def main():
    option_parser, opts, args = \
        parse_command_line_parameters(suppress_verbose=True, **script_info)
        
    input_dir = opts.input_dir
    parameter_fp = opts.parameter_fp
    read1_indicator = opts.read1_indicator
    read2_indicator = opts.read2_indicator
    match_barcodes = opts.match_barcodes
    barcode_indicator = opts.barcode_indicator
    leading_text = opts.leading_text
    trailing_text = opts.trailing_text
    include_input_dir_path = opts.include_input_dir_path
    output_dir = abspath(opts.output_dir)
    remove_filepath_in_name = opts.remove_filepath_in_name
    print_only = opts.print_only
    
    if remove_filepath_in_name and not include_input_dir_path:
        option_parser.error("If --remove_filepath_in_name is enabled, "
            "--include_input_dir_path must also be enabled.")

    if opts.parameter_fp:
        with open(opts.parameter_fp, 'U') as parameter_f:
            params_dict = parse_qiime_parameters(parameter_f)
        params_str = get_params_str(params_dict['join_paired_ends'])
    else:
        params_dict = {}
        params_str = ""

    create_dir(output_dir)
    
    all_files = []
    extensions = ['.fastq.gz', '.fastq', '.fq.gz', '.fq']
    
    for root, dir, fps in walk(input_dir):
        for fp in fps:
            for extension in extensions:
                if fp.endswith(extension):
                    all_files += [abspath(join(root, fp))]
        
    pairs, bc_pairs = get_pairs(all_files, read1_indicator, read2_indicator,
        match_barcodes, barcode_indicator)

    commands = create_commands_jpe(pairs, output_dir,
        params_str, leading_text, trailing_text, include_input_dir_path,
        remove_filepath_in_name, match_barcodes, bc_pairs)
        
    qiime_config = load_qiime_config()
    if print_only:
        command_handler = print_commands
    else:
        command_handler = call_commands_serially
    logger = WorkflowLogger(generate_log_fp(output_dir),
                            params=params_dict,
                            qiime_config=qiime_config)
    # Call the command handler on the list of commands
    command_handler(commands,
                    status_update_callback=no_status_updates,
                    logger=logger,
                    close_logger_on_success=True)
Example #2
0
    def test_create_commands_jpe_added_options(self):
        """ Properly creates commands with all optional parameters """

        pairs = {'dir1/f_read1.fastq':'dir1/r_read1.fastq',
            'dir2/f_read2.fastq':'dir2/r_read2.fastq'}
        base_output_dir = "output_dir/"
        optional_params = "-m OtherMethod"
        leading_text = "Echo"
        trailing_text = "| qsub COMMANDxxx"
        include_input_dir_path=True
        remove_filepath_in_name=True

        commands = create_commands_jpe(pairs, base_output_dir,
            optional_params, leading_text, trailing_text,
            include_input_dir_path, remove_filepath_in_name)

        actual_commands = []
        for n in commands:
            actual_commands.append(n[0][1])
        actual_commands = set(actual_commands)

        expected_commands = set(['Echo join_paired_ends.py -m OtherMethod -f dir2/f_read2.fastq -r dir2/r_read2.fastq -o output_dir/dir2 | qsub COMMANDxxx',
            'Echo join_paired_ends.py -m OtherMethod -f dir1/f_read1.fastq -r dir1/r_read1.fastq -o output_dir/dir1 | qsub COMMANDxxx'])

        self.assertEqual(actual_commands, expected_commands)
Example #3
0
    def test_create_commands_jpe_bcs(self):
        """ Properly creates commands with matched bcs """

        pairs = {'f_read1.fastq':'r_read1.fastq',
            'f_read2.fastq':'r_read2.fastq'}
        base_output_dir = "output_dir/"
        optional_params = ""
        leading_text = ""
        trailing_text = ""
        include_input_dir_path=False
        remove_filepath_in_name=False
        match_barcodes = True
        bc_pairs = {'f_read1.fastq':'b_read1.fastq',
            'f_read2.fastq':'b_read2.fastq'}

        commands = create_commands_jpe(pairs, base_output_dir,
            optional_params, leading_text, trailing_text,
            include_input_dir_path, remove_filepath_in_name,
            match_barcodes, bc_pairs)

        actual_commands = []
        for n in commands:
            actual_commands.append(n[0][1])
        actual_commands = set(actual_commands)

        expected_commands = set(['join_paired_ends.py  -b b_read1.fastq -f f_read1.fastq -r r_read1.fastq -o output_dir/f_read1 ',
            'join_paired_ends.py  -b b_read2.fastq -f f_read2.fastq -r r_read2.fastq -o output_dir/f_read2 '])

