmuts-compatible HDF5 file

Usage

Provide the HDF5 file and redirect the output to a file.

cmuts csv reactivity.h5 > reactivity.csv

Providing a FASTA populates the reference column with the corresponding name.

cmuts csv -f references.fasta reactivity.h5 > reactivity.csv

Input

Dataset	Input
mismatches/rate	if present
mismatches/error	if present
insertions/rate	if present
insertions/error	if present
deletions/rate	if present
deletions/error	if present
terminations/rate	if present
terminations/error	if present
coverage	required
sequence	required

All other datasets in an input are ignored.

Output

Each row is one position in one reference. The first three columns identify the position as follows.

Column	Meaning
reference	the reference number, or the name of the record in the FASTA
position	the position in the reference, counting from one
base	the base at that position, taken from the sequence dataset

Each column after these is one dataset of the input, under the name it has in the format. NaN values are converted to empty fields.

In ragged libraries references are not padded.

CLI Options

Arguments

Argument	Description
HDF5	the cmuts output to convert

Input

Option	Description
-f, --fasta FASTA	populate the reference field with the names from this file (default: the reference number)

Information

Option	Description
-h, --help	show this help and exit
-V, --version	show the version and exit

Advanced

Accepted, and left out of --help.

Option	Description
--dump-options	describe every argument as JSON and exit
--dump-layout	describe the input format as JSON and exit