Source code for tool.inps

"""
.. 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 shlex
import subprocess
import sys

from utils import logger

try:
    if hasattr(sys, '_run_from_cmdl') is True:
        raise ImportError
    from pycompss.api.parameter import FILE_IN, FILE_OUT, IN
    from pycompss.api.task import task
    from pycompss.api.api import compss_wait_on
except ImportError:
    logger.warn("[Warning] Cannot import \"pycompss\" API packages.")
    logger.warn("          Using mock decorators.")

    from utils.dummy_pycompss import FILE_IN, FILE_OUT, IN  # pylint: disable=ungrouped-imports
    from utils.dummy_pycompss import task  # pylint: disable=ungrouped-imports
    from utils.dummy_pycompss import compss_wait_on  # pylint: disable=ungrouped-imports

from basic_modules.tool import Tool
from basic_modules.metadata import Metadata


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

[docs]class inps(Tool): # pylint: disable=invalid-name """ Tool for peak calling for MNase-seq data """ 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("iNPS Peak Caller") Tool.__init__(self) if configuration is None: configuration = {} self.configuration.update(configuration)
[docs] @task( returns=int, bam_file=FILE_IN, peak_bed=FILE_OUT, inps_params=IN, isModifier=False) def inps_peak_calling(self, bam_file, peak_bed, inps_params): # pylint: disable=no-self-use """ Convert Bam to Bed then make Nucleosome peak calls. These are saved as bed files That can then get displayed on genome browsers. Parameters ---------- bam_file : str Location of the aligned sequences in bam format peak_bed : str Location of the collated bed file of nucleosome peak calls Returns ------- peak_bed : str Location of the collated bed file of nucleosome peak calls """ bed_file = bam_file + ".bed" # pyenv3 = os.path.join(os.path.expanduser("~"), "bin/py3") command_line_1 = 'bedtools bamtobed -i ' + bam_file command_line_2 = "iNPS " + " ".join(inps_params) command_line_2 = command_line_2 + " -i " + bed_file + " -o " + peak_bed + "_tmp" logger.info("iNPS - cmd1:", command_line_1) logger.info("iNPS - cmd2:", command_line_2) args = shlex.split(command_line_1) with open(bed_file, "w") as f_out: sub_proc = subprocess.Popen(args, stdout=f_out) sub_proc.wait() args = shlex.split(command_line_2) sub_proc = subprocess.Popen(args) sub_proc.wait() with open(peak_bed + "_tmp_Gathering.like_bed", "rb") as f_in: with open(peak_bed, "wb") as f_out: f_out.write(f_in.read()) return 0
[docs] def run(self, input_files, input_metadata, output_files): """ The main function to run iNPS for peak calling over a given BAM file and matching background BAM file. Parameters ---------- input_files : list List of input bam file locations where 0 is the bam data file and 1 is the matching background bam file metadata : dict Returns ------- output_files : list List of locations for the output files. output_metadata : list List of matching metadata dict objects """ command_params = [] if "inps_sp_param" in self.configuration: command_params = command_params + [ "--s_p", str(self.configuration["inps_sp_param"])] if "inps_pe_max_param" in self.configuration: command_params = command_params + [ "--pe_max", str(self.configuration["inps_pe_max_param"])] if "inps_pe_min_param" in self.configuration: command_params = command_params + [ "--pe_min", str(self.configuration["inps_pe_min_param"])] results = self.inps_peak_calling( input_files["bam"], output_files["bed"], command_params ) results = compss_wait_on(results) output_metadata = { "bed": Metadata( data_type=input_metadata['bam'].data_type, file_type="BED", file_path=output_files["bed"], sources=[input_metadata["bam"].file_path], taxon_id=input_metadata["bam"].taxon_id, meta_data={ "assembly": input_metadata["bam"].meta_data["assembly"], "tool": "inps" } ) } return (output_files, output_metadata)
# ------------------------------------------------------------------------------