        self.assertEqual(actual_commands, expected_commands)
Example #4
0
    def test_create_commands_jpe_added_options(self):
        """ Properly creates commands with all optional parameters """

        pairs = {'dir1/f_read1.fastq':'dir1/r_read1.fastq',
            'dir2/f_read2.fastq':'dir2/r_read2.fastq'}
        base_output_dir = "output_dir/"
        optional_params = "-m OtherMethod"
        leading_text = "Echo"
        trailing_text = "| qsub COMMANDxxx"
        include_input_dir_path=True
        remove_filepath_in_name=True

        commands = create_commands_jpe(pairs, base_output_dir,
            optional_params, leading_text, trailing_text,
            include_input_dir_path, remove_filepath_in_name)

        actual_commands = []
        for n in commands:
            actual_commands.append(n[0][1])
        actual_commands = set(actual_commands)

        expected_commands = set(['Echo join_paired_ends.py -m OtherMethod -f dir2/f_read2.fastq -r dir2/r_read2.fastq -o output_dir/dir2 | qsub COMMANDxxx',
            'Echo join_paired_ends.py -m OtherMethod -f dir1/f_read1.fastq -r dir1/r_read1.fastq -o output_dir/dir1 | qsub COMMANDxxx'])

        self.assertEqual(actual_commands, expected_commands)
Example #5
0
    def test_create_commands_jpe_bcs(self):
        """ Properly creates commands with matched bcs """

        pairs = {'f_read1.fastq':'r_read1.fastq',
            'f_read2.fastq':'r_read2.fastq'}
        base_output_dir = "output_dir/"
        optional_params = ""
        leading_text = ""
        trailing_text = ""
        include_input_dir_path=False
        remove_filepath_in_name=False
        match_barcodes = True
        bc_pairs = {'f_read1.fastq':'b_read1.fastq',
            'f_read2.fastq':'b_read2.fastq'}

        commands = create_commands_jpe(pairs, base_output_dir,
            optional_params, leading_text, trailing_text,
            include_input_dir_path, remove_filepath_in_name,
            match_barcodes, bc_pairs)

        actual_commands = []
        for n in commands:
            actual_commands.append(n[0][1])
        actual_commands = set(actual_commands)

        expected_commands = set(['join_paired_ends.py  -b b_read1.fastq -f f_read1.fastq -r r_read1.fastq -o output_dir/f_read1 ',
            'join_paired_ends.py  -b b_read2.fastq -f f_read2.fastq -r r_read2.fastq -o output_dir/f_read2 '])

        self.assertEqual(actual_commands, expected_commands)
Example #6
0
def main():
    option_parser, opts, args = \
        parse_command_line_parameters(suppress_verbose=True, **script_info)

    input_dir = opts.input_dir
    parameter_fp = opts.parameter_fp
    read1_indicator = opts.read1_indicator
    read2_indicator = opts.read2_indicator
    match_barcodes = opts.match_barcodes
    barcode_indicator = opts.barcode_indicator
    leading_text = opts.leading_text
    trailing_text = opts.trailing_text
    include_input_dir_path = opts.include_input_dir_path
    output_dir = abspath(opts.output_dir)
    remove_filepath_in_name = opts.remove_filepath_in_name
    print_only = opts.print_only

    if remove_filepath_in_name and not include_input_dir_path:
        option_parser.error("If --remove_filepath_in_name is enabled, "
                            "--include_input_dir_path must also be enabled.")

    if opts.parameter_fp:
        with open(opts.parameter_fp, 'U') as parameter_f:
            params_dict = parse_qiime_parameters(parameter_f)
        params_str = get_params_str(params_dict['join_paired_ends'])
    else:
        params_dict = {}
        params_str = ""

    create_dir(output_dir)

    all_files = []
    extensions = ['.fastq.gz', '.fastq', '.fq.gz', '.fq']

    for root, dir, fps in walk(input_dir):
        for fp in fps:
            for extension in extensions:
                if fp.endswith(extension):
                    all_files += [abspath(join(root, fp))]

    pairs, bc_pairs = get_pairs(all_files, read1_indicator, read2_indicator,
                                match_barcodes, barcode_indicator)

    commands = create_commands_jpe(pairs, output_dir, params_str, leading_text,
                                   trailing_text, include_input_dir_path,
                                   remove_filepath_in_name, match_barcodes,
                                   bc_pairs)

    qiime_config = load_qiime_config()
    if print_only:
        command_handler = print_commands
    else:
        command_handler = call_commands_serially
    logger = WorkflowLogger(generate_log_fp(output_dir),
                            params=params_dict,
                            qiime_config=qiime_config)
    # Call the command handler on the list of commands
    command_handler(commands,
                    status_update_callback=no_status_updates,
                    logger=logger,
                    close_logger_on_success=True)