#!/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.bs_seeker_aligner import bssAlignerTool
# ------------------------------------------------------------------------------
[docs]class process_bs_seeker_aligner(Workflow):
"""
Functions for downloading and processing whole genome bisulfate sequencings
(WGBS) files. Files are filtered, aligned and analysed for points of
methylation
"""
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 BS SEEKER2 - Aligning Reads")
if configuration is None:
configuration = {}
self.configuration.update(configuration)
[docs] def run(self, input_files, metadata, output_files):
"""
This pipeline processes paired-end FASTQ files to identify
methylated regions within the genome.
Parameters
----------
input_files : dict
List of strings for the locations of files. These should include:
genome_fa : str
Genome assembly in FASTA
fastq1 : str
Location for the first filtered FASTQ file for single or paired
end reads
fastq2 : str
Location for the second filtered FASTQ file if paired end reads
index : str
Location of the index file
metadata : dict
Input file meta data associated with their roles
genome_fa : dict
fastq1 : dict
fastq2 : dict
index : dict
output_files : dict
bam : str
bai : str
Returns
-------
bam|bai : str
Location of the alignment bam file and the associated index
"""
output_results_files = {}
output_metadata = {}
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")
logger.info("BS-Seeker2 Aligner")
bss_aligner = bssAlignerTool(self.configuration)
logger.progress("BSseeker2 Aligner", status="RUNNING")
bam, bam_meta = bss_aligner.run(
input_files, metadata,
{
"bam": output_files["bam"],
"bai": output_files["bai"]
})
logger.progress("BSseeker2 Aligner", status="DONE")
try:
output_results_files["bam"] = bam["bam"]
output_results_files["bai"] = bam["bai"]
output_metadata["bam"] = bam_meta["bam"]
output_metadata["bai"] = bam_meta["bai"]
tool_name = output_metadata["bam"].meta_data["tool"]
output_metadata["bam"].meta_data["tool_description"] = tool_name
output_metadata["bam"].meta_data["tool"] = "process_wgbs"
tool_name = output_metadata["bai"].meta_data["tool"]
output_metadata["bai"].meta_data["tool_description"] = tool_name
output_metadata["bai"].meta_data["tool"] = "process_bs_seeker_aligner"
except KeyError:
logger.fatal("BS SEEKER2 - Aligner failed")
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_bs_seeker_aligner,
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="BS-Seeker 2 Aligner")
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)