def test_fastq_context_manager(): filename = "tests/data/simple.fastq" with open(filename) as f: assert not f.closed reads = list(seqio.open(f)) assert not f.closed assert f.closed with seqio.FastqReader(filename) as sr: tmp_sr = sr assert not sr.fp.closed reads = list(sr) assert not sr.fp.closed assert tmp_sr.fp is None
def test_fastq_incomplete():
fastq = StringIO("@name\nACGT+\n")
with seqio.FastqReader(fastq) as fq:
list(fq)
def test_fastq_wrongformat():
with seqio.FastqReader("tests/data/withplus.fastq") as f:
reads = list(f)
def test_fastqreader_dos():
with seqio.FastqReader("tests/data/dos.fastq") as f:
dos_reads = list(f)
with seqio.FastqReader("tests/data/small.fastq") as f:
unix_reads = list(f)
assert dos_reads == unix_reads
def test_fastqreader():
with seqio.FastqReader("tests/data/simple.fastq") as f:
reads = list(f)
assert reads == simple_fastq