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
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
|
# Copyright 2009 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Unit tests for Bio.SeqIO.convert(...) function."""
from __future__ import print_function
import unittest
import warnings
from Bio import BiopythonWarning
from Bio.Seq import UnknownSeq
from Bio import SeqIO
from Bio.SeqIO import QualityIO
from Bio.SeqIO._convert import _converter as converter_dict
from Bio._py3k import StringIO
from Bio.Alphabet import generic_protein, generic_nucleotide, generic_dna
# TODO - share this with the QualityIO tests...
def truncation_expected(format):
if format in ["fastq-solexa", "fastq-illumina"]:
return 62
elif format in ["fastq", "fastq-sanger"]:
return 93
else:
return None
# Top level function as this makes it easier to use for debugging:
def check_convert(in_filename, in_format, out_format, alphabet=None):
records = list(SeqIO.parse(in_filename, in_format, alphabet))
# Write it out...
handle = StringIO()
qual_truncate = truncation_expected(out_format)
with warnings.catch_warnings():
if qual_truncate:
warnings.simplefilter('ignore', BiopythonWarning)
SeqIO.write(records, handle, out_format)
handle.seek(0)
# Now load it back and check it agrees,
records2 = list(SeqIO.parse(handle, out_format, alphabet))
compare_records(records, records2, qual_truncate)
# Finally, use the convert function, and check that agrees:
handle2 = StringIO()
with warnings.catch_warnings():
if qual_truncate:
warnings.simplefilter('ignore', BiopythonWarning)
SeqIO.convert(in_filename, in_format, handle2, out_format, alphabet)
# We could re-parse this, but it is simpler and stricter:
assert handle.getvalue() == handle2.getvalue()
def check_convert_fails(in_filename, in_format, out_format, alphabet=None):
qual_truncate = truncation_expected(out_format)
# We want the SAME error message from parse/write as convert!
err1 = None
try:
records = list(SeqIO.parse(in_filename, in_format, alphabet))
handle = StringIO()
with warnings.catch_warnings():
if qual_truncate:
warnings.simplefilter('ignore', BiopythonWarning)
SeqIO.write(records, handle, out_format)
handle.seek(0)
assert False, "Parse or write should have failed!"
except ValueError as err:
err1 = err
# Now do the conversion...
try:
handle2 = StringIO()
with warnings.catch_warnings():
if qual_truncate:
warnings.simplefilter('ignore', BiopythonWarning)
SeqIO.convert(in_filename, in_format, handle2, out_format, alphabet)
assert False, "Convert should have failed!"
except ValueError as err2:
assert str(err1) == str(err2), \
"Different failures, parse/write:\n%s\nconvert:\n%s" \
% (err1, err2)
# TODO - move this to a shared test module...
def compare_record(old, new, truncate=None):
"""Quality aware SeqRecord comparison.
This will check the mapping between Solexa and PHRED scores.
It knows to ignore UnknownSeq objects for string matching (i.e. QUAL files).
"""
if old.id != new.id:
raise ValueError("'%s' vs '%s' " % (old.id, new.id))
if old.description != new.description \
and (old.id + " " + old.description).strip() != new.description \
and new.description != "<unknown description>" \
and new.description != "": # e.g. tab format
raise ValueError("'%s' vs '%s' " % (old.description, new.description))
if len(old.seq) != len(new.seq):
raise ValueError("%i vs %i" % (len(old.seq), len(new.seq)))
if isinstance(old.seq, UnknownSeq) or isinstance(new.seq, UnknownSeq):
pass
elif str(old.seq) != str(new.seq):
if len(old.seq) < 200:
raise ValueError("'%s' vs '%s'" % (old.seq, new.seq))
else:
raise ValueError("'%s...' vs '%s...'" % (old.seq[:100], new.seq[:100]))
if "phred_quality" in old.letter_annotations \
and "phred_quality" in new.letter_annotations \
and old.letter_annotations["phred_quality"] != new.letter_annotations["phred_quality"]:
if truncate and [min(q, truncate) for q in old.letter_annotations["phred_quality"]] == \
[min(q, truncate) for q in new.letter_annotations["phred_quality"]]:
pass
else:
raise ValuerError("Mismatch in phred_quality")
if "solexa_quality" in old.letter_annotations \
and "solexa_quality" in new.letter_annotations \
and old.letter_annotations["solexa_quality"] != new.letter_annotations["solexa_quality"]:
if truncate and [min(q, truncate) for q in old.letter_annotations["solexa_quality"]] == \
[min(q, truncate) for q in new.letter_annotations["solexa_quality"]]:
pass
else:
raise ValueError("Mismatch in phred_quality")
if "phred_quality" in old.letter_annotations \
and "solexa_quality" in new.letter_annotations:
# Mapping from Solexa to PHRED is lossy, but so is PHRED to Solexa.
# Assume "old" is the original, and "new" has been converted.
converted = [round(QualityIO.solexa_quality_from_phred(q))
for q in old.letter_annotations["phred_quality"]]
if truncate:
converted = [min(q, truncate) for q in converted]
if converted != new.letter_annotations["solexa_quality"]:
print("")
print(old.letter_annotations["phred_quality"])
print(converted)
print(new.letter_annotations["solexa_quality"])
raise ValueError("Mismatch in phred_quality vs solexa_quality")
if "solexa_quality" in old.letter_annotations \
and "phred_quality" in new.letter_annotations:
