def test_color_conversions(self):
"""Test color translations.
"""
translator = ColorTranslator()
# Does the translate method correctly convert the passed argument?
assert translator.float1_color((0.5, 0.5, 0.5)) == translator.translate((0.5, 0.5, 0.5)), \
"Did not correctly translate colour from floating point RGB tuple"
assert translator.int255_color((1, 75, 240)) == translator.translate((1, 75, 240)), \
"Did not correctly translate colour from integer RGB tuple"
assert translator.artemis_color(7) == translator.translate(7), \
"Did not correctly translate colour from Artemis colour scheme"
assert translator.scheme_color(2) == translator.translate(2), \
"Did not correctly translate colour from user-defined colour scheme"
def __init__(self,
parent=None,
feature_id=None,
feature=None,
color=colors.lightgreen,
label=0,
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 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._feature = None # Bio.SeqFeature object to wrap
self.hide = 0 # show by default
self.sigil = 'BOX'
self.arrowhead_length = 1.0 # 100% 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 = 'start'
if feature is not None:
self.set_feature(feature)
def test_color_conversions(self):
"""Test color translations.
"""
translator = ColorTranslator()
# Does the translate method correctly convert the passed argument?
assert translator.float1_color((0.5, 0.5, 0.5)) == translator.translate((0.5, 0.5, 0.5)), \
"Did not correctly translate colour from floating point RGB tuple"
assert translator.int255_color((1, 75, 240)) == translator.translate((1, 75, 240)), \
"Did not correctly translate colour from integer RGB tuple"
assert translator.artemis_color(7) == translator.translate(7), \
"Did not correctly translate colour from Artemis colour scheme"
assert translator.scheme_color(2) == translator.translate(2), \
"Did not correctly translate colour from user-defined colour scheme"
def __init__(self, parent=None, feature_id=None, feature=None,
color=colors.lightgreen, label=0, 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 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._feature = None # Bio.SeqFeature object to wrap
self.hide = 0 # show by default
self.sigil = 'BOX'
self.arrowhead_length = 1.0 # 100% 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 = 'start'
if feature is not None:
self.set_feature(feature)
class Feature:
""" 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 (linear only)
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, 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 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._feature = None # Bio.SeqFeature object to wrap
self.hide = 0 # show by default
self.sigil = 'BOX'
self.arrowhead_length = 1.0 # 100% 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 = 'start'
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 = []
if self._feature.sub_features == []:
if '^' in str(self._feature.location._start):
self.hide = 1 # The GenBank parser doesn't behave properly, so don't show the feature
#print self._feature.location, dir(self._feature.location)
start, end = str(self._feature.location._start).split('^')
else:
start = str(self._feature.location._start) # Feature start
end = str(self._feature.location._end) # Feature end
while start[0] not in string.digits: # Remove extraneous leading chars
#print start
start = start[1:]
while end[0] not in string.digits:
#print end
end = end[1:]
while end[-1] not in string.digits:
#print end
end = end[:-1]
start, end = int(start), int(end)
#if start > end and self.strand == -1:
# start, end = end, start
self.locations.append((start, end))
bounds += [start, end]
else:
for subfeature in self._feature.sub_features:
if '^' in str(subfeature.location._start):
self.hide = 1
start, end = str(subfeature.location._start).split('^')
else:
start = str(subfeature.location._start) # Feature start
end = str(subfeature.location._end) # Feature end
while start[0] not in string.digits: # Remove extraneous leading chars
#print start
start = start[1:]
while end[0] not in string.digits:
#print end
end = end[1:]
try:
start, end = int(start), int(end)
except:
#print start, end
sys.exit(1)
#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
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)
# Artemis color used to be only a single integer, but as of
# Oct '04 appears to be dot-delimited. This is a quick fix to
# allow dot-delimited strings, but only use the first integer
artemis_color = self._feature.qualifiers['color'][0] # Local copy of string
if artemis_color.count('.'): # dot-delimited
artemis_color = artemis_color.split('.')[0] # Use only first integer
else: # Assume just an integer
artemis_color = artemis_color # Use integer
self.color = self._colortranslator.artemis_color(artemis_color)
self.name = self.type
for qualifier in self.name_qualifiers:
if qualifier in self._feature.qualifiers:
self.name = self._feature.qualifiers[qualifier][0]
break
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
class Feature:
""" 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 (linear only)
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,
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 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._feature = None # Bio.SeqFeature object to wrap
self.hide = 0 # show by default
self.sigil = 'BOX'
self.arrowhead_length = 1.0 # 100% 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 = 'start'
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 = []
if self._feature.sub_features == []:
if '^' in str(self._feature.location._start):
self.hide = 1 # The GenBank parser doesn't behave properly, so don't show the feature
#print self._feature.location, dir(self._feature.location)
start, end = str(self._feature.location._start).split('^')
else:
start = str(self._feature.location._start) # Feature start
end = str(self._feature.location._end) # Feature end
while start[
0] not in string.digits: # Remove extraneous leading chars
#print start
start = start[1:]
while end[0] not in string.digits:
#print end
end = end[1:]
while end[-1] not in string.digits:
#print end
end = end[:-1]
start, end = int(start), int(end)
#if start > end and self.strand == -1:
# start, end = end, start
self.locations.append((start, end))
bounds += [start, end]
else:
for subfeature in self._feature.sub_features:
if '^' in str(subfeature.location._start):
self.hide = 1
start, end = str(subfeature.location._start).split('^')
else:
start = str(subfeature.location._start) # Feature start
end = str(subfeature.location._end) # Feature end
while start[
0] not in string.digits: # Remove extraneous leading chars
#print start
start = start[1:]
while end[0] not in string.digits:
#print end
end = end[1:]
try:
start, end = int(start), int(end)
except:
#print start, end
sys.exit(1)
#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
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)
# Artemis color used to be only a single integer, but as of
# Oct '04 appears to be dot-delimited. This is a quick fix to
# allow dot-delimited strings, but only use the first integer
artemis_color = self._feature.qualifiers['color'][
0] # Local copy of string
if artemis_color.count('.'): # dot-delimited
artemis_color = artemis_color.split('.')[
0] # Use only first integer
else: # Assume just an integer
artemis_color = artemis_color # Use integer
self.color = self._colortranslator.artemis_color(artemis_color)
self.name = self.type
for qualifier in self.name_qualifiers:
if qualifier in self._feature.qualifiers:
self.name = self._feature.qualifiers[qualifier][0]
break
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
