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
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
|
# Copyright 2003-2008 by Leighton Pritchard. 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.
#
# Contact: Leighton Pritchard, Scottish Crop Research Institute,
# Invergowrie, Dundee, Scotland, DD2 5DA, UK
# L.Pritchard@scri.ac.uk
################################################################################
""" Feature module
Provides:
o Feature - class to wrap Bio.SeqFeature objects with drawing information
For drawing capabilities, this module uses reportlab to define colors:
http://www.reportlab.com
For dealing with biological information, the package uses BioPython:
http://www.biopython.org
"""
# ReportLab imports
from reportlab.lib import colors
# GenomeDiagram imports
from ._Colors import ColorTranslator
class Feature(object):
""" Class to wrap Bio.SeqFeature objects for GenomeDiagram
Provides:
Methods:
o __init__(self, parent=None, feature_id=None, feature=None,
color=colors.lightgreen) Called when the feature is
instantiated
o set_feature(self, feature) Wrap the passed feature
o get_feature(self) Return the unwrapped Bio.SeqFeature object
o set_color(self, color) Set the color in which the feature will
be drawn (accepts multiple formats: reportlab color.Color()
tuple and color.name, or integer representing Artemis color
o get_color(self) Returns color.Color tuple of the feature's color
o __getattr__(self, name) Catches attribute requests and passes them to
the wrapped Bio.SeqFeature object
Attributes:
o parent FeatureSet, container for the object
o id Unique id
o color color.Color, color to draw the feature
o hide Boolean for whether the feature will be drawn or not
o sigil String denoting the type of sigil to use for the feature.
Currently either "BOX" or "ARROW" are supported.
o arrowhead_length Float denoting length of the arrow head to be drawn,
relative to the bounding box height. The arrow shaft
takes up the remainder of the bounding box's length.
o arrowshaft_height Float denoting length of the representative arrow
shaft to be drawn, relative to the bounding box height.
The arrow head takes the full height of the bound box.
o name_qualifiers List of Strings, describes the qualifiers that may
contain feature names in the wrapped Bio.SeqFeature object
o label Boolean, 1 if the label should be shown
o label_font String describing the font to use for the feature label
o label_size Int describing the feature label font size
o label_color color.Color describing the feature label color
o label_angle Float describing the angle through which to rotate the
feature label in degrees (default = 45, linear only)
o label_position String, 'start', 'end' or 'middle' denoting where
to place the feature label. Leave as None for the default
which is 'start' for linear diagrams, and at the bottom of
the feature as drawn on circular diagrams.
o label_strand Integer -1 or +1 to explicitly place the label on the
forward or reverse strand. Default (None) follows th
feature's strand. Use -1 to put labels under (linear) or
inside (circular) the track, +1 to put them above (linear)
or outside (circular) the track.
o locations List of tuples of (start, end) ints describing where the
feature and any subfeatures start and end
o type String denoting the feature type
o name String denoting the feature name
o strand Int describing the strand on which the feature is found
"""
def __init__(self, parent=None, feature_id=None, feature=None,
color=colors.lightgreen, label=0, border=None, colour=None):
""" __init__(self, parent=None, feature_id=None, feature=None,
color=colors.lightgreen, label=0)
o parent FeatureSet containing the feature
o feature_id Unique id for the feature
o feature Bio.SeqFeature object to be wrapped
o color color.Color Color to draw the feature (overridden
by backwards compatible argument with UK spelling,
colour). Either argument is overridden if 'color'
is found in feature qualifiers
o border color.Color Color to draw the feature border, use
None for the same as the fill color, False for no border.
o label Boolean, 1 if the label should be shown
"""
# Let the UK spelling (colour) override the USA spelling (color)
if colour is not None:
color = colour
self._colortranslator = ColorTranslator()
# Initialise attributes
self.parent = parent
self.id = feature_id
self.color = color # default color to draw the feature
self.border = border
self._feature = None # Bio.SeqFeature object to wrap
self.hide = 0 # show by default
self.sigil = 'BOX'
self.arrowhead_length = 0.5 # 50% of the box height
self.arrowshaft_height = 0.4 # 40% of the box height
self.name_qualifiers = ['gene', 'label', 'name', 'locus_tag', 'product']
self.label = label
self.label_font = 'Helvetica'
self.label_size = 6
self.label_color = colors.black
self.label_angle = 45
self.label_position = None # Expect 'start', 'middle', or 'end' (plus aliases)
self.label_strand = None # Expect +1 or -1 if overriding this
if feature is not None:
self.set_feature(feature)
def set_feature(self, feature):
""" set_feature(self, feature)
o feature Bio.SeqFeature object to be wrapped
Defines the Bio.SeqFeature object to be wrapped
"""
self._feature = feature
self.__process_feature()
def __process_feature(self):
""" __process_feature(self)
Examine the feature to be wrapped, and set some of the Feature's
properties accordingly
"""
self.locations = []
bounds = []
# This will be a list of length one for simple FeatureLocation:
for location in self._feature.location.parts:
start = location.nofuzzy_start
end = location.nofuzzy_end
# if start > end and self.strand == -1:
# start, end = end, start
self.locations.append((start, end))
bounds += [start, end]
self.type = str(self._feature.type) # Feature type
# TODO - Strand can vary with subfeatures (e.g. mixed strand tRNA)
if self._feature.strand is None:
# This is the SeqFeature default (None), but the drawing code
# only expects 0, +1 or -1.
self.strand = 0
else:
self.strand = int(self._feature.strand) # Feature strand
if 'color' in self._feature.qualifiers: # Artemis color (if present)
self.color = self._colortranslator.artemis_color(
self._feature.qualifiers['color'][0])
self.name = self.type
for qualifier in self.name_qualifiers:
if qualifier in self._feature.qualifiers:
self.name = self._feature.qualifiers[qualifier][0]
break
# Note will be 0 to N for origin wrapping feature on genome of length N
self.start, self.end = min(bounds), max(bounds)
def get_feature(self):
""" get_feature(self) -> Bio.SeqFeature
Returns the unwrapped Bio.SeqFeature object
"""
return self._feature
def set_colour(self, colour):
"""Backwards compatible variant of set_color(self, color) using UK spelling."""
color = self._colortranslator.translate(colour)
self.color = color
def set_color(self, color):
""" set_color(self, color)
o color The color to draw the feature - either a colors.Color
object, an RGB tuple of floats, or an integer
corresponding to colors in colors.txt
Set the color in which the feature will be drawn
"""
# TODO - Make this into the set method for a color property?
color = self._colortranslator.translate(color)
self.color = color
def __getattr__(self, name):
""" __getattr__(self, name) -> various
If the Feature class doesn't have the attribute called for,
check in self._feature for it
"""
return getattr(self._feature, name) # try to get the attribute from the feature
################################################################################
# RUN AS SCRIPT
################################################################################
if __name__ == '__main__':
# Test code
gdf = Feature()
|
