def test_convert_tsv_tsv(self):
"""Test converting tsv to tsv."""
with TemporaryDirectory() as tmpdir:
convert(self.path / "unwrapped_quals.tsv",
Path(tmpdir) / "unwrapped_quals.tsv")
self.assertTxtsMatch(self.path / "unwrapped_quals.tsv",
Path(tmpdir) / "unwrapped_quals.tsv")
def test_convert_tsv_fa(self):
"""Test converting tsv to fasta."""
with TemporaryDirectory() as tmpdir:
convert(self.path / "unwrapped.tsv",
Path(tmpdir) / "unwrapped.fasta")
self.assertTxtsMatch(self.path / "unwrapped.fasta",
Path(tmpdir) / "unwrapped.fasta")
def test_convert_fa_fa(self):
"""Test converting fasta to fasta with dry_run=True.
Nothing should actually be written.
"""
with TemporaryDirectory() as tmpdir:
convert(self.path / "wrapped.fasta",
Path(tmpdir) / "unwrapped.fasta",
dry_run=True)
self.assertTrue(not (Path(tmpdir) / "unwrapped.fasta").exists())
def test_convert_csv_csv(self):
"""Test converting csv to csv."""
with TemporaryDirectory() as tmpdir:
convert(self.path / "unwrapped_quals.csv",
Path(tmpdir) / "unwrapped_quals.csv")
self.assertTxtsMatch(self.path / "unwrapped_quals.csv",
Path(tmpdir) / "unwrapped_quals.csv")
with TemporaryDirectory() as tmpdir:
convert(self.path / "unwrapped.csv",
Path(tmpdir) / "unwrapped_quals.csv",
dummyqual="I")
self.assertTxtsMatch(self.path / "unwrapped_quals.csv",
Path(tmpdir) / "unwrapped_quals.csv")
def test_convert_fq_fa(self):
"""Test converting fastq to fasta."""
with TemporaryDirectory() as tmpdir:
convert(self.path / "unwrapped.fastq",
Path(tmpdir) / "unwrapped.fasta")
self.assertTxtsMatch(self.path / "unwrapped.fasta",
Path(tmpdir) / "unwrapped.fasta")
with TemporaryDirectory() as tmpdir:
convert(self.path / "unwrapped.fastq",
Path(tmpdir) / "unwrapped.fasta.gz")
gunzip(Path(tmpdir) / "unwrapped.fasta.gz")
self.assertTxtsMatch(self.path / "unwrapped.fasta",
Path(tmpdir) / "unwrapped.fasta")
def test_convert_csv_fa(self):
"""Test converting csv to fasta.
It should understand how to pull from custom-named columns.
"""
with TemporaryDirectory() as tmpdir:
convert(self.path / "unwrapped.csv",
Path(tmpdir) / "unwrapped.fasta",
colmap={
"sequence_id": "SeqID",
"sequence": "Seq"
})
self.assertTxtsMatch(self.path / "unwrapped.fasta",
Path(tmpdir) / "unwrapped.fasta")
def test_convert_csv_fq(self):
"""Test converting csv to fastq.
Like the csv_fa case, but it should get quality scores from custom col too.
"""
with TemporaryDirectory() as tmpdir:
convert(self.path / "unwrapped_quals.csv",
Path(tmpdir) / "unwrapped.fastq",
colmap={
"sequence_id": "SeqID",
"sequence": "Seq",
"sequence_quality": "SeqQual"
})
self.assertTxtsMatch(self.path / "unwrapped.fastq",
Path(tmpdir) / "unwrapped.fastq")
def test_convert_fq_csv(self):
"""Test converting fastq to csv.
There should be three columns of output, one for sequence IDs, one for
sequences, and one for quality scores.
"""
with TemporaryDirectory() as tmpdir:
convert(self.path / "unwrapped.fastq",
Path(tmpdir) / "unwrapped.csv",
colmap={
"sequence_id": "SeqID",
"sequence": "Seq",
"sequence_quality": "SeqQual"
})
self.assertTxtsMatch(self.path / "unwrapped_quals.csv",
Path(tmpdir) / "unwrapped.csv")
def test_convert_fq_tsv(self):
"""Test converting fastq to tsv.
