kb_python.validate

Module Contents

Functions

validate_bus(path)	Verify if the provided BUS file is valid.
validate_mtx(path)	Verify if the provided Matrix Market (.mtx) file is valid.
validate(path)	Validate a file.
validate_files(pre=True, post=True)	Function decorator to validate input/output files.

Attributes

BUSTOOLS_INSPECT_PARSER
VALIDATORS

kb_python.validate.BUSTOOLS_INSPECT_PARSER

exception kb_python.validate.FileVerificationFailed

Bases: Exception

Common base class for all non-exit exceptions.

kb_python.validate.validate_bus(path)

Verify if the provided BUS file is valid.

A BUS file is considered valid when bustools inspect can read the file + it has > 0 BUS records.

Parameters

path (str) – path to BUS file

Raises

• FileVerificationFailed – if the file failed verification

• subprocess.CalledProcessError – if the bustools command failed

kb_python.validate.validate_mtx(path)

Verify if the provided Matrix Market (.mtx) file is valid.

A BUS file is considered valid when the file can be read with scipy.io.mmread.

Parameters

path (str) – path to mtx file

Raises

FileVerificationFailed – if the file failed verification

kb_python.validate.VALIDATORS

kb_python.validate.validate(path)

Validate a file.

This function is a wrapper around all validation functions. Given a path, it chooses the correct validation function. This function assumes the file exists.

Parameters

path (str) – path to file

Raises

FileVerificationFailed – if the file failed verification

kb_python.validate.validate_files(pre=True, post=True)

Function decorator to validate input/output files.

This function does not validate when the current run is a dry run.

Parameters

• pre (bool) – whether to validate input files, defaults to True

• post (bool) – whether to validate output files, defaults to True

Returns

wrapped function

Return type

function