#!/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.bowtie_indexer import bowtieIndexerTool
from tool.bwa_indexer import bwaIndexerTool
from tool.gem_indexer import gemIndexerTool
# ------------------------------------------------------------------------------
[docs]class process_genome(Workflow):
"""
Workflow to download and pre-index a given genome
"""
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 Genomes")
if configuration is None:
configuration = {}
self.configuration.update(configuration)
[docs] def run(self, input_files, metadata, output_files):
"""
Main run function for the indexing of genome assembly FASTA files. The
pipeline uses Bowtie2, BWA and GEM ready for use in pipelines that
rely on alignment.
Parameters
----------
input_files : dict
genome : str
List of file locations
metadata : dict
genome : dict
Required meta data
output_files : dict
bwa_index : str
Location of the BWA index archive files
bwt_index : str
Location of the Bowtie2 index archive file
gem_index : str
Location of the GEM index file
genome_gem : str
Location of a the FASTA file generated for the GEM indexing
step
Returns
-------
outputfiles : dict
List of locations for the output index files
output_metadata : dict
Metadata about each of the files
"""
output_files_generated = {}
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"]}
# Bowtie2 Indexer
logger.info("Generating indexes for Bowtie2")
bowtie2 = bowtieIndexerTool()
logger.progress("Bowtie2 Indexer", status="RUNNING")
bti, btm = bowtie2.run(
genome_input_file,
genome_input_meta,
{'index': output_files['bwt_index']}
)
logger.progress("Bowtie2 Indexer", status="DONE")
try:
output_files_generated['bwt_index'] = bti["index"]
output_metadata['bwt_index'] = btm['index']
tool_name = output_metadata['bwt_index'].meta_data['tool']
output_metadata['bwt_index'].meta_data['tool_description'] = tool_name
output_metadata['bwt_index'].meta_data['tool'] = "process_genome"
except KeyError:
logger.fatal("Bowtie2 indexer failed")
# BWA Indexer
logger.info("Generating indexes for BWA")
bwa = bwaIndexerTool()
logger.progress("BWA Indexer", status="RUNNING")
bwai, bwam = bwa.run(
genome_input_file,
genome_input_meta,
{'index': output_files['bwa_index']}
)
logger.progress("BWA Indexer", status="DONE")
try:
output_files_generated['bwa_index'] = bwai['index']
output_metadata['bwa_index'] = bwam['index']
tool_name = output_metadata['bwa_index'].meta_data['tool']
output_metadata['bwa_index'].meta_data['tool_description'] = tool_name
output_metadata['bwa_index'].meta_data['tool'] = "process_genome"
except KeyError:
logger.fatal("BWA indexer failed")
# GEM Indexer
logger.info("Generating indexes for GEM")
gem = gemIndexerTool()
logger.progress("GEM Indexer", status="RUNNING")
gemi, gemm = gem.run(
genome_input_file, genome_input_meta,
{
'index': output_files['gem_index']
}
)
logger.progress("GEM Indexer", status="DONE")
try:
output_files_generated['gem_index'] = gemi['index']
output_metadata['gem_index'] = gemm['index']
tool_name = output_metadata['gem_index'].meta_data['tool']
output_metadata['gem_index'].meta_data['tool_description'] = tool_name
output_metadata['gem_index'].meta_data['tool'] = "process_genome"
except KeyError:
logger.fatal("GEM indexer 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
logger.info("1. Instantiate and launch the App")
from apps.jsonapp import JSONApp
app = JSONApp()
result = app.launch(process_genome,
config,
in_metadata,
out_metadata)
# 2. The App has finished
logger.info("2. Execution finished; see " + out_metadata)
return result
# ------------------------------------------------------------------------------
if __name__ == "__main__":
# Set up the command line parameters
PARSER = argparse.ArgumentParser(description="Index the genome file")
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)