#!/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.bwa_aligner import bwaAlignerTool
# ------------------------------------------------------------------------------
[docs]class process_bwa(Workflow):
"""
Functions for aligning FastQ files with BWA ALN
"""
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 BWA Aligner")
if configuration is None:
configuration = {}
self.configuration.update(configuration)
[docs] def run(self, input_files, metadata, output_files):
"""
Main run function for aligning FastQ reads with BWA ALN.
Parameters
----------
input_files : dict
Location of the initial input files required by the workflow
genome : str
Genome FASTA file
index : str
Location of the BWA archived index files
loc : str
Location of the FASTQ reads files
fastq2 : str
[OPTIONAL] Location of the FASTQ reads file for paired end data
metadata : dict
Input file meta data associated with their roles
genome : str
index : str
loc : str
fastq2 : str
output_files : dict
Output file locations
bam : str
Output bam file location
Returns
-------
output_files : dict
Output file locations associated with their roles, for the output
bam : str
Aligned FASTQ short read file locations
output_metadata : dict
Output metadata for the associated files in output_files
bam : Metadata
"""
output_files_generated = {}
output_metadata = {}
logger.info("PROCESS ALIGNMENT - DEFINED OUTPUT:", output_files["bam"])
if "genome_public" in input_files:
input_files["genome"] = input_files.pop("genome_public")
metadata["genome"] = metadata.pop("genome_public")
if "index_public" in input_files:
input_files["index"] = input_files.pop("index_public")
metadata["index"] = metadata.pop("index_public")
bwa = bwaAlignerTool(self.configuration)
logger.progress("BWA ALN Aligner", status="RUNNING")
bwa_files, bwa_meta = bwa.run(
input_files, metadata,
{"output": output_files["bam"], "bai": output_files["bai"]}
)
logger.progress("BWA ALN Aligner", status="DONE")
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_bwa_aln"
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_bwa_aln"
except KeyError:
logger.fatal("BWA aligner failed")
return output_files_generated, 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_bwa,
config,
in_metadata,
out_metadata)
# 2. The App has finished
print("2. Execution finished; see " + out_metadata)
return result
# ------------------------------------------------------------------------------
if __name__ == "__main__":
# Set up the command line parameters
PARSER = argparse.ArgumentParser(description="BWA Alignment")
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)