def test_flash(pipeline_dir):
# Test using FLASH and parsing its log output
with chdir(pipeline_dir):
modify_configuration(settings=[("merge_program", "flash")])
run_snakemake(targets=["stats/reads.json"])
# Ensure FLASH was actually run
assert (pipeline_dir / "reads/2-flash.log").exists()
def init_testdata(directory):
run_init(
database="testdata/database",
reads1="testdata/reads.1.fastq.gz",
directory=str(directory),
)
with chdir(directory):
modify_configuration([("barcode_length_3prime", "21")])
def test_primers(pipeline_dir):
# Test whether specifying primer sequences leads to a SyntaxError
with chdir(pipeline_dir):
modify_configuration(settings=[
("forward_primers", "['CGTGA']"),
("reverse_primers", "['TTCAC']"),
], )
run_snakemake(dryrun=True)
def test_modify_configuration(pipeline_dir):
modify_configuration(
settings=[("d_coverage", "12"), ("j_discovery.allele_ratio", "0.37")],
path=str(pipeline_dir / "igdiscover.yaml"),
)
import ruamel.yaml
with open(pipeline_dir / "igdiscover.yaml") as f:
config = ruamel.yaml.safe_load(f)
assert config["d_coverage"] == 12
assert config["j_discovery"]["allele_ratio"] == 0.37
def test_modify_configuration(pipeline_dir):
modify_configuration(
settings=[("d_coverage", "12"), ("j_discovery.allele_ratio", "0.37")],
path=str(pipeline_dir / "igdiscover.yaml"),
)
from ruamel.yaml import YAML
yaml = YAML(typ="safe", pure=True)
with open(pipeline_dir / "igdiscover.yaml") as f:
config = yaml.load(f)
assert config["d_coverage"] == 12
assert config["j_discovery"]["allele_ratio"] == 0.37
def test_fastq_input(has_filtered_tab, tmp_path):
# Use merged reads from already-run pipeline as input for a new run
single_reads = has_filtered_tab / "reads" / "2-merged.fastq.gz"
directory = tmp_path / "singleend-fastq"
run_init(
database="testdata/database",
single_reads=str(single_reads),
directory=str(directory),
)
with chdir(directory):
modify_configuration([("barcode_length_3prime", "21")])
run_snakemake(targets=["stats/reads.json"])
def test_fasta_input(has_filtered_tab, tmp_path):
fasta_path = tmp_path / "justfasta.fasta"
convert_fastq_to_fasta(
has_filtered_tab / "reads" / "2-merged.fastq.gz",
fasta_path,
)
directory = tmp_path / "singleend-fasta"
run_init(
database="testdata/database",
single_reads=str(fasta_path),
directory=str(directory),
)
with chdir(directory):
modify_configuration([("barcode_length_3prime", "21")])
run_snakemake(targets=["stats/reads.json"])
def test_only_forward_primer(pipeline_dir):
# issue #107 (broken symlink)
with chdir(pipeline_dir):
modify_configuration(settings=[("forward_primers", "['CGTGA']")])
# Create some dummy files so we don’t need to run irrelevant steps of the pipeline
r = Path("reads")
r.mkdir()
with xopen(r / "2-merged.fastq.gz", "w") as f:
pass
s = Path("stats")
s.mkdir()
with open(s / "merging-successful", "w") as f:
pass
with open(s / "reads.json", "w") as f:
f.write('{"total": 0}')
with open(s / "trimmed.json", "w") as f:
f.write('{"trimmed": 0}')
run_snakemake(targets=["reads/sequences.fasta.gz"])