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process_bed.py
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/
process_bed.py
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#!/usr/bin/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
import h5py
from basic_modules.workflow import Workflow
from utils import logger
from utils import remap
from mg_process_files.tool.bed_indexer import bedIndexerTool
from mg_process_files.tool.bed_sorter import bedSortTool
# ------------------------------------------------------------------------------
class process_bed(Workflow):
"""
Workflow to index BED formatted files within the Multiscale Genomics (MuG)
Virtural Research Environment (VRE)
"""
def __init__(self, configuration=None):
"""
Initialise the tool with its configuration.
Parameters
----------
configuration : dict
a dictionary containing parameters that define how the operation
should be carried out, which are specific to each Tool.
"""
logger.info("Process BED file")
if configuration is None:
configuration = {}
self.configuration.update(configuration)
def run(self, input_files, metadata, output_files):
"""
Main run function to index the BED files ready for use in the RESTful
API. BED files are index in 2 different ways to allow for optimal data
retreival. The first is as a bigbed file, this allows the data to get
easily extracted as BED documents and served to the user. The second is
as an HDF5 file that is used to identify which bed files have
information at a given location. This is to help the REST clients make
only the required calls to the relevant BED files rather than needing to
pole all potential BED files.
Parameters
----------
inpout_files : list
List of file locations
metadata : list
Returns
-------
outputfiles : list
List of locations for the output BED and HDF5 files
"""
# Ensure that the file exists
f_check = h5py.File(input_files["hdf5_file"], "a")
f_check.close()
# Bed Sort
bst = bedSortTool()
bst_files, bst_meta = bst.run(
remap(input_files,
"bed"),
remap(metadata,
"bed"),
remap(output_files,
"sorted_bed")
)
# Bed Indexer
bit = bedIndexerTool()
bit_files, bit_meta = bit.run(
{
"bed": bst_files["sorted_bed"],
"chrom_size": input_files["chrom_size"],
"hdf5_file": input_files["hdf5_file"]
}, {
"bed": bst_meta["sorted_bed"],
"chrom_size": metadata["chrom_size"],
"hdf5_file": metadata["hdf5_file"]
}, {
"bb_file": output_files["bb_file"],
"hdf5_file": output_files["hdf5_file"]
}
)
return (bst_files + bit_files, bst_meta + bit_meta)
# ------------------------------------------------------------------------------
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_bed,
config,
in_metadata,
out_metadata)
# 2. The App has finished
logger.info("2. Execution finished; see " + out_metadata)
return result
# ------------------------------------------------------------------------------
if __name__ == "__main__":
import sys
sys._run_from_cmdl = True # pylint: disable=protected-access
# Set up the command line parameters
PARSER = argparse.ArgumentParser(description="Index BED 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")
# 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
RESULTS = main_json(CONFIG, IN_METADATA, OUT_METADATA)
print(RESULTS)