run_abridge

#! /usr/bin/env python3

########################################################################################################################################################
# Script for running abridge within docker container
########################################################################################################################################################

import argparse
import logging
import os
import pprint
import sys
import re
import time
import multiprocessing
import random
import glob
import time
import subprocess
from pprint import pformat
from argparse import RawTextHelpFormatter


def parseCommandLineArguments():
    parser = argparse.ArgumentParser( prog = "abridge", description = "Compress alignments for storage, decompress from compressed file, view alignments from random locations and generate coverages", formatter_class = RawTextHelpFormatter )
    required_named = parser.add_argument_group( 'Required arguments' )
    optional_named = parser.add_argument_group( 'Optional arguments' )

    # Required arguments

    required_named.add_argument( "-o", "--output_directory", help = "Enter the name of the output directory. If nothing is specified then the compressed file will be put in the same location as the input samfile" )
    input_group = parser.add_mutually_exclusive_group()
    input_group.add_argument( "-isam", "--inputfilename", help = "Enter the name of the alignment file you wish to compress. Alignments in SAM format only is expected. Ensure that the file is sorted by coordinate. Also, files must have the header section with the reference information available. You can compress only one file at a time." )
    input_group.add_argument( "-iabr", "--inputabrfilenames", help = "Enter the name of the compressed alignment files you wish to merge. These files must be compressed using abridge. You can decompress only one file at a time." )
    required_named.add_argument( "-g", "--genome", help = "Enter a single fasta file for the reference" )

    compress_decompress_group = parser.add_mutually_exclusive_group()
    compress_decompress_group.add_argument( "-cmp", "--compress", help = "Set this option if you wish to compress the alignment file", action = "store_true" )
    compress_decompress_group.add_argument( "-dcmp", "--decompress", help = "Set this option if you wish to decompress the alignment file", action = "store_true" )
    compress_decompress_group.add_argument( "-r", "--random", help = "Retrieve alignments from random locations", action = "store_true" )
    compress_decompress_group.add_argument( "-H", "--header", help = "Print only the header of reference sequences during decompression", action = "store_true" )

    # Optional arguments
    # optional_named.add_argument( "-l", "--level", help = "This can accept an integer from the set (1,2,3). If level is set to 1 then abridge will perform the fastest but low compression. abridge will use brotli to compress. Decompression will be fast. Setting level to 2 will prompt abridge to perform the medium level compression using 7z. Compression will take time but decompression will be fast. If level is set to 3 then abridge will perform the best compression using 7paq. Both compression and decompression will take average time to complete", type = int, default = 2 )
    optional_named.add_argument( "-ss", "--ignore_alignment_scores", help = "Request abrigde to store the quality scores and the alignment score", action = "store_true" )
    optional_named.add_argument( "-igqual", "--ignore_quality_scores", help = "Ignore all quality scores", action = "store_true" )
    optional_named.add_argument( "-qual", "--quality", help = "Enter dummy quality scores while decompressing", default = 'I' )
    optional_named.add_argument( "-gsc", "--ignore_soft_clippings", help = "No soft clippings will be stored. Read will be trimmed down to only the portion which matched to nucleotides in the reference", action = "store_true" )
    optional_named.add_argument( "-gm", "--ignore_mismatches", help = "All mismatches will be ignored", action = "store_true" )
    optional_named.add_argument( "-gs", "--ignore_sequence", help = "No nucleotide sequence will be produced during decompression", action = "store_true" )
    optional_named.add_argument( "-gu", "--ignore_unmapped_reads", help = "Request abridge to discard all reads that are unmapped", action = "store_true" )
    # optional_named.add_argument( "-sq", "--save_all_quality_scores", help = "Request abridge to save all quality scores", action = 'store_true' )
    # optional_named.add_argument( "-aq", "--save_exact_quality_scores", help = "Adjust quality scores for matched bases to achieve better encoding. For more details please check ...", action = "store_true" )
    optional_named.add_argument( "-q", "--quiet", help = "Prevent abridge from printing any log information. By default logging is enables", action = "store_true" )
    optional_named.add_argument( "-n", "--cpu", help = "Enter the number of CPU cores to be used. This option will be used during compression or decompression.", default = 1 )
    optional_named.add_argument( "-run_diagnostics", "--run_diagnostics", help = "abridge will run diagnostics on the cigar compression and decompression. It will exit on discovery of any discrepancies", action = "store_true" )
    optional_named.add_argument( "-p", "--positions", help = "Enter the position as chromosome:start-end from which reads will be retrieved" )
    optional_named.add_argument( "-rp", "--read_prefix", help = "Enter a read prefix for decompression - valid only for random access" )
    optional_named.add_argument( "--keep_intermediate_error_files", "-keep_intermediate_error_files", help = "Set this argument if you wish to preserve the intermediate error files to assess time and memory usage. Default behaviour is to delete those", action = "store_true" )
    optional_named.add_argument( "--test", "-test", help = "Set this option to test run the software with example data", action = "store_true" )
    optional_named.add_argument( "--error_directory", "-edir", help = "Enter a directory where all error files will be stored. If nothing is specified then error files will be stored in the output directory" )
    optional_named.add_argument( "--framework", "-fm", help = "Enter your choice of framework", choices = ["docker", "singularity"], default = "docker" )
    optional_named.add_argument( "--force", "-force", help = "Setting this argument will remove the output directory and start the computation from scratch", action = "store_true" )

