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
|
#################################################################################
# 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.
#################################################################################
__all__ = [ "BaseRegionsMixin",
"ExtraBaseRegionsMixin",
"ADAPTER_REGION",
"INSERT_REGION",
"HQ_REGION" ]
# Region types
ADAPTER_REGION = 0
INSERT_REGION = 1
HQ_REGION = 2
# Interval arithmetic
def intersectRanges(r1, r2):
b1, e1 = r1
b2, e2 = r2
b, e = max(b1, b2), min(e1, e2)
return (b, e) if (b < e) else None
def removeNones(lst):
return filter(lambda x: x!=None, lst)
class BaseRegionsMixin(object):
"""
Mixin class for "ZMW" client classes providing access to base
regions and reads sliced to those regions.
Requires the client subclass to provide 'regionsTable' and 'read'
(subrange slicing) methods with the correct semantics.
The "...Region[s]" calls here return one or more intervals ((int, int));
*All accessors in this mixin class implicitly clip regions to the
HQ region.*
"""
@property
def hqRegion(self):
"""
Return the HQ region interval.
The HQ region is an interval of basecalls where the basecaller has
inferred that a single sequencing reaction is taking place.
Secondary analysis should only use subreads within the HQ
region. Methods in this class, with the exception of the
"NoQC" methods, return data appropriately clipped/filtered to
the HQ region.
"""
rt = self.regionTable
hqRows = rt[rt.regionType == HQ_REGION]
assert len(hqRows) == 1
hqRow = hqRows[0]
return hqRow.regionStart, hqRow.regionEnd
def _unclippedInsertRegions(self):
return [ (region.regionStart, region.regionEnd)
for region in self.regionTable
if region.regionType == INSERT_REGION ]
@property
def insertRegions(self):
"""
Get insert regions as intervals, clipped to the HQ region
"""
hqRegion = self.hqRegion
return removeNones([ intersectRanges(hqRegion, region)
for region in self._unclippedInsertRegions() ])
@property
def subreads(self):
"""
Get the subreads as a list of ZmwRead objects. Restricts focus,
and clips to, the HQ region. This method can be used by
production code.
"""
return [ self.read(readStart, readEnd)
for (readStart, readEnd) in self.insertRegions ]
def _unclippedAdapterRegions(self):
return [ (region.regionStart, region.regionEnd)
for region in self.regionTable
if region.regionType == ADAPTER_REGION ]
@property
def adapterRegions(self):
"""
Get adapter regions as intervals, performing clipping to the HQ region
"""
hqRegion = self.hqRegion
return removeNones([ intersectRanges(hqRegion, region)
for region in self._unclippedAdapterRegions() ])
@property
def adapters(self):
"""
Get the adapter hits as a list of ZmwRead objects. Restricts
focus, and clips to, the HQ region. This method can be used
by production code.
"""
return [ self.read(readStart, readEnd)
for (readStart, readEnd) in self.adapterRegions ]
class ExtraBaseRegionsMixin(BaseRegionsMixin):
"""
Mixin class for a "ZMW" class providing the basic region
accessors, and additional region accessors that do not clip to the
HQ region.
These accessors only make sense for bas.h5 ZMW objects, where we
have access to region information extending beyond the HQ region.
In the BAM world, "regions" are all inherently clipped to HQ by
design of PPA.
Requires 'readNoQC' accessor
"""
@property
def adapterRegionsNoQC(self):
"""
Get adapter regions as intervals, without clipping to the HQ
region. Don't use this unless you know what you're doing.
"""
return self._unclippedAdapterRegions()
@property
def adaptersNoQC(self):
"""
Get the adapters, including data beyond the bounds of the HQ
region.
.. warning::
It is not recommended that production code use this method
as we make no guarantees about what happens outside of the
HQ region.
"""
return [ self.read(readStart, readEnd)
for (readStart, readEnd) in self.adapterRegionsNoQC ]
@property
def insertRegionsNoQC(self):
"""
Get insert regions as intervals, without clipping to the HQ
region. Don't use this unless you know what you're doing.
"""
return self._unclippedInsertRegions()
@property
def subreadsNoQC(self):
"""
Get the subreads, including data beyond the bounds of the HQ region.
.. warning::
It is not recommended that production code use this method
as we make no guarantees about what happens outside of the
HQ region.
"""
return [ self.read(readStart, readEnd)
for (readStart, readEnd) in self.insertRegionsNoQC ]
|
