def remove_intermediate_files(self, out_dir, workflow_name):
"""Remove intermediate files from the output directory.
Parameters
----------
out_dir : str
The output directory.
"""
misc = Misc()
misc.remove_intermediate_files(out_dir, workflow_name)
self.logger.info('Done.')
def check_install(self):
""" Verify all GTDB-Tk data files are present.
Raises
------
ReferenceFileMalformed
If one or more reference files are malformed.
"""
self.logger.info("Running install verification")
misc = Misc()
misc.check_install()
self.logger.info('Done.')
def export_msa(self, options):
"""Export the untrimmed archaeal or bacterial MSA file.
Parameters
----------
options : argparse.Namespace
The CLI arguments input by the user.
"""
misc = Misc()
misc.export_msa(options.domain, options.output)
self.logger.info('Done.')
def convert_to_itol(self, options):
"""Convert Tree to iTOL format.
Parameters
----------
options : argparse.Namespace
The CLI arguments input by the user.
"""
check_file_exists(options.input_tree)
r = Misc()
r.convert_to_itol(options.input_tree, options.output_tree)
self.logger.info('Done.')
def remove_labels(self, options):
"""Remove labels from tree.
Parameters
----------
options : argparse.Namespace
The CLI arguments input by the user.
"""
check_file_exists(options.input_tree)
r = Misc()
r.remove_labels(options.input_tree, options.output_tree)
self.logger.info('Done.')
def trim_msa(self, options):
""" Trim an untrimmed archaea or bacterial MSA file.
Parameters
----------
options : argparse.Namespace
The CLI arguments input by the user.
"""
if options.reference_mask in ['bac', 'arc']:
mask_type = "reference"
mask_id = options.reference_mask
else:
mask_type = "file"
mask_id = options.mask_file
misc = Misc()
misc.trim_msa(options.untrimmed_msa, mask_type,
mask_id, options.output)
self.logger.info('Done.')