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
|
# Copyright 1999 by Jeffrey Chang. 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.
import os
import sys
import unittest
from types import *
import warnings
warnings.filterwarnings("ignore", category=DeprecationWarning)
from Bio import Fasta
warnings.resetwarnings()
from Bio import SeqRecord
from Bio import Seq
from Bio import Alphabet
from Bio.Alphabet import IUPAC
class RecordTest(unittest.TestCase):
def test_record_basic(self):
"""Basic test on Record
"""
def pbool(b):
if b:
return 1
return 0
r = Fasta.Record()
assert pbool(type(r.title) is StringType) # StringType
assert pbool(type(r.sequence) is StringType) # StringType
class ParserTest(unittest.TestCase):
def setUp(self):
files = ["f001", "f002"]
self.handles = []
for filename in files:
self.handles.append(open(os.path.join("Fasta", filename)))
self.lengths = {0 : (96, 79),
1 : (100, 633)}
def tearDown(self):
for handle in self.handles:
handle.close()
def test_record_parser(self):
"""Basic operation of the Record Parser.
"""
parser = Fasta.RecordParser()
for index in range(len(self.handles)):
handle = self.handles[index]
rec = parser.parse(handle)
assert isinstance(rec, Fasta.Record)
assert len(rec.title) == self.lengths[index][0]
assert len(rec.sequence) == self.lengths[index][1]
def test_sequence_parser(self):
"""Basic operation of the Sequence Parser.
"""
parser = Fasta.SequenceParser()
for index in range(len(self.handles)):
handle = self.handles[index]
rec = parser.parse(handle)
assert isinstance(rec, SeqRecord.SeqRecord)
assert isinstance(rec.seq, Seq.Seq)
assert rec.seq.alphabet == Alphabet.generic_alphabet
assert len(rec.seq) == self.lengths[index][1]
assert len(rec.description) == self.lengths[index][0]
def test_sequence_alphabet(self):
"""Setting the alphabet for the Sequence Parser.
"""
parser = Fasta.SequenceParser(alphabet =
IUPAC.unambiguous_dna)
rec = parser.parse(self.handles[0])
assert rec.seq.alphabet == IUPAC.unambiguous_dna
def test_sequence_title_convert(self):
"""Test title conversion for the Sequence Parser.
"""
def test_title2ids(title):
return "id", "name", "description"
parser = Fasta.SequenceParser(title2ids = test_title2ids)
rec = parser.parse(self.handles[0])
assert rec.id == "id"
assert rec.name == "name"
assert rec.description == "description"
class IteratorTest(unittest.TestCase):
def setUp(self):
self.test_handle = open(os.path.join('Fasta', 'f002'))
def tearDown(self):
self.test_handle.close()
def test_basic_iterator(self):
"""Ensure the Fasta iterator works returning text.
"""
i = Fasta.Iterator(self.test_handle)
rec_info = {0 : ">gi|1348912|gb|G26680|G26680",
1 : ">gi|1348917|gb|G26685|G26685",
2 : ">gi|1592936|gb|G29385|G29385"}
for rec_num in range(3):
rec = i.next()
lines = rec.split("\n")
title_part = lines[0].split()
assert title_part[0] == rec_info[rec_num]
# make sure we keep getting None when the iterator is done
assert i.next() is None
assert i.next() is None
def test_new_iterator(self):
"""Ensure the Fasta iterator works like a Python 2.2 iterator.
"""
n = 0
iterator = Fasta.Iterator(self.test_handle)
for rec in iter(iterator):
n += 1
assert n == 3
def test_record_iterator(self):
"""Test the iterator with a Record Parser.
"""
parser = Fasta.RecordParser()
iterator = Fasta.Iterator(self.test_handle, parser)
for rec in iter(iterator):
assert isinstance(rec, Fasta.Record)
def test_sequence_iterator(self):
"""Test the iterator with a Sequence Parser.
"""
parser = Fasta.SequenceParser()
iterator = Fasta.Iterator(self.test_handle, parser)
for rec in iter(iterator):
assert isinstance(rec, SeqRecord.SeqRecord)
def test_parsing_comments(self):
"""Parse FASTA files with # style comment lines in them.
"""
handle = open(os.path.join("Fasta", "f003"))
iterator = Fasta.Iterator(handle, Fasta.RecordParser())
num_recs = 0
for rec in iter(iterator):
num_recs += 1
assert num_recs == 2
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)
|
