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)
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)
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)
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)
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)
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)