    # Suppressed arguments
    parser.add_argument( "--logfilename", "-logfilename", help = argparse.SUPPRESS )  # Name of the logfile
    parser.add_argument( "--files_for_removal", "-files_for_removal", help = argparse.SUPPRESS )  # Files will be removed later
    parser.add_argument( "--softwares", "-softwares", help = argparse.SUPPRESS )  # Software paths
    parser.add_argument( "--single_ended", "-single_ended", help = argparse.SUPPRESS )
    parser.add_argument( "--reference_to_length", "-num_of_reference_sequences", help = argparse.SUPPRESS )
    parser.add_argument( "--outputfilename", "-outputfilena", help = argparse.SUPPRESS )
    parser.add_argument( "--compile_programs", "-compile_programs", action = "store_true", help = argparse.SUPPRESS )  # Force abridge to compile the C programs

    # Future enhancements
    compress_decompress_group.add_argument( "-ov", "--generate_overlapping_coverage", help = argparse.SUPPRESS, action = "store_true" )  # Future - This option can be used in conjuction with --positions to construct coverage from a specific location # help="Enter the name of the compressed file from which you wish to generate an overlapping coverage of reads ",
    compress_decompress_group.add_argument( "-nov", "--generate_non_overlapping_coverage", help = argparse.SUPPRESS, action = "store_true" )  # help="Enter the name of the compressed file from which you wish to generate a non-overlapping coverage of reads "

    # Options for generating coverage
    optional_named.add_argument( "-d", "--d", help = argparse.SUPPRESS, action = "store_true" )  # help = "Report the depth at each position in each A feature. Positions reported are one based.  Each position and depth follow the complete A feature.",
    optional_named.add_argument( "-bg", "--bg", help = argparse.SUPPRESS, action = "store_true" )
    optional_named.add_argument( "-bga", "--bga", help = argparse.SUPPRESS, action = "store_true" )
    optional_named.add_argument( "-split", "--split", help = argparse.SUPPRESS, action = "store_true" )  # help = "Treat \"split\" BAM or BED12 entries as distinct BED intervals.",
    optional_named.add_argument( "-mem", "--max_memory", help = argparse.SUPPRESS, default = 10 )  # help="Enter the maximum memory allowed (in GB)"
    optional_named.add_argument( "-t", "--produce_tags", help = argparse.SUPPRESS, nargs = "*" )  # help="Enter a comma separated list of tags that you want abridge to produce during decompression. By default abridge will generate NH, MD and XS tags."
    return parser.parse_args()


def runDockerCommand( name, version, image_location, container_name, volumes, command , cpus = 1, memory = '1g' ):
    """
    Runs the command in a docker container
    """

    # Runs the main command
    docker_cmd = f" docker run "
    # docker_cmd += f" -ti "
    docker_cmd += f" -v /var/run/docker.sock:/var/run/docker.sock"
    docker_cmd += f" -v /usr/bin/docker:/usr/bin/docker --privileged=true "
    docker_cmd += f" --rm "
    docker_cmd += f" --cpus={cpus}"
    docker_cmd += f" --memory='{memory}'"
    # docker_cmd += f" --name {container_name}"
    for mapping in volumes:
        docker_cmd += f" -v {mapping}"
    docker_cmd += f" {image_location}:{version} "
    docker_cmd += f" bash -c {command}"
    os.system( docker_cmd )
    # print( docker_cmd )


def runSingularityCommand( name, version, image_location, container_name, volumes, command , cpus = 1, memory = '1g' ):
    """
    Runs the command in a Singularity container
    """

