#!/usr/bin/env python
"""
.. See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
"""
from __future__ import print_function
import argparse
from basic_modules.workflow import Workflow
from utils import logger
from mg_process_macs2.tool.macs2 import Macs2
# ------------------------------------------------------------------------------
[docs]class process_macs2(Workflow): # pylint: disable=invalid-name,too-few-public-methods
"""
Functions for demonstrating the pipeline set up.
"""
configuration = {}
def __init__(self, configuration=None):
"""
Initialise the tool with its configuration.
Parameters
----------
configuration : dict
a dictionary containing parameters that define how the operation
should be carried out, which are specific to each Tool.
"""
logger.info("Processing Test")
if configuration is None:
configuration = {}
self.configuration.update(configuration)
[docs] def run(self, input_files, metadata, output_files):
"""
Main run function for processing a test file.
Parameters
----------
input_files : dict
Dictionary of file locations
metadata : list
Required meta data
output_files : dict
Locations of the output files to be returned by the pipeline
Returns
-------
output_files : dict
Locations for the output txt
output_metadata : dict
Matching metadata for each of the files
"""
# Initialise the test tool
macs2_handle = Macs2(self.configuration)
macs2_files, macs2_meta = macs2_handle.run(input_files, metadata, output_files)
return (macs2_files, macs2_meta)
# ------------------------------------------------------------------------------
def main_json(config, in_metadata, out_metadata):
"""
Main function
-------------
This function launches the app using configuration written in
two json files: config.json and input_metadata.json.
"""
# 1. Instantiate and launch the App
logger.info("1. Instantiate and launch the App")
from apps.jsonapp import JSONApp
app = JSONApp()
result = app.launch(process_macs2,
config,
in_metadata,
out_metadata)
# 2. The App has finished
logger.info("2. Execution finished; see " + out_metadata)
return result
# ------------------------------------------------------------------------------
if __name__ == "__main__":
# Set up the command line parameters
PARSER = argparse.ArgumentParser(description="Index the genome file")
PARSER.add_argument("--config", help="Configuration file")
PARSER.add_argument("--in_metadata", help="Location of input metadata file")
PARSER.add_argument("--out_metadata", help="Location of output metadata file")
PARSER.add_argument("--local", action="store_const", const=True, default=False)
# Get the matching parameters from the command line
ARGS = PARSER.parse_args()
CONFIG = ARGS.config
IN_METADATA = ARGS.in_metadata
OUT_METADATA = ARGS.out_metadata
LOCAL = ARGS.local
if LOCAL:
import sys
sys._run_from_cmdl = True # pylint: disable=protected-access
RESULTS = main_json(CONFIG, IN_METADATA, OUT_METADATA)
print(RESULTS)