#!/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 tool.inps import inps
# ------------------------------------------------------------------------------
[docs]class process_iNPS(Workflow):
"""
Functions for improved nucleosome positioning algorithm
(iNPS). Bam Files are analysed for peaks for nucleosome positioning
"""
configuration = {}
def __init__(self, configuration=None):
"""
Initialise the class
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 iNPS")
if configuration is None:
configuration = {}
self.configuration.update(configuration)
[docs] def run(self, input_files, metadata, output_files):
"""
This pipeline processes bam files to identify
nucleosome regions within the genome and generates bed files.
Parameters
----------
input_files : dict
bam_file : str
Location of the aligned sequences in bam format
output_files : dict
peak_bed : str
Location of the collated bed file of nucleosome peak calls
Returns
-------
peak_bed : str
Location of the collated bed file of nucleosome peak calls
"""
output_results_files = {}
output_metadata = {}
logger.info("iNPS")
# Process the MNAse-seq reads to find nucleosome
logger.info("iNPS")
inps_r = inps(self.configuration)
logger.progress("iNPS Peak Caller", status="RUNNING")
bamf, bed_meta = inps_r.run(
{"bam": input_files["bam"]},
{"bam": metadata["bam"]},
{"bed": output_files["bed"]}
)
logger.progress("iNPS Peak Caller", status="DONE")
try:
output_results_files["bed"] = bamf["bed"]
output_metadata["bed"] = bed_meta["bed"]
tool_name = output_metadata["bed"].meta_data["tool"]
output_metadata["bed"].meta_data["tool_description"] = tool_name
output_metadata["bed"].meta_data["tool"] = "process_iNPS"
except KeyError:
logger.fatal("iNPS : Error while processing")
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
print("1. Instantiate and launch the App")
from apps.jsonapp import JSONApp
app = JSONApp()
result = app.launch(process_iNPS,
config,
in_metadata,
out_metadata)
# 2. The App has finished
print("2. Execution finished; see " + out_metadata)
print(result)
return result
# ------------------------------------------------------------------------------
if __name__ == "__main__":
# Set up the command line parameters
PARSER = argparse.ArgumentParser(description="iNPS peak calling")
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)