def test_sra2fastq_gz(method):
infile = "SRR390728"
outfile = bioconvert_data("SRR390728_1.fastq")
outfile2 = bioconvert_data("SRR390728_2.fastq")
with TempFile(suffix=".fastq.gz") as tempfile:
converter = SRA2FASTQ(infile, tempfile.name, True)
converter(method=method)
outbasename, ext = os.path.splitext(tempfile.name)
if ext == ".gz":
outbasename, ext = os.path.splitext(outbasename)
with gzip.open(outbasename + "_1.fastq.gz",
'rb') as f_in, open(outbasename + "_1.fastq",
'wb') as f_out:
shutil.copyfileobj(f_in, f_out)
with gzip.open(outbasename + "_2.fastq.gz",
'rb') as f_in, open(outbasename + "_2.fastq",
'wb') as f_out:
shutil.copyfileobj(f_in, f_out)
# Check that the output is correct with a checksum
assert md5(outbasename + "_1.fastq") == md5(outfile)
assert md5(outbasename + "_2.fastq") == md5(outfile2)