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"