def test_creat_commands_slf_exception(self):
all_files = ['sample1_r1.fastq', 'sample2_r1.fastq']
demultiplexing_method = 'sampleid_by_file'
output_dir = 'foo-boo-loo-bloop'
with self.assertRaises(IOError):
actual_command = create_commands_slf(all_files,
demultiplexing_method,
output_dir)[0][0][1]
def test_create_commands_slf_by_sampleID(self):
""" Properly creates commands for SampleIDs options """
all_files = ['sample1_r1.fastq', 'sample2_r1.fastq']
demultiplexing_method = 'sampleid_by_file'
output_dir = "sl_out"
actual_command = create_commands_slf(all_files, demultiplexing_method,
output_dir)[0][0][1]
expected_command = "split_libraries_fastq.py -i sample1_r1.fastq,sample2_r1.fastq --sample_ids sample1,sample2 -o sl_out --barcode_type 'not-barcoded'"
self.assertEqual(actual_command, expected_command)
def test_create_commands_slf_by_sampleID(self):
""" Properly creates commands for SampleIDs options """
all_files = ['sample1_r1.fastq', 'sample2_r1.fastq']
demultiplexing_method = 'sampleid_by_file'
output_dir = "sl_out"
actual_command = create_commands_slf(all_files, demultiplexing_method,
output_dir)[0][0][1]
expected_command = "split_libraries_fastq.py -i sample1_r1.fastq,sample2_r1.fastq --sample_ids sample1,sample2 -o sl_out --barcode_type 'not-barcoded'"
self.assertEqual(actual_command, expected_command)
def test_create_commands_slf_mapping_barcodes(self):
""" Properly creates commands for barcode/mapping files option """
all_files = {'sample1_r1.fastq':('sample1_mapping.txt',
'sample1_bc.fastq'), 'sample2_r1.fastq':('sample2_mapping.txt',
'sample2_bc.fastq')}
demultiplexing_method = 'mapping_barcode_files'
output_dir = "sl_out"
actual_command = create_commands_slf(all_files, demultiplexing_method,
output_dir)[0][0][1]
expected_command = "split_libraries_fastq.py -i sample1_r1.fastq,sample2_r1.fastq --barcode_read_fps sample1_mapping.txt,sample2_mapping.txt --mapping_fps sample1_bc.fastq,sample2_bc.fastq -o sl_out "
self.assertEqual(actual_command, expected_command)
def test_create_commands_slf_mapping_barcodes(self):
""" Properly creates commands for barcode/mapping files option """
all_files = {'sample1_r1.fastq':('sample1_mapping.txt',
'sample1_bc.fastq'), 'sample2_r1.fastq':('sample2_mapping.txt',
'sample2_bc.fastq')}
demultiplexing_method = 'mapping_barcode_files'
output_dir = "sl_out"
actual_command = create_commands_slf(all_files, demultiplexing_method,
output_dir)[0][0][1]
expected_command = "split_libraries_fastq.py -i sample1_r1.fastq,sample2_r1.fastq --barcode_read_fps sample1_mapping.txt,sample2_mapping.txt --mapping_fps sample1_bc.fastq,sample2_bc.fastq -o sl_out "
self.assertEqual(actual_command, expected_command)
def test_create_commands_slf_by_sampleID(self):
""" Properly creates commands for SampleIDs options """
all_files = ['sample1_r1.fastq', 'sample2_r1.fastq']
demultiplexing_method = 'sampleid_by_file'
# the output directory has to exist
output_dir = self.temp_dir
actual_command = create_commands_slf(all_files, demultiplexing_method,
output_dir)[0][0][1]
expected = ("split_libraries_fastq.py -i {output_dir}/seqs.txt -o "
"{output_dir} --read_arguments_from_file --sample_ids "
"{output_dir}/sample_ids.txt --barcode_type "
"'not-barcoded' ").format(output_dir=output_dir)
self.assertEqual(actual_command, expected)
def test_create_commands_slf_added_options(self):
""" Properly creates slf commands with added parameters """
all_files = ['sample1/sample_r1.fastq', 'sample2/sample_r1.fastq']
demultiplexing_method = 'sampleid_by_file'
output_dir = "sl_out"
params = "--max_bad_run_length 15"
leading_text = "echo"
trailing_text = " | qsub -N BigErn -k oe"
include_input_dir_path = True
remove_filepath_in_name = True
actual_command = create_commands_slf(all_files, demultiplexing_method,
output_dir, params, leading_text, trailing_text,
include_input_dir_path, remove_filepath_in_name)[0][0][1]
expected_command = "echo split_libraries_fastq.py --max_bad_run_length 15 -i sample1/sample_r1.fastq,sample2/sample_r1.fastq --sample_ids sample1,sample2 -o sl_out | qsub -N BigErn -k oe --barcode_type 'not-barcoded'"
self.assertEqual(actual_command, expected_command)
def test_create_commands_slf_added_options(self):
""" Properly creates slf commands with added parameters """
all_files = ['sample1/sample_r1.fastq', 'sample2/sample_r1.fastq']
demultiplexing_method = 'sampleid_by_file'
output_dir = "sl_out"
params = "--max_bad_run_length 15"
leading_text = "echo"
trailing_text = " | qsub -N BigErn -k oe"
include_input_dir_path = True
remove_filepath_in_name = True
actual_command = create_commands_slf(all_files, demultiplexing_method,
output_dir, params, leading_text, trailing_text,
include_input_dir_path, remove_filepath_in_name)[0][0][1]
