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
|
import pysam
import unittest
import os
import gzip
import shutil
from TestUtils import checkURL
DATADIR = "pysam_data"
class TestFastaFile(unittest.TestCase):
sequences = {
'chr1':
"CACTAGTGGCTCATTGTAAATGTGTGGTTTAACTCGTCCATGGCCCAGCATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTGGCTGAGGGGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTGGCAAGCTAGAGTCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTAATGAAAACTATATTTATGCTATTCAGTTCTAAATATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAACAACCTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAGTTACCAAATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTTCTTCCAAAGATGAAACGCGTAACTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCAATGGACCTGTGATATCTGGATTCTGGGAAATTCTTCATCCTGGACCCTGAGAGATTCTGCAGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAGCCATCACAATGAACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCAACCTCATACACACACATGGTTTAGGGGTATAATACCTCTACATGGCTGATTATGAAAACAATGTTCCCCAGATACCATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATTTGCCTTCAGACCCTACACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTTTCCCATCATGAAGCACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAGGTGCACTAATGCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAATACATGAGATTATTAGGAAATGCTTTACTGTCATAACTATGAAGAGACTATTGCCAGATGAACCACACATTAATACTATGTTTCTTATCTGCACATTACTACCCTGCAATTAATATAATTGTGTCCATGTACACACGCTGTCCTATGTACTTATCATGACTCTATCCCAAATTCCCAATTACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACATAATCCCACGCTTCCTATGGAAAGGTTGTTGGGAGATTTTTAATGATTCCTCAATGTTAAAATGTCTATTTTTGTCTTGACACCCAACTAATATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCGTCTTCTTA",
'chr2':
"TTCAAATGAACTTCTGTAATTGAAAAATTCATTTAAGAAATTACAAAATATAGTTGAAAGCTCTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGAATTAACCCAGTCAGACAAAAATAAAGAAAAAAATTTTAAAAATGAACAGAGCTTTCAAGAAGTATGAGATTATGTAAAGTAACTGAACCTATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACTATCTAAAGTCAACATGAAGGAAAAAAATTCTAAAATCAGCAAGAGAAAAGCATACAGTCATCTATAAAGGAAATCCCATCAGAATAACAATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAAGAGATTGGATCTAATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGTTATGCCCTGCTAAACTAAGCATCATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGATAATTCATCATCACTAAACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATACTCACCATCATAAATACACACAAAAGTACAAAACTCACAGGTTTTATAAAACAATTGAGACTACAGAGCAACTAGGTAAAAAATTAACATTACAACAGGAACAAAACCTCATATATCAATATTAACTTTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAGATATAGATTGGCAGAACAGATTTAAAAACATGAACTAACTATATGCTGTTTACAAGAAACTCATTAATAAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAAACCAAATGAGAGAAGGAGTAGCTATACTTATATCAGATAAAGCACACTTTAAATCAACAACAGTAAAATAAAACAAAGGAGGTCATCATACAATGATAAAAAGATCAATTCAGCAAGAAGATATAACCATCCTACTAAATACATATGCACCTAACACAAGACTACCCAGATTCATAAAACAAATACTACTAGACCTAAGAGGGATGAGAAATTACCTAATTGGTACAATGTACAATATTCTGATGATGGTTACACTAAAAGCCCATACTTTACTGCTACTCAATATATCCATGTAACAAATCTGCGCTTGTACTTCTAAATCTATAAAAAAATTAAAATTTAACAAAAGTAAATAAAACACATAGCTAAAACTAAAAAAGCAAAAACAAAAACTATGCTAAGTATTGGTAAAGATGTGGGGAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAGTATAAATTGTTTTCCACTTTGGAAAACAATTTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTTTGCATGCCAGAAAAAAATATTTACAGTAACT",
}
def setUp(self):
self.file = pysam.FastaFile(os.path.join(DATADIR, "ex1.fa"))
def testFetch(self):
for id, seq in list(self.sequences.items()):
self.assertEqual(seq, self.file.fetch(id))
for x in range(0, len(seq), 10):
self.assertEqual(seq[x:x + 10], self.file.fetch(id, x, x + 10))
# test x:end
self.assertEqual(seq[x:], self.file.fetch(id, x))
# test 0:x
self.assertEqual(seq[:x], self.file.fetch(id, None, x))
# unknown sequence raises IndexError
self.assertRaises(KeyError, self.file.fetch, "chr12")
def testOutOfRangeAccess(self):
'''test out of range access.'''
