#!/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 CHiC.tool.bam2chicago_tool import bam2chicagoTool
################################################
[docs]class process_bam2chicago(Workflow):
"""
This class creates .chinput files.
input files for CHiCAGO
"""
def __init__(self, configuration=None):
"""
initiate the class
Parameters
----------
configuration: dict
dictionary with parameters for different Tools, indicating
how to run each of them
"""
logger.info("Initialising process_bam2chicago")
if configuration is None:
configuration = {}
self.configuration.update(configuration)
[docs] def run(self, input_files, metadata, output_files):
"""
This is the main function that run the tools to create
.chinput files
Parameters
----------
input_files: dict
BAM: str
path to BAM files
RMAP: str
path to RMAP file
BAITMAP: str
path to BAITMAP file
metadata: dict
input metadata
Returns
-------
bool
output_metadata: dict
metadata for .chinput file
"""
try:
bam2chicago_caller = bam2chicagoTool(self.configuration)
output_files_bam2chicago, output_metadata_bam2chicago = bam2chicago_caller.run(
input_files, metadata, output_files
)
return output_files_bam2chicago, output_metadata_bam2chicago
except IOError:
logger.fatal("process_bam2chicago failed to generate .chinput files")
#############################################################
def main_json(config, in_metadata, out_metadata):
"""
Alternative main function
This function launch the app using the configuration written
in two json files: config_process_rmapBaitmap.json and
input_process_rmapBaitmap.json
"""
#Instantiate and lauch the app
print("1. Instantiate and launch the App")
from apps.jsonapp import JSONApp
app = JSONApp()
results = app.launch(process_bam2chicago,
config,
in_metadata,
out_metadata)
#2. The App has finished
print("2. Execution finished: see " + out_metadata)
print(results)
return results
#########################################################################
if __name__ == "__main__":
#set up the command line parameters
PARSER = argparse.ArgumentParser(
description="Pipeline to generate .chinput file")
PARSER.add_argument("--config", help="Configuration file")
PARSER.add_argument(
"--in_metadata", help="Location of 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 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)