How to use the refgenie.exceptions.RefgenieError function in refgenie
To help you get started, we’ve selected a few refgenie examples, based on popular ways it is used in public projects.
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databio / refgenie / refgenie / exceptions.py View on Github 
""" Exception for when a genome config filepath doesn't point to a file. """
def __init__(self, conf_file=None):
"""
Create the error message, using optionally an attempt filepath.
:param str conf_file: path attempted to be used as genome config file
"""
msg = "You must provide a config file either as an argument or via an environment variable: {}"\
.format(", ".join(CFG_ENV_VARS))
if conf_file:
msg = "Not a file {} -- {}.".format(conf_file, msg)
super(MissingGenomeConfigError, self).__init__(msg)
class MissingFolderError(RefgenieError):
def __init__(self, folder):
"""
Create the error message.
:param str folder: path attempted to be used as folder to save a file to
"""
super(MissingFolderError, self).__init__(folder)from refgenconf import CFG_ENV_VARS
__all__ = ["RefgenieError", "MissingGenomeConfigError"]
class RefgenieError(Exception):
""" Base refgenie exception type """
pass
class MissingGenomeConfigError(RefgenieError):
""" Exception for when a genome config filepath doesn't point to a file. """
def __init__(self, conf_file=None):
"""
Create the error message, using optionally an attempt filepath.
:param str conf_file: path attempted to be used as genome config file
"""
msg = "You must provide a config file either as an argument or via an environment variable: {}"\
.format(", ".join(CFG_ENV_VARS))
if conf_file:
msg = "Not a file {} -- {}.".format(conf_file, msg)
super(MissingGenomeConfigError, self).__init__(msg)
class MissingFolderError(RefgenieError):refgenie
Refgenie creates a standardized folder structure for reference genome files and indexes. You can download pre-built genomes or build your own for any fasta file