Like fq_csv, but tab-separated.
"""
with TemporaryDirectory() as tmpdir:
convert(self.path / "unwrapped.fastq",
Path(tmpdir) / "unwrapped.tsv")
self.assertTxtsMatch(self.path / "unwrapped_quals.tsv",
Path(tmpdir) / "unwrapped.tsv")
with TemporaryDirectory() as tmpdir:
convert(self.path / "unwrapped.fastq",
Path(tmpdir) / "unwrapped.tsv.gz")
gunzip(Path(tmpdir) / "unwrapped.tsv.gz")
self.assertTxtsMatch(self.path / "unwrapped_quals.tsv",
Path(tmpdir) / "unwrapped.tsv")
def test_convert_fq_fq(self):
"""Test converting fastq to fastq.
This shouldn't change anything.
"""
with TemporaryDirectory() as tmpdir:
convert(self.path / "unwrapped.fastq",
Path(tmpdir) / "unwrapped.fastq")
self.assertTxtsMatch(self.path / "unwrapped.fastq",
Path(tmpdir) / "unwrapped.fastq")
with TemporaryDirectory() as tmpdir:
convert(self.path / "unwrapped.fastq",
Path(tmpdir) / "unwrapped.fastq.gz")
gunzip(Path(tmpdir) / "unwrapped.fastq.gz")
self.assertTxtsMatch(self.path / "unwrapped.fastq",
Path(tmpdir) / "unwrapped.fastq")
def test_convert_fa_csv(self):
"""Test converting fasta to csv.
There should be two columns of output, one for sequence IDs and one for
sequences.
"""
with TemporaryDirectory() as tmpdir:
convert(self.path / "wrapped.fasta",
Path(tmpdir) / "unwrapped.csv")
self.assertTxtsMatch(self.path / "unwrapped.csv",
Path(tmpdir) / "unwrapped.csv")
with TemporaryDirectory() as tmpdir:
convert(self.path / "wrapped.fasta",
Path(tmpdir) / "unwrapped.csv.gz")
gunzip(Path(tmpdir) / "unwrapped.csv.gz")
self.assertTxtsMatch(self.path / "unwrapped.csv",
Path(tmpdir) / "unwrapped.csv")
def test_convert_fa_fq(self):
"""Test converting fasta to fastq.
This should fake the quality scores, with a warning if the dummy score
isn't explicitly set.
"""
with TemporaryDirectory() as tmpdir:
with self.assertLogs(level="WARNING"):
convert(self.path / "wrapped.fasta",
Path(tmpdir) / "unwrapped.fastq")
self.assertTxtsMatch(self.path / "unwrapped.fastq",
Path(tmpdir) / "unwrapped.fastq")
with TemporaryDirectory() as tmpdir:
convert(self.path / "wrapped.fasta",
Path(tmpdir) / "unwrapped.fastq",
dummyqual="I")
self.assertTxtsMatch(self.path / "unwrapped.fastq",
Path(tmpdir) / "unwrapped.fastq")
with TemporaryDirectory() as tmpdir:
convert(self.path / "wrapped.fasta",
Path(tmpdir) / "unwrapped.fastq.gz",
dummyqual="I")
gunzip(Path(tmpdir) / "unwrapped.fastq.gz")
self.assertTxtsMatch(self.path / "unwrapped.fastq",
Path(tmpdir) / "unwrapped.fastq")
def test_convert_fa_csv(self):
"""Test converting fasta to csv.
There should be two columns of output, one for sequence IDs and one for
sequences, with custom column names.
