#!/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 Bam_QC.tool.bamqc import bamQC
# ------------------------------------------------------------------------------
[docs]class process_bamqc(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 BamQC")
if configuration is None:
configuration = {}
self.configuration.update(configuration)
[docs] def run(self, input_files, metadata, output_files):
"""
This pipeline analyses a given bam file and produces html file
as the reporting output file.
Parameters
----------
input_files : dict
Dictionary of file locations. These should include:
bam : str
Location for the bam file
metadata : list
Required meta data
output_files : dict
Locations of the output html files returned by the pipeline
Returns
-------
output_files : dict
Locations for the output html
output_metadata : dict
Matching metadata for each of the files
"""
output_results_files = {}
output_metadata = {}
logger.info("bamqc")
# Initialise the test tool
bamqc_handle = bamQC(self.configuration)
logger.progress("BamQC", status="RUNNING")
bqc_files, bqc_meta = bamqc_handle.run(input_files, metadata, output_files)
try:
output_results_files["html"] = bqc_files["html"]
output_metadata["html"] = bqc_meta["html"]
tool_name = output_metadata["html"].meta_data["tool"]
output_metadata["html"].meta_data["tool_description"] = tool_name
output_metadata["html"].meta_data["tool"] = "process_bamqc"
except KeyError:
logger.fatal("BamQC: Error while running")
return {}, {}
return (output_results_files, output_metadata)
# ------------------------------------------------------------------------------
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_bamqc,
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="BamQC Pipeline")
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)