Source code for tool.tb_model

"""
.. 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 sys
import glob
import os
from subprocess import PIPE, Popen

from basic_modules.tool import Tool

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
    # from pycompss.api.constraint import constraint
except ImportError:
    logger.info("[Warning] Cannot import \"pycompss\" API packages.")
    logger.info("          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 utils.dummy_pycompss import constraint

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


[docs]class tbModelTool(Tool): # pylint: disable=invalid-name """ Tool for normalizing an adjacency matrix """ def __init__(self): """ Init function """ logger.info("TADbit - Modeling") Tool.__init__(self)
[docs] @task(optimize_only=IN, hic_contacts_matrix_norm=FILE_IN, resolution=IN, gen_pos_chrom_name=IN, gen_pos_begin=IN, gen_pos_end=IN, num_mod_comp=IN, num_mod_keep=IN, max_dist=IN, upper_bound=IN, lower_bound=IN, cutoff=IN, workdir=IN, model_dir=FILE_OUT) def tb_model(self, optimize_only, hic_contacts_matrix_norm, resolution, # pylint: disable=too-many-locals,too-many-statements,unused-argument,no-self-use,too-many-arguments gen_pos_chrom_name, gen_pos_begin, gen_pos_end, num_mod_comp, num_mod_keep, max_dist, upper_bound, lower_bound, cutoff, workdir, metadata, ncpus=1): """ Function to normalize to a given resolution the Hi-C matrix Parameters ---------- optimize_only: bool True if only optimize, False for computing the models and stats hic_contacts_matrix_norm : str Location of the tab-separated normalized matrix resolution : str Resolution of the Hi-C gen_pos_chrom_name : str Coordinates of the genomic region to model. gen_pos_begin : int Genomic coordinate from which to start modeling. gen_pos_end : int Genomic coordinate where to end modeling. num_mod_comp : int Number of models to compute for each optimization step. num_mod_comp : int Number of models to keep. max_dist : str Range of numbers for optimal maxdist parameter, i.e. 400:1000:100; or just a single number e.g. 800; or a list of numbers e.g. 400 600 800 1000. upper_bound : int Range of numbers for optimal upfreq parameter, i.e. 0:1.2:0.3; or just a single number e.g. 0.8; or a list of numbers e.g. 0.1 0.3 0.5 0.9. lower_bound : int Range of numbers for optimal low parameter, i.e. -1.2:0:0.3; or just a single number e.g. -0.8; or a list of numbers e.g. -0.1 -0.3 -0.5 -0.9. cutoff : str Range of numbers for optimal cutoff distance. Cutoff is computed based on the resolution. This cutoff distance is calculated taking as reference the diameter of a modeled particle in the 3D model. i.e. 1.5:2.5:0.5; or just a single number e.g. 2; or a list of numbers e.g. 2 2.5. workdir : str Location of working directory ncpus : str Number of cpus to use Returns ------- tadkit_models : str Location of TADkit json file modeling_stats : str Location of the folder with the modeling files and stats """ # chr_hic_data = read_matrix(matrix_file, resolution=int(resolution)) logger.info("TB MODELING: {0},{1},{2},{3},{4},{5},{6},{7},{8},{9},{10},{11}".format( hic_contacts_matrix_norm, resolution, gen_pos_chrom_name, gen_pos_begin, gen_pos_end, num_mod_comp, num_mod_keep, max_dist, upper_bound, lower_bound, cutoff, workdir)) try: beg = int(float(gen_pos_begin) / int(resolution)) end = int(float(gen_pos_end) / int(resolution)) if end - beg <= 2: logger.fatal('"beg" and "end" parameter should be given in ' + 'genomic coordinates, not bin') raise Exception('"beg" and "end" parameter should be given in ' + 'genomic coordinates, not bin') except ValueError: pass except TypeError: pass name = '{0}_{1}_{2}'.format(gen_pos_chrom_name, gen_pos_begin, gen_pos_end) if not os.path.exists(os.path.join(workdir, name)): os.makedirs(os.path.join(workdir, name)) # ======================================================================= # _cmd = [ # 'model_and_analyze.py', # '--norm', hic_contacts_matrix_norm, # '--res', resolution, # '--maxdist', max_dist, # '--upfreq', upper_bound, # '--lowfreq='+lower_bound, # '--dcutoff', cutoff, # '--ncpus', str(ncpus), # '--assembly', metadata["assembly"], # '--species', metadata["species"], # '--project', metadata["project"], # '--fig_format', 'png' # ] # if len(gen_pos_chrom_name) > 0: # _cmd.append('--crm') # _cmd.append(gen_pos_chrom_name) # if len(gen_pos_begin) > 0 and len(gen_pos_end) > 0: # _cmd.append('--beg') # _cmd.append(str(gen_pos_begin)) # _cmd.append('--end') # _cmd.append(str(gen_pos_end)) # if optimize_only: # _cmd.append('--nmodels_opt') # _cmd.append(str(num_mod_comp)) # _cmd.append('--nkeep_opt') # _cmd.append(str(num_mod_keep)) # _cmd.append('--optimize_only') # _cmd.append('--outdir') # _cmd.append(workdir) # else: # _cmd.append('--nmodels_opt') # _cmd.append('0') # _cmd.append('--nkeep_opt') # _cmd.append('0') # _cmd.append('--nmodels_mod') # _cmd.append(str(num_mod_comp)) # _cmd.append('--nkeep_mod') # _cmd.append(str(num_mod_keep)) # _cmd.append('--outdir') # _cmd.append(workdir) # ======================================================================= _cmd = [ 'tadbit', 'model', '--workdir', os.path.join(workdir, name), '--input_matrix', hic_contacts_matrix_norm, '--reso', resolution, '--maxdist', max_dist, '--upfreq', upper_bound, '--lowfreq='+lower_bound, '--dcutoff', cutoff, '--cpu', str(ncpus), '--assembly', metadata["assembly"], '--species', metadata["species"], '--project', metadata["project"], '--fig_format', 'png' ] if gen_pos_chrom_name: _cmd.append('--crm') _cmd.append(gen_pos_chrom_name) if gen_pos_begin and gen_pos_end: _cmd.append('--beg') _cmd.append(str(gen_pos_begin)) _cmd.append('--end') _cmd.append(str(gen_pos_end)) _cmd.append('--nmodels') _cmd.append(str(num_mod_comp)) _cmd.append('--nkeep') _cmd.append(str(num_mod_keep)) if optimize_only: _cmd.append('--optimize') else: _cmd.append('--model') _cmd.append('--force') _cmd.append('--analyze') output_metadata = {} logger.info(' '.join(_cmd)) out, err = Popen(_cmd, stdout=PIPE, stderr=PIPE).communicate() logger.info(out) logger.info(err) output_folder = os.listdir(os.path.join(workdir, name, '06_model'))[0] output_files = [os.path.join(workdir, name, '06_model', output_folder)] if not optimize_only: os.chdir(os.path.join(workdir, name, '06_model', output_folder)) for fl_file in glob.glob("*.json"): output_files.append(fl_file) break for fl_file in glob.glob("*optimal_params*"): os.unlink(fl_file) return (output_files, output_metadata)
[docs] def run(self, input_files, input_metadata, output_files): # pylint: disable=too-many-locals """ The main function for the normalization of the Hi-C matrix to a given resolution Parameters ---------- input_files : list hic_contacts_matrix_norm : str Location of the tab-separated normalized matrix metadata : dict optimize_only: bool True if only optimize, False for computing the models and stats gen_pos_chrom_name : str Coordinates of the genomic region to model. resolution : str Resolution of the Hi-C gen_pos_begin : int Genomic coordinate from which to start modeling. gen_pos_end : int Genomic coordinate where to end modeling. num_mod_comp : int Number of models to compute for each optimization step. num_mod_comp : int Number of models to keep. max_dist : str Range of numbers for optimal maxdist parameter, i.e. 400:1000:100; or just a single number e.g. 800; or a list of numbers e.g. 400 600 800 1000. upper_bound : int Range of numbers for optimal upfreq parameter, i.e. 0:1.2:0.3; or just a single number e.g. 0.8; or a list of numbers e.g. 0.1 0.3 0.5 0.9. lower_bound : int Range of numbers for optimal low parameter, i.e. -1.2:0:0.3; or just a single number e.g. -0.8; or a list of numbers e.g. -0.1 -0.3 -0.5 -0.9. cutoff : str Range of numbers for optimal cutoff distance. Cutoff is computed based on the resolution. This cutoff distance is calculated taking as reference the diameter of a modeled particle in the 3D model. i.e. 1.5:2.5:0.5; or just a single number e.g. 2; or a list of numbers e.g. 2 2.5. workdir : str Location of working directory ncpus : str Number of cpus to use Returns ------- output_files : list List of locations for the output files. output_metadata : list List of matching metadata dict objects """ hic_contacts_matrix_norm = input_files[0] ncpus = 1 if 'ncpus' in input_metadata: ncpus = input_metadata['ncpus'] optimize_only = input_metadata["optimize_only"] gen_pos_chrom_name = input_metadata['gen_pos_chrom_name'] resolution = input_metadata['resolution'] gen_pos_begin = input_metadata['gen_pos_begin'] gen_pos_end = input_metadata['gen_pos_end'] num_mod_comp = input_metadata['num_mod_comp'] num_mod_keep = input_metadata['num_mod_keep'] max_dist = input_metadata['max_dist'] upper_bound = input_metadata['upper_bound'] lower_bound = input_metadata['lower_bound'] cutoff = input_metadata['cutoff'] root_name = os.path.dirname(os.path.abspath(hic_contacts_matrix_norm)) if 'workdir' in input_metadata: root_name = input_metadata['workdir'] project_metadata = {} project_metadata["species"] = input_metadata["species"] project_metadata["assembly"] = input_metadata["assembly"] project_metadata["project"] = os.path.basename(os.path.normpath(input_metadata["project"])) # input and output share most metadata output_files, output_metadata = self.tb_model(optimize_only, hic_contacts_matrix_norm, resolution, gen_pos_chrom_name, gen_pos_begin, gen_pos_end, num_mod_comp, num_mod_keep, max_dist, upper_bound, lower_bound, cutoff, root_name, project_metadata, ncpus) return (output_files, output_metadata)