genomepy.utils

Utility functions

Functions

check_ucsc_tools([tools])	Check if UCSC tools for gene annotation conversion are installed.
cleanpath(path)	Expand any path input to a literal path output
cmd_ok(cmd)	Returns True if cmd can be run.
get_genomename(name)	return the name of the genome without path or extensions
get_genomes_dir([genomes_dir, check_exist])	import genomes_dir if none is given, and check validity
get_localname(name[, localname])	Returns the safe version of the given localname.
get_remotename(name)	try to get the name from the url
mkdir_p(path)	'mkdir -p' in Python
rm_rf(path)	'rm -rf' in Python
run_index_cmd(name, cmd)	Run command, show errors if the returncode is non-zero.
safe(name)	Replace spaces with underscores.
try_except_pass(errors, func, *args, **kwargs)	try to return FUNC with ARGS, pass on ERRORS