def convert(shock_url, shock_id, handle_url, handle_id, input_filename, output_filename, level=logging.INFO, logger=None):
"""
Converts FASTA file to KBaseAssembly.SingleEndLibrary json string.
Args:
shock_url: A url for the KBase SHOCK service.
handle_url: A url for the KBase Handle Service.
shock_id: A KBase SHOCK node id.
handle_id: A KBase Handle id.
input_filename: A file name for the input FASTA data.
output_filename: A file name where the output JSON string should be stored.
level: Logging level, defaults to logging.INFO.
"""
if logger is None:
logger = script_utils.getStderrLogger(__file__)
logger.info("Starting conversion of FASTA to KBaseAssembly.SingleEndLibrary.")
token = os.environ.get('KB_AUTH_TOKEN')
logger.info("Gathering information.")
handles = script_utils.getHandles(logger, shock_url, handle_url, [shock_id], [handle_id],token)
assert len(handles) != 0
objectString = json.dumps({"handle" : handles[0]}, sort_keys=True, indent=4)
return objectString
def convert(
workspace_service_url,
shock_service_url,
handle_service_url,
workspace_name,
object_name,
working_directory,
level=logging.INFO,
logger=None,
):
"""
Converts KBaseAssembly.SingleEndLibrary to a Fasta file of assembledDNA.
Args:
workspace_service_url : A url for the KBase Workspace service
shock_service_url: A url for the KBase SHOCK service.
handle_service_url: A url for the KBase Handle Service.
workspace_name : Name of the workspace
object_name : Name of the object in the workspace
working_directory : The working directory for where the output file should be stored.
level: Logging level, defaults to logging.INFO.
"""
if not os.path.isdir(args.working_directory):
raise Exception("The working directory does not exist {0} does not exist".format(working_directory))
md5 = None
if logger is None:
logger = script_utils.getStderrLogger(__file__)
logger.info("Starting conversion of KBaseAssembly.SingleEndLibrary to FASTA.")
token = os.environ.get("KB_AUTH_TOKEN")
logger.info("Gathering information.")
ws_client = biokbase.workspace.client.Workspace("https://kbase.us/services/ws")
single_end_library = ws_client.get_objects([{"workspace": workspace_name, "name": object_name}])[0]["data"]
shock_id = None
if "handle" in single_end_library and "id" in single_end_library["handle"]:
shock_id = single_end_library["handle"]["id"]
if shock_id is None:
raise Exception("There was not shock id found.")
# if "handle" in ws_object and "remote_md5" in single_end_library['handle']:
# md5 = single_end_library['handle']['remote_md5']
script_utils.download_file_from_shock(logger, shock_service_url, shock_id, working_directory, token)
logger.info("Conversion completed.")
def convert(workspace_service_url, shock_service_url, handle_service_url, workspace_name, object_name, working_directory, level=logging.INFO, logger=None):
"""
Converts KBaseAssembly.SingleEndLibrary to a Fasta file of assembledDNA.
Args:
workspace_service_url : A url for the KBase Workspace service
shock_service_url: A url for the KBase SHOCK service.
handle_service_url: A url for the KBase Handle Service.
workspace_name : Name of the workspace
object_name : Name of the object in the workspace
working_directory : The working directory for where the output file should be stored.
level: Logging level, defaults to logging.INFO.
"""
if not os.path.isdir(args.working_directory):
raise Exception("The working directory does not exist {0} does not exist".format(working_directory))
md5 = None
if logger is None:
logger = script_utils.getStderrLogger(__file__)
logger.info("Starting conversion of KBaseAssembly.SingleEndLibrary to FASTA.")
token = os.environ.get('KB_AUTH_TOKEN')
logger.info("Gathering information.")
ws_client = biokbase.workspace.client.Workspace('https://kbase.us/services/ws')
single_end_library = ws_client.get_objects([{'workspace':workspace_name,'name':object_name}])[0]['data']
shock_id = None
if "handle" in single_end_library and "id" in single_end_library['handle']:
shock_id = single_end_library['handle']['id']
if shock_id is None:
raise Exception("There was not shock id found.")
# if "handle" in ws_object and "remote_md5" in single_end_library['handle']:
# md5 = single_end_library['handle']['remote_md5']
script_utils.download_file_from_shock(logger, shock_service_url, shock_id, working_directory, token)
logger.info("Conversion completed.")
if __name__ == "__main__":
parser = argparse.ArgumentParser(prog='trns_transform_KBaseAssembly.FA-to-KBaseAssembly.SingleEndLibrary',
description='Converts FASTA file to KBaseAssembly.SingleEndLibrary json string.',
epilog='Authors: Matt Henderson')
parser.add_argument('-s', '--shock_url', help='Shock url', action='store', type=str, default='https://kbase.us/services/shock-api/', nargs='?')
parser.add_argument('-n', '--handle_url', help='Handle service url', action='store', type=str, default='https://kbase.us/services/handle_service/', nargs='?')
parser.add_argument('-f','--input_filename', help ='Input file name', action='store', type=str, nargs='?', required=False)
parser.add_argument('-o', '--output_filename', help='Output file name', action='store', type=str, nargs='?', required=True)
parser.add_argument('-r','--reference_name',help='Reference name', action='store', type=str, nargs='?',default=None)
data_id = parser.add_mutually_exclusive_group(required=True)
data_id.add_argument('-i', '--shock_id', help='Shock node id', action='store', type=str, nargs='?')
data_id.add_argument('-d','--handle_id', help ='Handle id', action= 'store', type=str, nargs='?')
args = parser.parse_args()
logger = script_utils.getStderrLogger(__file__)
try:
ret_json = json.loads(convert(args.shock_url, args.shock_id, args.handle_url, args.handle_id, args.input_filename, args.output_filename,logger=logger))
if args.reference_name is not None:
ret_json["reference_name"] = args.reference_name
logger.info("Writing out JSON.")
with open(args.output_filename, "w") as outFile:
outFile.write(json.dumps(ret_json,sort_keys = True, indent = 4))
logger.info("Conversion completed.")
except:
logger.exception("".join(traceback.format_exc()))
sys.exit(1)
sys.exit(0)
