Source code for process_bsgenome

#!/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.forge_bsgenome import bsgenomeTool


# ------------------------------------------------------------------------------

[docs]class process_bsgenome(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 Genome") 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 Location of the FASTA input file metadata : dict genome : dict Required meta data output_files : dict BSgenome : str Location of a the BSgenome R package 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 = {} genome_input_file = {"genome": input_files["genome"]} genome_input_meta = {"genome": metadata["genome"]} if "genome_public" in input_files: genome_input_file = {"genome": input_files["genome_public"]} genome_input_meta = {"genome": metadata["genome_public"]} # BSgenome logger.info("Generating BSgenome") bsg = bsgenomeTool(self.configuration) logger.progress("BSgenome Indexer", status="RUNNING") bsgi, bsgm = bsg.run(genome_input_file, genome_input_meta, output_files) logger.progress("BSgenome Indexer", status="DONE") try: for file_key in ["bsgenome", "chrom_size", "genome_2bit", "seed_file"]: output_files_generated[file_key] = bsgi[file_key] output_metadata[file_key] = bsgm[file_key] tool_name = output_metadata[file_key].meta_data['tool'] output_metadata[file_key].meta_data['tool_description'] = tool_name output_metadata[file_key].meta_data['tool'] = "process_bsgenome" except KeyError: logger.fatal("BSgenome 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_bsgenome, 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="Generate BSgenome files") 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)