#!/usr/bin/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_files.tool.json_3d_indexer import json3dIndexerTool
# ------------------------------------------------------------------------------
[docs]class process_json_3d(Workflow):
"""
Workflow to index JSON formatted files within the Multiscale Genomics (MuG)
Virtural Research Environment (VRE) that have been generated as part of the
Hi-C analysis pipeline to model the 3D structure of the genome within the
nucleus of the cell.
"""
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("Process 3D Models file")
if configuration is None:
configuration = {}
self.configuration.update(configuration)
[docs] def run(self, input_files, metadata, output_files):
"""
Main run function to index the 3D JSON files that have been generated
as part of the Hi-C analysis pipeline to model the 3D structure of the
genome within the nucleus of the cellready for use in the RESTful API.
Parameters
----------
files_ids : list
file : str
Location of the tar.gz file of JSON files representing the 3D
models of the nucleus
metadata : list
Returns
-------
outputfiles : list
List with the location of the HDF5 index file for the given dataset
"""
j3dit = json3dIndexerTool()
hdf5_idx, hdf5_meta = j3dit.run(
{
"modles": input_files["models"],
}, {
"models": metadata["models"],
}, {
"index": output_files["index"]
}
)
return (hdf5_idx, hdf5_meta)
# ------------------------------------------------------------------------------
def main_json(config, in_metadata, out_metadata):
"""
Alternative 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_json_3d,
config,
in_metadata,
out_metadata)
# 2. The App has finished
logger.info("2. Execution finished; see " + out_metadata)
return result
# ------------------------------------------------------------------------------
if __name__ == "__main__":
import sys
sys._run_from_cmdl = True # pylint: disable=protected-access
# Set up the command line parameters
PARSER = argparse.ArgumentParser(description="Index BED 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")
# 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
RESULTS = main_json(CONFIG, IN_METADATA, OUT_METADATA)