def __init__(self, exe_path, logger):
"""Instantiate with location of executable"""
self._logger = logger
self._no_run = False
if not is_exe(exe_path):
self._logger.error("No join_paired_ends.py script (exiting)")
sys.exit(1)
self._exe_path = exe_path
def __init__(self, exe_path, logger):
"""Instantiate with location of executable"""
self._logger = logger
self._no_run = False
if not is_exe(exe_path):
self._logger.error("No blastclust at %s (exiting)" % exe_path)
sys.exit(1)
self._exe_path = exe_path
def __init__(self, exe_path, logger):
"""Instantiate with location of executable"""
self._logger = logger
self._no_run = False
if not is_exe(exe_path):
self._logger.error("No pick_closed_reference_otus.py script " + "(exiting)")
sys.exit(1)
self._exe_path = exe_path
def __init__(self, exe_path, logger):
"""Instantiate with location of executable"""
self._logger = logger
self._no_run = False
if not is_exe(exe_path):
self._logger.error("No SWARM program in PATH (exiting)")
sys.exit(1)
self._exe_path = exe_path
def __init__(self, exe_path, logger):
"""Instantiate with location of executable"""
self._logger = logger
self._no_run = False
if not is_exe(exe_path):
self._logger.error("No trim_quality script available (exiting)")
sys.exit(1)
self._exe_path = exe_path
self.format = 'fastq'
def __init__(self, exe_path, logger):
"""Instantiate with location of executable"""
self._logger = logger
self._no_run = False
if not is_exe(exe_path):
msg = ["trimmomatic executable not valid", "trimming of reads will not be run"]
for m in msg:
self._logger.warning(m)
self._no_run = True
self._exe_path = exe_path
def __init__(self, exe_path, logger):
"""Instantiate with location of executable"""
self._logger = logger
self._no_run = False
if not is_exe(exe_path):
self._logger.error("No convert_format script available (exiting)")
sys.exit(1)
self._exe_path = exe_path
self.informat = "fastq"
self.outformat = "fasta"
