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
|
#################################################################################
# Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
#
# All rights reserved.
#
# 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 Pacific Biosciences nor the names of its
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
# 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 PACIFIC BIOSCIENCES OR
# ITS 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.
#################################################################################
# Base classes for readers and writers.
# Author: David Alexander
from __future__ import absolute_import
import gzip
from os.path import abspath, expanduser
__all__ = [ "ReaderBase", "WriterBase" ]
def isFileLikeObject(o):
return hasattr(o, "read") and hasattr(o, "write")
def getFileHandle(filenameOrFile, mode="r"):
"""
Given a filename not ending in ".gz", open the file with the
appropriate mode.
Given a filename ending in ".gz", return a filehandle to the
unzipped stream.
Given a file object, return it unless the mode is incorrect--in
that case, raise an exception.
"""
assert mode in ("r", "w")
if isinstance(filenameOrFile, basestring):
filename = abspath(expanduser(filenameOrFile))
if filename.endswith(".gz"):
return gzip.open(filename, mode)
else:
return open(filename, mode)
elif isFileLikeObject(filenameOrFile):
return filenameOrFile
else:
raise Exception("Invalid type to getFileHandle")
class ReaderBase(object):
def __init__(self, f):
"""
Prepare for iteration through the records in the file
"""
self.file = getFileHandle(f, "r")
if hasattr(self.file, "name"):
self.filename = self.file.name
else:
self.filename = "(anonymous)"
def close(self):
"""
Close the underlying file
"""
self.file.close()
def __enter__(self):
return self
def __exit__(self, exc_type, exc_value, traceback):
self.close()
def __repr__(self):
return "<%s for %s>" % (type(self).__name__, self.filename)
class WriterBase(object):
def __init__(self, f):
"""
Prepare for output to the file
"""
self.file = getFileHandle(f, "w")
if hasattr(self.file, "name"):
self.filename = self.file.name
else:
self.filename = "(anonymous)"
def close(self):
"""
Close the underlying file
"""
self.file.close()
def __enter__(self):
return self
def __exit__(self, exc_type, exc_value, traceback):
self.close()
def __repr__(self):
return "<%s for %s>" % (type(self).__name__, self.filename)
|