# Mapping from Solexa to PHRED is lossy, but so is PHRED to Solexa.
# Assume "old" is the original, and "new" has been converted.
converted = [round(QualityIO.phred_quality_from_solexa(q))
for q in old.letter_annotations["solexa_quality"]]
if truncate:
converted = [min(q, truncate) for q in converted]
if converted != new.letter_annotations["phred_quality"]:
print(old.letter_annotations["solexa_quality"])
print(converted)
print(new.letter_annotations["phred_quality"])
raise ValueError("Mismatch in solexa_quality vs phred_quality")
return True
def compare_records(old_list, new_list, truncate_qual=None):
"""Check two lists of SeqRecords agree, raises a ValueError if mismatch."""
if len(old_list) != len(new_list):
raise ValueError("%i vs %i records" % (len(old_list), len(new_list)))
for old, new in zip(old_list, new_list):
if not compare_record(old, new, truncate_qual):
return False
return True
class ConvertTests(unittest.TestCase):
"""Cunning unit test where methods are added at run time."""
def simple_check(self, filename, in_format, out_format, alphabet):
check_convert(filename, in_format, out_format, alphabet)
def failure_check(self, filename, in_format, out_format, alphabet):
check_convert_fails(filename, in_format, out_format, alphabet)
tests = [
("Quality/example.fastq", "fastq", None),
("Quality/example.fastq", "fastq-sanger", generic_dna),
("Quality/tricky.fastq", "fastq", generic_nucleotide),
("Quality/sanger_93.fastq", "fastq-sanger", None),
("Quality/sanger_faked.fastq", "fastq-sanger", generic_dna),
("Quality/solexa_faked.fastq", "fastq-solexa", generic_dna),
("Quality/illumina_faked.fastq", "fastq-illumina", generic_dna),
("EMBL/U87107.embl", "embl", None),
("EMBL/TRBG361.embl", "embl", None),
("GenBank/NC_005816.gb", "gb", None),
("GenBank/cor6_6.gb", "genbank", None),
]
for filename, format, alphabet in tests:
for (in_format, out_format) in converter_dict:
if in_format != format:
continue
def funct(fn, fmt1, fmt2, alpha):
f = lambda x: x.simple_check(fn, fmt1, fmt2, alpha)
f.__doc__ = "Convert %s from %s to %s" % (fn, fmt1, fmt2)
return f
setattr(ConvertTests, "test_%s_%s_to_%s"
% (filename.replace("/", "_").replace(".", "_"), in_format, out_format),
funct(filename, in_format, out_format, alphabet))
del funct
# Fail tests:
tests = [
("Quality/error_diff_ids.fastq", "fastq", None),
("Quality/error_long_qual.fastq", "fastq", None),
("Quality/error_no_qual.fastq", "fastq", None),
("Quality/error_qual_del.fastq", "fastq", None),
("Quality/error_qual_escape.fastq", "fastq", None),
("Quality/error_qual_null.fastq", "fastq", None),
("Quality/error_qual_space.fastq", "fastq", None),
("Quality/error_qual_tab.fastq", "fastq", None),
("Quality/error_qual_unit_sep.fastq", "fastq", None),
("Quality/error_qual_vtab.fastq", "fastq", None),
("Quality/error_short_qual.fastq", "fastq", None),
("Quality/error_spaces.fastq", "fastq", None),
("Quality/error_tabs.fastq", "fastq", None),
("Quality/error_trunc_at_plus.fastq", "fastq", None),
("Quality/error_trunc_at_qual.fastq", "fastq", None),
("Quality/error_trunc_at_seq.fastq", "fastq", None),
("Quality/error_trunc_in_title.fastq", "fastq", generic_dna),
("Quality/error_trunc_in_seq.fastq", "fastq", generic_nucleotide),
("Quality/error_trunc_in_plus.fastq", "fastq", None),
("Quality/error_trunc_in_qual.fastq", "fastq", generic_dna),
("Quality/error_double_seq.fastq", "fastq", generic_dna),
("Quality/error_double_qual.fastq", "fastq", generic_dna),
]
for filename, format, alphabet in tests:
for (in_format, out_format) in converter_dict:
if in_format != format:
continue
if in_format in ["fastq", "fastq-sanger", "fastq-solexa", "fastq-illumina"] \
and out_format in ["fasta", "tab"] and filename.startswith("Quality/error_qual_"):
# TODO? These conversions don't check for bad characters in the quality,
# and in order to pass this strict test they should.
continue
def funct(fn, fmt1, fmt2, alpha):
f = lambda x: x.failure_check(fn, fmt1, fmt2, alpha)
f.__doc__ = "Convert %s from %s to %s" % (fn, fmt1, fmt2)
return f
setattr(ConvertTests, "test_%s_%s_to_%s"
% (filename.replace("/", "_").replace(".", "_"), in_format, out_format),
funct(filename, in_format, out_format, alphabet))
del funct
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
