def test_generate_per_sample_fastq_command_error_barcodes(self):
fd, fp = mkstemp()
close(fd)
with open(fp, 'w') as f:
f.write(MAPPING_FILE)
self._clean_up_files.append(fp)
forward_seqs = ["s1.fastq.gz", "s2.fastq.gz", "s3.fastq.gz"]
reverse_seqs = [
"s1_rev.fastq.gz", "s2_rev.fastq.gz", "s3_rev.fastq.gz"
]
barcode_fps = [
"s1_barcodes.fastq.gz", "s2_barcodes.fastq.gz",
"s3_barcodes.fastq.gz"
]
mapping_file = fp
output_dir = "/output/dir"
params_str = (
"--max_bad_run_length 3 --min_per_read_length_fraction 0.75 "
"--sequence_max_n 0 --phred_quality_threshold 3 "
"--barcode_type golay_12 --max_barcode_errors 1.5 "
"--rev_comp_mapping_barcodes")
with self.assertRaises(ValueError):
generate_per_sample_fastq_command(forward_seqs, reverse_seqs,
barcode_fps, mapping_file,
output_dir, params_str)
def test_generate_per_sample_fastq_command_regex(self):
fd, fp = mkstemp()
close(fd)
with open(fp, 'w') as f:
f.write(MAPPING_FILE)
self._clean_up_files.append(fp)
forward_seqs = ["1_s1.fastq.gz", "1_s2.fastq.gz", "1_s3.fastq.gz"]
reverse_seqs = ["1_s1_rev.fastq.gz", "1_s2_rev.fastq.gz",
"1_s3_rev.fastq.gz"]
barcode_fps = []
mapping_file = fp
output_dir = "/output/dir"
params_str = (
"--max_bad_run_length 3 --min_per_read_length_fraction 0.75 "
"--sequence_max_n 0 --phred_quality_threshold 3 "
"--barcode_type golay_12 --max_barcode_errors 1.5 "
"--rev_comp_mapping_barcodes")
obs = generate_per_sample_fastq_command(
forward_seqs, reverse_seqs, barcode_fps,
mapping_file, output_dir, params_str)
exp = ("split_libraries_fastq.py --store_demultiplexed_fastq -i "
"1_s1.fastq.gz,1_s2.fastq.gz,1_s3.fastq.gz --sample_ids "
"SKB8.640193,SKD8.640184,SKB7.640196 -o /output/dir "
"--max_bad_run_length 3 --min_per_read_length_fraction 0.75 "
"--sequence_max_n 0 --phred_quality_threshold 3 "
"--barcode_type golay_12 --max_barcode_errors 1.5 "
"--rev_comp_mapping_barcodes")
self.assertEqual(obs, exp)
def test_generate_per_sample_fastq_command(self):
fd, fp = mkstemp()
close(fd)
with open(fp, 'w') as f:
f.write(MAPPING_FILE)
self._clean_up_files.append(fp)
forward_seqs = ["s1.fastq.gz", "s2.fastq.gz", "s3.fastq.gz"]
reverse_seqs = [
"s1_rev.fastq.gz", "s2_rev.fastq.gz", "s3_rev.fastq.gz"
]
barcode_fps = []
mapping_file = fp
output_dir = "/output/dir"
params_str = (
"--max_bad_run_length 3 --min_per_read_length_fraction 0.75 "
"--sequence_max_n 0 --phred_quality_threshold 3 "
"--barcode_type golay_12 --max_barcode_errors 1.5 "
"--rev_comp_mapping_barcodes")
obs = generate_per_sample_fastq_command(forward_seqs, reverse_seqs,
barcode_fps, mapping_file,
output_dir, params_str)
exp = ("split_libraries_fastq.py --store_demultiplexed_fastq -i "
"s1.fastq.gz,s2.fastq.gz,s3.fastq.gz --sample_ids "
"SKB8.640193,SKD8.640184,SKB7.640196 -o /output/dir "
"--max_bad_run_length 3 --min_per_read_length_fraction 0.75 "
"--sequence_max_n 0 --phred_quality_threshold 3 "
"--barcode_type golay_12 --max_barcode_errors 1.5 "
"--rev_comp_mapping_barcodes")
self.assertEqual(obs, exp)
def test_generate_per_sample_fastq_command_error_prefixes(self):
fd, fp = mkstemp()
close(fd)
with open(fp, 'w') as f:
f.write(MAPPING_FILE)
self._clean_up_files.append(fp)
forward_seqs = ["s1.fastq.gz", "s2.fastq.gz", "sX.fastq.gz"]
reverse_seqs = ["s1_rev.fastq.gz", "s2_rev.fastq.gz",
"sX_rev.fastq.gz"]
barcode_fps = []
mapping_file = fp
output_dir = "/output/dir"
params_str = (
"--max_bad_run_length 3 --min_per_read_length_fraction 0.75 "
"--sequence_max_n 0 --phred_quality_threshold 3 "
"--barcode_type golay_12 --max_barcode_errors 1.5 "
"--rev_comp_mapping_barcodes")
with self.assertRaises(ValueError):
generate_per_sample_fastq_command(
forward_seqs, reverse_seqs, barcode_fps,
mapping_file, output_dir, params_str)