expected_command = "echo split_libraries_fastq.py --max_bad_run_length 15 -i sample1/sample_r1.fastq,sample2/sample_r1.fastq --sample_ids sample1,sample2 -o sl_out | qsub -N BigErn -k oe --barcode_type 'not-barcoded'"
self.assertEqual(actual_command, expected_command)
def test_create_commands_slf_mapping_barcodes(self):
""" Properly creates commands for barcode/mapping files option """
all_files = {'sample1_r1.fastq':('sample1_mapping.txt',
'sample1_bc.fastq'), 'sample2_r1.fastq':('sample2_mapping.txt',
'sample2_bc.fastq')}
demultiplexing_method = 'mapping_barcode_files'
# the output directory has to exist
output_dir = self.temp_dir
actual_command = create_commands_slf(all_files, demultiplexing_method,
output_dir)[0][0][1]
expected = ("split_libraries_fastq.py -i {output_dir}/seqs.txt -o "
"{output_dir} --read_arguments_from_file "
"--barcode_read_fps {output_dir}/barcodes.txt "
"--mapping_fps {output_dir}/maps.txt ").format(
output_dir=output_dir)
self.assertEqual(actual_command, expected)
def test_create_commands_slf_added_options(self):
""" Properly creates slf commands with added parameters """
all_files = ['sample1/sample_r1.fastq', 'sample2/sample_r1.fastq']
demultiplexing_method = 'sampleid_by_file'
# the output directory has to exist
output_dir = self.temp_dir
params = "--max_bad_run_length 15"
leading_text = "echo"
trailing_text = " | qsub -N BigErn -k oe"
include_input_dir_path = True
remove_filepath_in_name = True
actual_command = create_commands_slf(all_files, demultiplexing_method,
output_dir, params, leading_text, trailing_text,
include_input_dir_path, remove_filepath_in_name)[0][0][1]
expected = ("echo split_libraries_fastq.py --max_bad_run_length 15 -i "
"{output_dir}/seqs.txt -o {output_dir} "
"--read_arguments_from_file --sample_ids "
"{output_dir}/sample_ids.txt --barcode_type 'not-barcoded'"
" | qsub -N BigErn -k oe").format(output_dir=output_dir)
self.assertEqual(actual_command, expected)
def main():
option_parser, opts, args =\
parse_command_line_parameters(suppress_verbose=True, **script_info)
input_dir = opts.input_dir
demultiplexing_method = opts.demultiplexing_method
parameter_fp = opts.parameter_fp
read_indicator = opts.read_indicator
barcode_indicator = opts.barcode_indicator
mapping_indicator = opts.mapping_indicator
mapping_extensions = opts.mapping_extensions.split(',')
sampleid_indicator = opts.sampleid_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 enabled, "
"--include_input_dir_path must 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['split_libraries_fastq'])
else:
params_dict = {}
params_str = ""
create_dir(output_dir)
all_fastq = []
all_mapping = []
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_fastq += [abspath(join(root, fp))]
if demultiplexing_method == 'mapping_barcode_files':
for root, dir, fps in walk(input_dir):
for fp in fps:
for mapping_extension in mapping_extensions:
if fp.endswith(mapping_extension):
all_mapping += [abspath(join(root, fp))]
all_files = get_matching_files(all_fastq, all_mapping, read_indicator,
barcode_indicator, mapping_indicator)
else:
all_files = all_fastq
commands = create_commands_slf(all_files, demultiplexing_method,
output_dir, params_str, leading_text,
trailing_text, include_input_dir_path,
remove_filepath_in_name, sampleid_indicator)
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 main():
option_parser, opts, args =\
parse_command_line_parameters(suppress_verbose=True, **script_info)
input_dir = opts.input_dir
demultiplexing_method = opts.demultiplexing_method
parameter_fp = opts.parameter_fp
read_indicator = opts.read_indicator
barcode_indicator = opts.barcode_indicator
mapping_indicator = opts.mapping_indicator
mapping_extensions = opts.mapping_extensions.split(',')
sampleid_indicator = opts.sampleid_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 enabled, "
"--include_input_dir_path must 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['split_libraries_fastq'])
else:
params_dict = {}
params_str = ""
create_dir(output_dir)
all_fastq = []
all_mapping = []
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_fastq += [abspath(join(root, fp))]
if demultiplexing_method == 'mapping_barcode_files':
for root, dir, fps in walk(input_dir):
for fp in fps:
for mapping_extension in mapping_extensions:
if fp.endswith(mapping_extension):
all_mapping += [abspath(join(root, fp))]
all_files = get_matching_files(all_fastq, all_mapping,
read_indicator, barcode_indicator, mapping_indicator)
else:
all_files = all_fastq
commands = create_commands_slf(all_files, demultiplexing_method, output_dir,
params_str, leading_text, trailing_text, include_input_dir_path,
remove_filepath_in_name, sampleid_indicator)
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)