Spaces:
No application file
No application file
File size: 8,047 Bytes
b7731cd |
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 |
# Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
#
# Contact: Leighton Pritchard, The James Hutton Institute,
# Invergowrie, Dundee, Scotland, DD2 5DA, UK
# [email protected]
################################################################################
"""Feature module.
Provides:
- Feature - class to wrap Bio.SeqFeature objects with drawing information
For drawing capabilities, this module uses reportlab to define colors:
http://www.reportlab.com
"""
# ReportLab imports
from reportlab.lib import colors
# GenomeDiagram imports
from ._Colors import ColorTranslator
class Feature:
"""Class to wrap Bio.SeqFeature objects for GenomeDiagram.
Attributes:
- parent FeatureSet, container for the object
- id Unique id
- color color.Color, color to draw the feature
- hide Boolean for whether the feature will be drawn or not
- sigil String denoting the type of sigil to use for the feature.
Currently either "BOX" or "ARROW" are supported.
- 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.
- 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.
- name_qualifiers List of Strings, describes the qualifiers that may
contain feature names in the wrapped Bio.SeqFeature object
- label Boolean, 1 if the label should be shown
- label_font String describing the font to use for the feature label
- label_size Int describing the feature label font size
- label_color color.Color describing the feature label color
- label_angle Float describing the angle through which to rotate the
feature label in degrees (default = 45, linear only)
- 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.
- 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.
- locations List of tuples of (start, end) ints describing where the
feature and any subfeatures start and end
- type String denoting the feature type
- name String denoting the feature name
- 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,
):
"""Initialize.
Arguments:
- parent FeatureSet containing the feature
- feature_id Unique id for the feature
- feature Bio.SeqFeature object to be wrapped
- 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
- border color.Color Color to draw the feature border, use
None for the same as the fill color, False for no border.
- 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()
# Initialize 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):
"""Define the Bio.SeqFeature object to be wrapped."""
self._feature = feature
self.__process_feature()
def __process_feature(self):
"""Examine wrapped feature and set some properties accordingly (PRIVATE)."""
self.locations = []
bounds = []
# This will be a list of length one for a SimpleLocation:
for location in self._feature.location.parts:
start = int(location.start)
end = int(location.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):
"""Return 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 the color in which the feature will be drawn.
Arguments:
- color The color to draw the feature - either a colors.Color
object, an RGB tuple of floats, or an integer corresponding a
colors in colors.txt
"""
# TODO - Make this into the set method for a color property?
color = self._colortranslator.translate(color)
self.color = color
def __getattr__(self, name):
"""Get attribute by name.
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()
|