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Fix demux to_ascii for fasta files #1170

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Merged
merged 2 commits into from
May 15, 2015
Merged

Fix demux to_ascii for fasta files #1170

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7bb933c
Simplify use of contexts in tests
May 8, 2015
b04394c
BUG: make to_ascii work with fasta files
May 8, 2015
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5 changes: 4 additions & 1 deletion qiita_ware/demux.py
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Original file line number Diff line number Diff line change
Expand Up @@ -438,7 +438,10 @@ def to_ascii(demux, samples=None):
for samp, idx, seq, qual, bc_ori, bc_cor, bc_err in fetch(demux, samples):
seq_id = id_fmt % {'sample': samp, 'idx': idx, 'bc_ori': bc_ori,
'bc_cor': bc_cor, 'bc_diff': bc_err}
yield formatter(seq_id, seq, qual.astype(np.uint8))
if qual is not None:
qual = qual.astype(np.uint8)

yield formatter(seq_id, seq, qual)


def to_per_sample_ascii(demux, samples=None):
Expand Down
43 changes: 28 additions & 15 deletions qiita_ware/test/test_demux.py
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Original file line number Diff line number Diff line change
Expand Up @@ -246,11 +246,9 @@ def test_to_hdf5(self):
with tempfile.NamedTemporaryFile('r+', suffix='.fna',
delete=False) as f:
f.write(seqdata)
f.flush()
f.close()

to_hdf5(f.name, self.hdf5_file)
self.to_remove.append(f.name)
self.to_remove.append(f.name)
to_hdf5(f.name, self.hdf5_file)

npt.assert_equal(self.hdf5_file['a/sequence'][:], np.array(["x", "xy",
"xyz"]))
Expand Down Expand Up @@ -283,14 +281,30 @@ def test_to_ascii(self):
with tempfile.NamedTemporaryFile('r+', suffix='.fq',
delete=False) as f:
f.write(fqdata)
f.flush()
f.close()
to_hdf5(f.name, self.hdf5_file)
self.to_remove.append(f.name)

exp = [(b"@a_0 orig_bc=abc new_bc=abc bc_diffs=0\nxyz\n+\nABC\n"),
(b"@b_0 orig_bc=abw new_bc=wbc bc_diffs=4\nqwe\n+\nDFG\n"),
(b"@b_1 orig_bc=abw new_bc=wbc bc_diffs=4\nqwe\n+\nDEF\n")]
self.to_remove.append(f.name)
to_hdf5(f.name, self.hdf5_file)

exp = [b"@a_0 orig_bc=abc new_bc=abc bc_diffs=0\nxyz\n+\nABC\n",
b"@b_0 orig_bc=abw new_bc=wbc bc_diffs=4\nqwe\n+\nDFG\n",
b"@b_1 orig_bc=abw new_bc=wbc bc_diffs=4\nqwe\n+\nDEF\n"]

obs = list(to_ascii(self.hdf5_file, samples=['a', 'b']))
self.assertEqual(obs, exp)

def test_to_ascii_fasta(self):
with tempfile.NamedTemporaryFile('r+', suffix='.fna',
delete=False) as f:
f.write(seqdata)

self.to_remove.append(f.name)
to_hdf5(f.name, self.hdf5_file)

exp = [b">a_0 orig_bc=abc new_bc=abc bc_diffs=0\nx\n",
b">a_1 orig_bc=aby new_bc=ybc bc_diffs=2\nxy\n",
b">a_2 orig_bc=abz new_bc=zbc bc_diffs=3\nxyz\n",
b">b_0 orig_bc=abx new_bc=xbc bc_diffs=1\nxyz\n",
b">b_1 orig_bc=abw new_bc=wbc bc_diffs=4\nabcd\n"]

obs = list(to_ascii(self.hdf5_file, samples=['a', 'b']))
self.assertEqual(obs, exp)
Expand All @@ -299,10 +313,9 @@ def test_to_per_sample_ascii(self):
with tempfile.NamedTemporaryFile('r+', suffix='.fq',
delete=False) as f:
f.write(fqdata)
f.flush()
f.close()
to_hdf5(f.name, self.hdf5_file)
self.to_remove.append(f.name)

self.to_remove.append(f.name)
to_hdf5(f.name, self.hdf5_file)

exp = [('a', [(b"@a_0 orig_bc=abc new_bc=abc bc_diffs=0\nxyz\n+\n"
"ABC\n")]),
Expand Down