#!/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 utils import remap
from tool.bwa_aligner import bwaAlignerTool
from tool.inps import inps
# ------------------------------------------------------------------------------
[docs]class process_mnaseseq(Workflow):
"""
Functions for downloading and processing Mnase-seq FastQ files. Files are
downloaded from the European Nucleotide Archive (ENA), then aligned,
filtered and analysed for peak calling
"""
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 MNase-Seq")
if configuration is None:
configuration = {}
self.configuration.update(configuration)
[docs] def run(self, input_files, metadata, output_files):
"""
Main run function for processing MNase-Seq FastQ data. Pipeline aligns
the FASTQ files to the genome using BWA. iNPS is then used for peak
calling to identify nucleosome position sites within the genome.
Parameters
----------
files_ids : list
List of file locations
metadata : list
Required meta data
Returns
-------
outputfiles : list
List of locations for the output bam, bed and tsv files
"""
output_metadata = {}
if "genome_public" in input_files:
align_input_files = remap(
input_files, genome="genome_public", loc="loc", index="index_public")
align_input_file_meta = remap(
metadata, genome="genome_public", loc="loc", index="index_public")
else:
align_input_files = remap(input_files, "genome", "loc", "index")
align_input_file_meta = remap(metadata, "genome", "loc", "index")
bwa = bwaAlignerTool()
logger.progress("BWA ALN Aligner", status="RUNNING")
bwa_files, bwa_meta = bwa.run(
align_input_files, align_input_file_meta,
{"output": output_files["bam"], "bai": output_files["bai"]}
)
logger.progress("BWA ALN Aligner", status="DONE")
output_files_generated = {}
try:
output_files_generated["bam"] = bwa_files["bam"]
output_metadata["bam"] = bwa_meta["bam"]
tool_name = output_metadata['bam'].meta_data['tool']
output_metadata['bam'].meta_data['tool_description'] = tool_name
output_metadata['bam'].meta_data['tool'] = "process_mnaseseq"
output_files_generated["bai"] = bwa_files["bai"]
output_metadata["bai"] = bwa_meta["bai"]
tool_name = output_metadata['bai'].meta_data['tool']
output_metadata['bai'].meta_data['tool_description'] = tool_name
output_metadata['bai'].meta_data['tool'] = "process_mnaseseq"
except KeyError:
logger.fatal("BWA Alignment failed")
inps_tool = inps()
logger.progress("iNPS Peak Caller", status="RUNNING")
inps_files, inps_meta = inps_tool.run(
remap(bwa_files, "bam"),
remap(bwa_meta, "bam"),
{"bed": output_files["bed"]}
)
logger.progress("iNPS Peak Caller", status="DONE")
try:
output_files_generated["bed"] = inps_files["bed"]
output_metadata["bed"] = inps_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_mnaseseq"
except KeyError:
logger.fatal("BWA Alignment failed")
print("MNASESEQ RESULTS:", output_metadata)
return output_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_mnaseseq,
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="MNase-seq 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)