    # Runs the main command
    singularity_cmd = f" singularity exec  "
    # singularity_cmd += f" --hostname {container_name}"
    for mapping in volumes:
        singularity_cmd += f" -B {mapping}"
    singularity_cmd += f" abridge_{version}.sif "
    singularity_cmd += f" bash -c {command}"
    os.system( singularity_cmd )
    # print( singularity_cmd )


def runDockerOrSingularityInParallel( eachinput ):

    compress_cmd, decompress1_cmd, decompress2_cmd, container_name, volumes_list, framework_of_choice = eachinput

    if framework_of_choice == "docker":
        runDockerCommand( name = "abridge",
                            version = "1.0.0",
                            image_location = "sagnikbanerjee15/abridge",
                            container_name = f"{container_name}_compress",
                            volumes = volumes_list,
                            command = compress_cmd,
                            cpus = "1",
                            memory = '3g'
            )

        runDockerCommand( name = "abridge",
                            version = "1.0.0",
                            image_location = "sagnikbanerjee15/abridge",
                            container_name = f"{container_name}_compress",
                            volumes = volumes_list,
                            command = decompress1_cmd,
                            cpus = "1",
                            memory = '3g'
            )

        runDockerCommand( name = "abridge",
                            version = "1.0.0",
                            image_location = "sagnikbanerjee15/abridge",
                            container_name = f"{container_name}_compress",
                            volumes = volumes_list,
                            command = decompress2_cmd,
                            cpus = "1",
                            memory = '3g'
            )

    elif framework_of_choice == "singularity":

        runSingularityCommand( name = "abridge",
                            version = "1.0.0",
                            image_location = "sagnikbanerjee15/abridge",
                            container_name = f"{container_name}_compress",
                            volumes = volumes_list,
                            command = compress_cmd,
                            cpus = "1",
                            memory = '3g'
            )

        runSingularityCommand( name = "abridge",
                            version = "1.0.0",
                            image_location = "sagnikbanerjee15/abridge",
                            container_name = f"{container_name}_decompress1",
                            volumes = volumes_list,
                            command = decompress1_cmd,
                            cpus = "1",
                            memory = '3g'
            )

        runSingularityCommand( name = "abridge",
                            version = "1.0.0",
                            image_location = "sagnikbanerjee15/abridge",
                            container_name = f"{container_name}_decompress2",
                            volumes = volumes_list,
                            command = decompress2_cmd,
                            cpus = "1",
                            memory = '3g'
            )


def main():
    commandLineArg = sys.argv
    if len( commandLineArg ) == 1:
        print( "Please use the --help option to get usage information" )
    options = parseCommandLineArguments()

    if options.test == False and ( options.genome is None or options.output_directory is None or ( options.inputfilename is None and options.compress is True ) or ( options.inputabrfilenames is None and options.decompress is True ) ):
        print( "You must enter the genome, the samfile to compress and container name" )
        return
    else:
        if options.output_directory is None:
            print( "Please enter a valid output directory" )
            return

    if options.error_directory is None:
        options.error_directory = options.output_directory
    output_filename = f"{options.error_directory}.output"
    error_filename = f"{options.error_directory}.error"

    os.system( f"mkdir -p {options.output_directory}" )
    os.system( f"which docker > {options.output_directory}/find_docker" )
    os.system( f"which singularity > {options.output_directory}/find_singularity" )

    docker_installed = 1 if "Command not found" not in open( f"{options.output_directory}/find_docker", "r" ).read() else 0
    singularity_installed = 1 if "Command not found" not in open( f"{options.output_directory}/find_singularity", "r" ).read() else 0

    if docker_installed == 0 and singularity_installed == 0:
        print( "You need to have either docker or singularity installed" )
        sys.exit()

    framework_of_choice = ""
    if options.framework == "docker":
        if docker_installed == 1:
            framework_of_choice = "docker"
        else:
            framework_of_choice = "singularity"

    if options.framework == "singularity":
        if singularity_installed == 1:
            framework_of_choice = "singularity"
        else:
            framework_of_choice = "docker"

    if options.force == True:
        os.system( f"rm -rf {options.output_directory}" )
    os.system( f"mkdir -p {options.output_directory}/singularity_images" )

