1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
|
import gzip
import struct
import textwrap
from pytest import raises
from io import BytesIO
import dnaio
from dnaio import UnknownFileFormat, FileFormatError
from dnaio._core import paired_fastq_heads
from dnaio.chunks import (
_bam_head,
_fastq_head,
_fasta_head,
read_chunks,
read_paired_chunks,
_paired_fasta_heads,
)
def test_fasta_head():
assert _fasta_head(b"") == 0
assert _fasta_head(b">1\n") == 0
assert _fasta_head(b">1\n3") == 0
assert _fasta_head(b">1\n3\n") == 0
assert _fasta_head(b">1\n3\n>") == 5
assert _fasta_head(b">1\n3\n>6") == 5
assert _fasta_head(b">1\n3\n>6\n") == 5
assert _fasta_head(b">1\n3\n>6\n8") == 5
assert _fasta_head(b">1\n3\n>6\n8\n") == 5
assert _fasta_head(b">1\n3\n>6\n8\n0") == 5
assert _fasta_head(b">1\n3\n>6\n8\n0\n") == 5
assert _fasta_head(b">1\n3\n>6\n8\n0\n>") == 12
def test_fasta_head_with_comment():
assert _fasta_head(b"#") == 0
assert _fasta_head(b"#\n") == 0
assert _fasta_head(b"#\n>") == 2
assert _fasta_head(b"#\n>3") == 2
assert _fasta_head(b"#\n>3\n") == 2
assert _fasta_head(b"#\n>3\n5") == 2
assert _fasta_head(b"#\n>3\n5\n") == 2
assert _fasta_head(b"#\n>3\n5\n>") == 7
def test_bam_head():
assert _bam_head(struct.pack("<Ix", 32)) == 0
assert _bam_head(struct.pack("<I32x", 32)) == 36
assert _bam_head(struct.pack("<I32xI32x", 32, 33)) == 36
assert _bam_head(struct.pack("<I32xI33x", 32, 33)) == 73
def test_paired_fasta_heads():
def pheads(buf1, buf2):
return _paired_fasta_heads(buf1, buf2, len(buf1), len(buf2))
assert pheads(b"", b"") == (0, 0)
assert pheads(b">r", b">r") == (0, 0)
assert pheads(b">r\nA\n>s", b">r") == (0, 0)
assert pheads(b">r\nA\n>s", b">r\nCT\n>s") == (5, 6)
assert pheads(b">r\nA\n>s\nG\n>t\n", b">r\nCT\n>s") == (5, 6)
buf1 = (
textwrap.dedent(
"""
>1
a
b
>2
c
>3
uv
"""
)
.strip()
.encode()
)
buf2 = (
textwrap.dedent(
"""
>1
def
>2
gh
i
>3
"""
)
.strip()
.encode()
)
assert pheads(buf1, buf2) == (
len(b">1\na\nb\n>2\nc\n"),
len(b">1\ndef\n>2\ngh\ni\n"),
)
def test_paired_fastq_heads():
buf1 = b"first\nsecond\nthird\nfourth\nfifth"
buf2 = b"a\nb\nc\nd\ne\nf\ng"
assert paired_fastq_heads(buf1, buf2, len(buf1), len(buf2)) == (
len(b"first\nsecond\nthird\nfourth\n"),
len(b"a\nb\nc\nd\n"),
)
assert paired_fastq_heads(b"abc", b"def", 3, 3) == (0, 0)
assert paired_fastq_heads(b"abc\n", b"def", 4, 3) == (0, 0)
assert paired_fastq_heads(b"abc", b"def\n", 3, 4) == (0, 0)
assert paired_fastq_heads(b"\n\n\n\n", b"\n\n\n\n", 4, 4) == (4, 4)
def test_fastq_head():
assert _fastq_head(b"") == 0
assert _fastq_head(b"A\n") == 0
assert _fastq_head(b"A\nB") == 0
assert _fastq_head(b"A\nB\n") == 0
assert _fastq_head(b"A\nB\nC") == 0
assert _fastq_head(b"A\nB\nC\n") == 0
assert _fastq_head(b"A\nB\nC\nD") == 0
assert _fastq_head(b"A\nB\nC\nD\n") == 0
assert _fastq_head(b"A\nB\nC\nD\nE") == 0
assert _fastq_head(b"A\nB\nC\nD\nE\n") == 0
assert _fastq_head(b"A\nB\nC\nD\nE\nF") == 0
assert _fastq_head(b"A\nB\nC\nD\nE\nF\n") == 0
assert _fastq_head(b"A\nB\nC\nD\nE\nF\nG") == 0
assert _fastq_head(b"A\nB\nC\nD\nE\nF\nG\n") == 0
assert _fastq_head(b"A\nB\nC\nD\nE\nF\nG\nH") == 0
assert _fastq_head(b"A\nB\nC\nD\nE\nF\nG\nH\n") == 16
assert _fastq_head(b"A\nB\nC\nD\nE\nF\nG\nH\nI") == 16
assert _fastq_head(b"A\nB\nC\nD\nE\nF\nG\nH\nI\n") == 16
def test_read_paired_chunks_empty_input(tmp_path):
empty_fastq = tmp_path / "empty.fastq"
empty_fastq.write_text("")
with open(empty_fastq, "rb") as f1:
with open(empty_fastq, "rb") as f2:
chunks = list(read_paired_chunks(f1, f2))
assert len(chunks) == 0
def test_read_paired_chunks_fastq():
with open("tests/data/paired.1.fastq", "rb") as f1:
with open("tests/data/paired.2.fastq", "rb") as f2:
for c1, c2 in read_paired_chunks(f1, f2, buffer_size=128):
print(c1, c2)
def test_paired_chunks_fasta(tmp_path):
for i in (1, 2):
with dnaio.open(f"tests/data/paired.{i}.fastq") as infile:
with dnaio.open(tmp_path / f"{i}.fasta", mode="w") as outfile:
for record in infile:
record.qualities = None
outfile.write(record)
with open(tmp_path / "1.fasta", "rb") as r1:
with open(tmp_path / "2.fasta", "rb") as r2:
for c1, c2 in read_paired_chunks(r1, r2, buffer_size=128):
print(c1.tobytes(), c2.tobytes())
def test_paired_chunks_different_number_of_records():
record = b"@r\nAA\n+\n##\n"
buf1 = record
buf2 = record * 3
it = read_paired_chunks(BytesIO(buf1), BytesIO(buf2), 16)
assert next(it) == (record, record)
with raises(FileFormatError) as error:
next(it)
error.match("more data found in the other file")
def test_read_chunks():
for data in [b"@r1\nACG\n+\nHHH\n", b">r1\nACGACGACG\n"]:
assert [m.tobytes() for m in read_chunks(BytesIO(data))] == [data]
# Buffer too small
with raises(OverflowError):
list(read_chunks(BytesIO(data), buffer_size=4))
def test_read_chunks_empty():
assert list(read_chunks(BytesIO(b""))) == []
def test_invalid_file_format():
with raises(UnknownFileFormat):
list(read_chunks(BytesIO(b"invalid format")))
def test_read_chunks_bam():
with gzip.open("tests/data/simple.unaligned.bam", "rb") as f:
for i, chunk in enumerate(read_chunks(f, 70)):
if i == 0:
assert b"Myheader" in chunk.tobytes()
if i == 1:
assert b"AnotherHeader" in chunk.tobytes()
if i == 2:
assert b"YetAnotherHeader" in chunk.tobytes()
assert b"RGZA\x00" in chunk.tobytes()
|