"""
with self.subTest(
"both custom columns"), TemporaryDirectory() as tmpdir:
convert(self.path / "wrapped.fasta",
Path(tmpdir) / "unwrapped.csv",
colmap={
"sequence_id": "SeqID",
"sequence": "Seq"
})
self.assertTxtsMatch(self.path / "unwrapped.csv",
Path(tmpdir) / "unwrapped.csv")
with self.subTest("one custom column"), TemporaryDirectory() as tmpdir:
convert(self.path / "wrapped.fasta",
Path(tmpdir) / "unwrapped.csv",
colmap={"sequence_id": "SeqID"})
self.assertTxtsMatch(self.path / "unwrapped.alt1.csv",
Path(tmpdir) / "unwrapped.csv")
with self.subTest("no custom columns"), TemporaryDirectory() as tmpdir:
convert(self.path / "wrapped.fasta",
Path(tmpdir) / "unwrapped.csv",
colmap={})
self.assertTxtsMatch(self.path / "unwrapped.alt2.csv",
Path(tmpdir) / "unwrapped.csv")
def test_convert_csv_fq(self):
"""Test converting csv to fastq."""
with TemporaryDirectory() as tmpdir:
convert(self.path / "unwrapped_quals.csv",
Path(tmpdir) / "unwrapped.fastq")
self.assertTxtsMatch(self.path / "unwrapped.fastq",
Path(tmpdir) / "unwrapped.fastq")
with TemporaryDirectory() as tmpdir:
with self.assertLogs(level="WARNING"):
convert(self.path / "unwrapped.csv",
Path(tmpdir) / "unwrapped.fastq")
self.assertTxtsMatch(self.path / "unwrapped.fastq",
Path(tmpdir) / "unwrapped.fastq")
with TemporaryDirectory() as tmpdir:
convert(self.path / "unwrapped.csv",
Path(tmpdir) / "unwrapped.fastq",
dummyqual="I")
self.assertTxtsMatch(self.path / "unwrapped.fastq",
Path(tmpdir) / "unwrapped.fastq")
def test_convert_fa_fa(self):
"""Test converting fasta to fasta.
This should just reformat by unwrapping.
"""
with TemporaryDirectory() as tmpdir:
# fasta -> fasta
convert(self.path / "wrapped.fasta",
Path(tmpdir) / "unwrapped.fasta")
self.assertTxtsMatch(self.path / "unwrapped.fasta",
Path(tmpdir) / "unwrapped.fasta")
# fasta.gz -> fasta
gzip(Path(tmpdir) / "unwrapped.fasta")
convert(
Path(tmpdir) / "unwrapped.fasta.gz",
Path(tmpdir) / "unwrapped.fasta")
self.assertTxtsMatch(self.path / "unwrapped.fasta",
Path(tmpdir) / "unwrapped.fasta")
with TemporaryDirectory() as tmpdir:
# fasta -> fasta.gz
convert(self.path / "wrapped.fasta",
Path(tmpdir) / "unwrapped.fasta.gz")
gunzip(Path(tmpdir) / "unwrapped.fasta.gz")
self.assertTxtsMatch(self.path / "unwrapped.fasta",
Path(tmpdir) / "unwrapped.fasta")
# fasta.gz -> fasta.gz
gzip(Path(tmpdir) / "unwrapped.fasta")
convert(
Path(tmpdir) / "unwrapped.fasta.gz",
Path(tmpdir) / "unwrapped2.fasta.gz")
self.assertGzipsMatch(
Path(tmpdir) / "unwrapped.fasta.gz",
Path(tmpdir) / "unwrapped2.fasta.gz")
# to stdout, but we need the format
with self.assertRaises(IgSeqError):
convert(self.path / "wrapped.fasta", "-")
# now, with the format
stdout, stderr = self.redirect_streams(
lambda: convert(self.path / "wrapped.fasta", "-", fmt_out="fa"))
with open(self.path / "unwrapped.fasta") as f_in:
stdout_exp = f_in.read()
self.assertEqual(stdout, stdout_exp)
self.assertEqual(stderr, "")
# or as gz
stdout, stderr = self.redirect_streams(
lambda: convert(self.path / "wrapped.fasta", "-", fmt_out="fagz"))
with open(self.path / "unwrapped.fasta") as f_in:
stdout_exp = f_in.read()
with gzopen(BytesIO(stdout), "rt", "ascii") as f_in:
stdout_txt = f_in.read()
self.assertEqual(stdout_txt, stdout_exp)
self.assertEqual(stderr, "")