process_gff3.py

#!/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.gff3_indexer import gff3IndexerTool
from mg_process_files.tool.gff3_sorter import gff3SortTool

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


class process_gff3(Workflow):
    """
    Workflow to index WIG 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 GFF3 file")
        if configuration is None:
            configuration = {}
        self.configuration.update(configuration)

    def run(self, input_files, metadata, output_files):
        """
        Main run function to index the WIG files ready for use in the RESTful
        API. WIG files are indexed in 2 different ways to allow for optimal data
        retreival. The first is as a Tabix file, this allows the data to get
        easily extracted as GFF3 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 GFF3 files rather than needing
        to pole all potential GFF3 files.

        Parameters
        ----------
        files_ids : list
            List of file locations
        metadata : list

        Returns
        -------
        outputfiles : list
            List of locations for the output wig and HDF5 files
        """

        # Ensure that the file exists
        f_check = h5py.File(input_files["hdf5_file"], "a")
        f_check.close()

        # GFF3 Sort
        gst = gff3SortTool()
        gst_files, gst_meta = gst.run(
            remap(input_files,
                  "gff3"),
            remap(metadata,
                  "gff3"),
            remap(output_files,
                  "sorted_gff3")
        )

        # GFF3 Indexer
        tbi = gff3IndexerTool()
        tbi_files, tbi_meta = tbi.run(
            {
                "gff3": gst_files["sorted_gff3"],
                "chrom_size": input_files["chrom_size"],
                "hdf5_file": input_files["hdf5_file"]
            }, {
                "gff3": gst_meta["sorted_gff3"],
                "chrom_size": metadata["chrom_size"],
                "hdf5_file": metadata["hdf5_file"]
            }, {
                "gz_file": output_files["gz_file"],
                "tbi_file": output_files["tbi_file"],
                "hdf5_file": output_files["hdf5_file"]
            }
        )

        return (gst_files + tbi_files, gst_meta + tbi_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_gff3,
                        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)