    ########################################################################################################################
    # Pull down docker or singularity images
    ########################################################################################################################

    list_of_softwares_with_versions = {"samtools":"1.14",
                                       "zpaq":"715",
                                       "fclqc":"latest",
                                       "abridge":"1.1.0"}

    if framework_of_choice == "docker":
        for software in list_of_softwares_with_versions:
            version = list_of_softwares_with_versions[software]
            os.system( f"docker pull ghcr.io/sagnikbanerjee15/docker_tools_and_pipelines/{software}:{version}" )
    else:
        for software in list_of_softwares_with_versions:
            version = list_of_softwares_with_versions[software]
            os.system( f"singularity pull {options.output_directory}/singularity_images/{software}:{version} docker://ghcr.io/sagnikbanerjee15/docker_tools_and_pipelines/{software}:{version}" )

    if options.test == True:
        pool = multiprocessing.Pool( processes = int( options.cpu ) )
        allinputs = []
        # Setting up commands for testing
        for level in ["1", "2", "3"]:  # 3 iterations
            # if level != "3": continue
            for inputfilename in ["/software/Abridge/example/SRR13711353_SE_100000.sam", "/software/Abridge/example/SRR13711353_PE_100000.sam"]:  # 2 iterations
                # if "PE" not in inputfilename:continue
                for ignore_alignment_scores in [0, 1]:  # 2 iterations
                    for ignore_quality_scores in [0, 1]:  # 2 iterations
                        for ignore_soft_clippings in [0, 1]:  # 2 iterations
                            for ignore_mismatches in [0, 1]:  # 2 iterations
                                for ignore_unmapped_reads in [0, 1]:  # 2 iterations
                                    for save_all_quality_scores in [0, 1]:  # 2 iterations
                                        for save_exact_quality_scores in [0, 1]:  # 2 iterations

                                            command_set = []
                                            inputfilename_without_location = inputfilename.split( "/" )[-1][:-4]
                                            output_directory_name = f"{options.output_directory}/"
                                            output_directory_name += f"{inputfilename_without_location}_"
                                            output_directory_name += f"compress_level_{level}_"
                                            output_directory_name += f"ignore_alignment_scores_{ignore_alignment_scores}_"
                                            output_directory_name += f"ignore_quality_scores_{ignore_quality_scores}_"
                                            output_directory_name += f"ignore_soft_clippings_{ignore_soft_clippings}_"
                                            output_directory_name += f"ignore_mismatches_{ignore_mismatches}_"
                                            output_directory_name += f"ignore_unmapped_reads_{ignore_unmapped_reads}_"
                                            output_directory_name += f"save_all_quality_scores_{save_all_quality_scores}_"
                                            output_directory_name += f"save_exact_quality_scores_{save_exact_quality_scores}_"
                                            output_directory_name += f"{framework_of_choice}"

                                            os.system( f"mkdir -p {output_directory_name}" )
                                            os.system( f"chmod a+x {output_directory_name}" )

                                            volumes_list = [f"{options.output_directory}:{options.output_directory}"]

                                            cmd = f" \" "
                                            cmd += f" abridge "
                                            cmd += f" --keep_intermediate_error_files "
                                            cmd += f" --compress "
                                            cmd += f" --genome /software/Abridge/example/arath_1.fa "
                                            cmd += f" --inputfilename {inputfilename} "
                                            cmd += f" --output_directory {output_directory_name} "
                                            cmd += f" --level {level} "
                                            if ignore_alignment_scores == 1:
                                                cmd += f" --ignore_alignment_scores "
                                            if ignore_quality_scores == 1:
                                                cmd += f" --ignore_quality_scores "
                                            if ignore_soft_clippings == 1:
                                                cmd += f" --ignore_soft_clippings "
                                            if ignore_mismatches == 1:
                                                cmd += f" --ignore_mismatches "
                                            if ignore_unmapped_reads == 1:
                                                cmd += f" --ignore_unmapped_reads "
                                            if save_all_quality_scores == 1:
                                                cmd += f" --save_all_quality_scores "
                                            if save_exact_quality_scores == 1:
                                                cmd += f" --save_exact_quality_scores "

                                            cmd += f" 1> {output_directory_name}.output "
                                            cmd += f" 2> {output_directory_name}.error "
                                            cmd += f" \" "
                                            command_set.append( cmd )
                                            # print( cmd )
                                            # os.system(cmd)

                                            volumes_list = list( set( volumes_list ) )

