#!/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.bs_seeker_indexer import bssIndexerTool
# ------------------------------------------------------------------------------
[docs]class process_bs_seeker_index(Workflow):
"""
Functions for aligning FastQ files with BWA
"""
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 Index")
if configuration is None:
configuration = {}
self.configuration.update(configuration)
[docs] def run(self, input_files, metadata, output_files):
"""
Main run function for generatigng the index files required by BS Seeker2.
Parameters
----------
input_files : dict
List of strings for the locations of files. These should include:
genome_fa : str
Genome assembly in FASTA
metadata : dict
Input file meta data associated with their roles
genome : 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
index : str
"""
output_results_files = {}
output_metadata = {}
if "genome_public" in input_files:
genome_input_file = {"genome": input_files["genome_public"]}
genome_input_meta = {"genome": metadata["genome_public"]}
else:
genome_input_file = {"genome": input_files["genome"]}
genome_input_meta = {"genome": metadata["genome"]}
logger.info("WGBS - BS-Seeker2 Index")
# Build the matching WGBS genome index
builder = bssIndexerTool(self.configuration)
logger.progress("BSseeker2 Indexer", status="RUNNING")
genome_idx, gidx_meta = builder.run(
genome_input_file,
genome_input_meta,
remap(output_files, "index")
)
logger.progress("BSseeker2 Indexer", status="DONE")
output_results_files["index"] = genome_idx["index"]
output_metadata["index"] = gidx_meta["index"]
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_index,
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="BS Seeker2 Indexer")
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)