# out of range access returns an empty string
for contig, s in self.sequences.items():
self.assertEqual(self.file.fetch(contig, len(s), len(s) + 1), "")
def testFetchErrors(self):
self.assertRaises(ValueError, self.file.fetch)
self.assertRaises(ValueError, self.file.fetch, "chr1", -1, 10)
self.assertRaises(ValueError, self.file.fetch, "chr1", 20, 10)
self.assertRaises(KeyError, self.file.fetch, "chr3", 0, 100)
def testLength(self):
self.assertEqual(len(self.file), 2)
def testSequenceLengths(self):
self.assertEqual(1575, self.file.get_reference_length("chr1"))
self.assertEqual(1584, self.file.get_reference_length("chr2"))
def tearDown(self):
self.file.close()
class TestFastaFilePathIndex(unittest.TestCase):
filename = os.path.join(DATADIR, "ex1.fa")
def testGarbageIndex(self):
self.assertRaises(NotImplementedError,
pysam.FastaFile,
self.filename,
filepath_index="garbage.fa.fai")
return
self.assertRaises(ValueError,
pysam.FastaFile,
self.filename,
filepath_index="garbage.fa.fai")
def testOpenWithoutIndex(self):
faidx = pysam.FastaFile(self.filename)
faidx.close()
def testOpenWithStandardIndex(self):
self.assertRaises(NotImplementedError,
pysam.FastaFile,
self.filename,
filepath_index=self.filename + ".fai")
return
faidx = pysam.FastaFile(self.filename,
filepath_index=self.filename + ".fai")
faidx.close()
def testOpenWithOtherIndex(self):
return
tmpfilename = "tmp_" + os.path.basename(self.filename)
shutil.copyfile(self.filename, tmpfilename)
faidx = pysam.FastaFile(tmpfilename,
filepath_index=self.filename + ".fai")
faidx.close()
# index should not be auto-generated
self.assertFalse(os.path.exists(tmpfilename + ".fai"))
os.unlink(tmpfilename)
class TestFastaFilePathIndexCompressed(TestFastaFilePathIndex):
filename = os.path.join(DATADIR, "ex1.fa.gz")
class TestFastxFileFastq(unittest.TestCase):
filetype = pysam.FastxFile
filename = "faidx_ex1.fq"
persist = True
def setUp(self):
self.file = self.filetype(os.path.join(DATADIR, self.filename),
persist=self.persist)
self.has_quality = self.filename.endswith('.fq')
def tearDown(self):
self.file.close()
def checkFirst(self, s):
# test first entry
self.assertEqual(s.sequence, "GGGAACAGGGGGGTGCACTAATGCGCTCCACGCCC")
self.assertEqual(s.name, "B7_589:1:101:825:28")
if self.has_quality:
self.assertEqual(s.quality, "<<86<<;<78<<<)<;4<67<;<;<74-7;,;8,;")
self.assertEqual(list(s.get_quality_array()),
[ord(x) - 33 for x in s.quality])
self.assertEqual(str(s),
"@B7_589:1:101:825:28\n"
"GGGAACAGGGGGGTGCACTAATGCGCTCCACGCCC\n"
"+\n"
"<<86<<;<78<<<)<;4<67<;<;<74-7;,;8,;")
else:
self.assertEqual(s.quality, None)
self.assertEqual(s.get_quality_array(), None)
self.assertEqual(str(s),
">B7_589:1:101:825:28\n"
"GGGAACAGGGGGGTGCACTAATGCGCTCCACGCCC")
def checkLast(self, s):
self.assertEqual(s.sequence, "TAATTGAAAAATTCATTTAAGAAATTACAAAATAT")
self.assertEqual(s.name, "EAS56_65:8:64:507:478")
if self.has_quality:
self.assertEqual(s.quality, "<<<<<;<<<<<<<<<<<<<<<;;;<<<;<<8;<;<")
self.assertEqual(list(s.get_quality_array()),
[ord(x) - 33 for x in s.quality])
else:
self.assertEqual(s.quality, None)
self.assertEqual(s.get_quality_array(), None)
def testCounts(self):
self.assertEqual(len([x for x in self.file]), 3270)
def testMissingFile(self):
self.assertRaises(IOError, self.filetype, "nothere.fq")
def testSequence(self):
first = self.file.__next__()
self.checkFirst(first)
for last in self.file:
pass
self.checkLast(last)
# test for persistence
if self.persist:
self.checkFirst(first)
else:
self.checkLast(first)
def testManager(self):
with self.filetype(os.path.join(DATADIR, self.filename),
persist=self.persist) as inf:
first = inf.__next__()
self.checkFirst(first)
for last in inf:
pass
self.checkLast(last)
self.assertEqual(inf.closed, True)
# Test for backwards compatibility
class TestFastqFileFastq(TestFastxFileFastq):
filetype = pysam.FastqFile
# Test for backwards compatibility
class TestFastxFileFasta(TestFastxFileFastq):
filetype = pysam.FastqFile
filename = "faidx_ex1.fa"
class TestFastxFileFastqStream(TestFastxFileFastq):
persist = False
class TestFastxFileWithEmptySequence(unittest.TestCase):
"""see issue 204:
iteration over fastq file with empty sequence stops prematurely
"""
filetype = pysam.FastxFile
filename = "faidx_empty_seq.fq.gz"
def testIteration(self):
fn = os.path.join(DATADIR, self.filename)
with gzip.open(fn) as inf:
ref_num = len(list(inf)) / 4
with self.filetype(fn) as f:
l = len(list(f))
self.assertEqual(ref_num, l)
if __name__ == "__main__":
unittest.main()
|
