#!/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.makeDesignFiles import makeDesignFilesTool
#####################################################
[docs]class process_design(Workflow):
"""
This class generates the Design files and chinput files,
imput for CHiCAGO. Starting from rmap and baitmap and capture
HiC BAM files.
"""
def __init__(self, configuration=None):
"""
Initiate the class
Parameters
----------
Configuration: dict
dictionary with parameters for different tools from the class
indicating how to run each of them.
"""
logger.info("Generating CHiCAGO input Design files")
if configuration is None:
configuration = {}
self.configuration.update(configuration)
[docs] def run(self, input_files, metadata, output_files):
"""
Main function to run the tools, MakeDesignFiles_Tool.py and
bam2chicago_Tool.py
Parameters
----------
input_files: dict
designDir: path to the folder with .rmap and .baitmap files
rmapFile: path to the .rmap file
baitmapFile: path to the .baitmap file
bamFile: path to the capture HiC bamfiles
metadata: dict
input metadata
output_files: dict
outPrefixDesign : Path and name of the output prefix,
recommend to be the same as rmap and baitmap files.
sample_name: Path and name of the .chinput file
Returns
-------
bool
output_metadata
"""
try:
design_caller = makeDesignFilesTool(self.configuration)
design_out, design_meta = design_caller.run(
{
"RMAP" : input_files["RMAP"],
"BAITMAP": input_files["BAITMAP"]
},
{
"RMAP" : metadata["RMAP"],
"BAITMAP" : metadata["BAITMAP"]
},
{
"nbpb" : output_files["nbpb"],
"npb" : output_files["npb"],
"poe" : output_files["poe"]
}
)
logger.info("design files succesfully generated =)")
return design_out, design_meta
except IOError:
logger.fatal("process_makeDesign failed to" +
"generate design files")
#############################################################
def main_json(config, in_metadata, out_metadata):
"""
Alternative main function
This function lauch the app using the configuration written
in two json files:
"""
#1.Instantiate and launch the app
print("Instantiate and launch the App")
from apps.jsonapp import JSONApp
app = JSONApp()
results = app.launch(process_design,
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 .baitmap 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)