def test_more_samples(method):
for sample_name in ["sample_v2", "sample_v3", "sample_v4"]:
if method == "GATB" and sample_name in ["sample_v3", "sample_v2"]:
# GATB long headers bug
continue
infile = bioconvert_data("{}.fastq".format(sample_name))
expected_outfile = bioconvert_data("{}.fasta".format(sample_name))
with TempFile(suffix=".fasta") as expected_unwrapped:
Fastq2Fasta.unwrap_fasta(
expected_outfile, expected_unwrapped.name, strip_comment=True)
md5out = md5(expected_unwrapped.name)
# One temporary file for the fasta created using the method
# and one for an unwrapped version.
# Some methods may output multi-line fasta, so we need to
# compare md5 sums of unwrapped versions.
with TempFile(suffix=".fasta") as outfile, \
TempFile(suffix=".fasta") as unwrapped:
convert = Fastq2Fasta(infile, outfile.name)
convert(method=method)
Fastq2Fasta.unwrap_fasta(
outfile.name, unwrapped.name, strip_comment=True)
assert md5(unwrapped.name) == md5out, \
"{} failed for {}".format(method, sample_name)
def test_conv(method):
infile = bioconvert_data("test_fastq2fasta_v1.fastq")
expected_outfile = bioconvert_data("test_fastq2fasta_v1.fasta")
with TempFile(suffix=".fasta") as expected_unwrapped:
Fastq2Fasta.unwrap_fasta(
expected_outfile, expected_unwrapped.name, strip_comment=True)
md5out = md5(expected_unwrapped.name)
# One temporary file for the fasta created using the method
# and one for an unwrapped version.
# Some methods may output multi-line fasta, so we need to
# compare md5 sums of unwrapped versions.
with TempFile(suffix=".fasta") as outfile, \
TempFile(suffix=".fasta") as unwrapped:
convert = Fastq2Fasta(infile, outfile.name)
convert(method=method)
Fastq2Fasta.unwrap_fasta(
outfile.name, unwrapped.name, strip_comment=True)
assert md5(unwrapped.name) == md5out, \
"{} failed".format(method)