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
|
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2010-2015, Michigan State University.
# Copyright (C) 2015, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
#
# * Neither the name of the Michigan State University nor the names
# of its contributors may be used to endorse or promote products
# derived from this software without specific prior written
# permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project@idyll.org
from __future__ import print_function
from __future__ import absolute_import
import khmer
from screed.fasta import fasta_iter
from nose.plugins.attrib import attr
from . import khmer_tst_utils as utils
def teardown():
utils.cleanup()
def load_fa_seq_names(filename):
fp = open(filename)
records = list(fasta_iter(fp))
names = [r['name'] for r in records]
return names
class Test_Filter(object):
def test_abund(self):
ht = khmer.Countgraph(10, 4 ** 10, 1)
filename = utils.get_test_data('test-abund-read.fa')
outname = utils.get_temp_filename('test_abund.out')
ht.consume_fasta(filename)
try:
ht.consume_fasta()
assert 0, "should fail"
except TypeError as err:
print(str(err))
try:
ht.consume_fasta("nonexistent")
assert 0, "should fail"
except OSError as err:
print(str(err))
ht.output_fasta_kmer_pos_freq(filename, outname)
try:
ht.output_fasta_kmer_pos_freq()
assert 0, "should fail"
except TypeError as err:
print(str(err))
fd = open(outname, "r")
output = fd.readlines()
assert len(output) == 1
output = output[0]
output = output.strip().split()
assert ['1'] * (114 - 10 + 1) == output
fd.close()
|
