process_bamqc.py

#!/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 Bam_QC.tool.bamqc import bamQC

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

class process_bamqc(Workflow):  # pylint: disable=invalid-name,too-few-public-methods
    """
    Functions for demonstrating the pipeline set up.
    """

    configuration = {}

    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("Processing BamQC")
        if configuration is None:
            configuration = {}

        self.configuration.update(configuration)

    def run(self, input_files, metadata, output_files):
        """
        This pipeline analyses a given bam file and produces html file
        as the reporting output file.

        Parameters
        ----------
        input_files : dict
           Dictionary of file locations. These should include:

            bam : str
                Location for the bam file

        metadata : list
           Required meta data

        output_files : dict
           Locations of the output html files returned by the pipeline

        Returns
        -------
        output_files : dict
           Locations for the output html
        output_metadata : dict
           Matching metadata for each of the files
        """

        output_results_files = {}
        output_metadata = {}

        logger.info("bamqc")
        # Initialise the test tool
        bamqc_handle = bamQC(self.configuration)
        logger.progress("BamQC", status="RUNNING")
        bqc_files, bqc_meta = bamqc_handle.run(input_files, metadata, output_files)

        try:
            output_results_files["html"] = bqc_files["html"]
            output_metadata["html"] = bqc_meta["html"]
            tool_name = output_metadata["html"].meta_data["tool"]
            output_metadata["html"].meta_data["tool_description"] = tool_name
            output_metadata["html"].meta_data["tool"] = "process_bamqc"

        except KeyError:
            logger.fatal("BamQC: Error while running")
            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
    logger.info("1. Instantiate and launch the App")
    from apps.jsonapp import JSONApp
    app = JSONApp()
    result = app.launch(process_bamqc,
                        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="BamQC Pipeline")
    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)