                                            output_directory_name_without_location = output_directory_name.split( "/" )[-1]
                                            for ignore_sequence in [0, 1]:  # 2 iterations
                                                output_directory_name = f"{options.output_directory}/"
                                                output_directory_name += f"{inputfilename_without_location}_"
                                                output_directory_name += f"decompress_level_{level}_"
                                                output_directory_name += f"ignore_alignment_scores_{ignore_alignment_scores}_"
                                                output_directory_name += f"ignore_quality_scores_{ignore_quality_scores}_"
                                                output_directory_name += f"ignore_soft_clippings_{ignore_soft_clippings}_"
                                                output_directory_name += f"ignore_mismatches_{ignore_mismatches}_"
                                                output_directory_name += f"ignore_unmapped_reads_{ignore_unmapped_reads}_"
                                                output_directory_name += f"save_all_quality_scores_{save_all_quality_scores}_"
                                                output_directory_name += f"save_exact_quality_scores_{save_exact_quality_scores}_"
                                                output_directory_name += f"{framework_of_choice}_"
                                                output_directory_name += f"ignore_sequence_{ignore_sequence}"

                                                cmd = f" \" "
                                                cmd += f" abridge "
                                                cmd += f" --keep_intermediate_error_files "
                                                cmd += f" --decompress "
                                                cmd += f" --genome /software/Abridge/example/arath_1.fa "
                                                cmd += f" --inputabrfilenames {output_directory_name.split('_ignore_sequence_')[0].replace('decompress','compress')}/{inputfilename_without_location}.abridge "
                                                cmd += f" --output_directory {output_directory_name} "
                                                if ignore_sequence == 1:
                                                    cmd += " --ignore_sequence "

                                                cmd += f" 1> {output_directory_name}.output"
                                                cmd += f" 2> {output_directory_name}.error"
                                                cmd += f" \" "
                                                # print( cmd )
                                                command_set.append( cmd )

                                            command_set.append( output_directory_name.replace( "/", "-" )[1:] )
                                            command_set.append( volumes_list )
                                            command_set.append( framework_of_choice )
                                            # if len( allinputs ) < 1:
                                            allinputs.append( command_set )
                                            # if len( allinputs ) >= 10: break
        pool.map( runDockerOrSingularityInParallel, allinputs )

    else:
        volumes_list = [f"{'/'.join(options.genome.split('/')[:-1])}:{'/'.join(options.genome.split('/')[:-1])}",
                                                 f"{options.output_directory}:{options.output_directory}",
                                                 f"{options.error_directory}:{options.error_directory}",
                                                 ]

        cmd = f" \" "
        cmd += f" abridge "
        if options.keep_intermediate_error_files == True:
            cmd += f" --keep_intermediate_error_files "
        if options.compress == True:
            cmd += f" --compress "
            cmd += f" --inputfilename {options.inputfilename} "
            volumes_list.append( f"{'/'.join(options.inputfilename.split('/')[:-1])}:{'/'.join(options.inputfilename.split('/')[:-1])}", )
        elif options.decompress == True:
            cmd += f" --decompress "
            cmd += f" --inputabrfilenames {options.inputabrfilenames} "
            volumes_list.append( f"{'/'.join(options.inputabrfilenames.split('/')[:-1])}:{'/'.join(options.inputabrfilenames.split('/')[:-1])}", )
        cmd += f" --genome {options.genome} "
        cmd += f" --output_directory {options.output_directory} "
        if options.ignore_alignment_scores == True:
            cmd += f" --ignore_alignment_scores "
        if options.ignore_quality_scores == True:
            cmd += f" --ignore_quality_scores "
        if options.ignore_soft_clippings == True:
            cmd += f" --ignore_soft_clippings "
        if options.ignore_mismatches == True:
            cmd += f" --ignore_mismatches "
        if options.ignore_unmapped_reads == True:
            cmd += f" --ignore_unmapped_reads "
        cmd += f" --framework {framework_of_choice}"
        cmd += f" 1> {output_filename}"
        cmd += f" 2> {error_filename}"
        cmd += f" \" "

        volumes_list = list( set( volumes_list ) )

        # os.system( cmd )

        if framework_of_choice == "docker":
            runDockerCommand( name = "abridge",
                                version = list_of_softwares_with_versions['abridge'],
                                image_location = f"ghcr.io/sagnikbanerjee15/docker_tools_and_pipelines/abridge",
                                container_name = f"{options.output_directory.split('/')[-1]}",
                                volumes = volumes_list,
                                command = cmd,
                                cpus = options.cpu,
                                memory = '100g'
                )

        elif framework_of_choice == "singularity":
            runSingularityCommand( name = "abridge",
                                version = list_of_softwares_with_versions['abridge'],
                                image_location = "ghcr.io/sagnikbanerjee15/docker_tools_and_pipelines/abridge",
                                container_name = f"{options.output_directory.split('/')[-1]}",
                                volumes = volumes_list,
                                command = cmd,
                                cpus = options.cpu,
                                memory = '100g'
                )


if __name__ == "__main__":
    main()