Package Bio :: Package Graphics :: Package GenomeDiagram :: Module _Feature :: Class Feature
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Class Feature

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object --+
         |
        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. 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

Instance Methods [hide private]
 
__init__(self, parent=None, feature_id=None, feature=None, color=colors.lightgreen, label=0)
o parent FeatureSet containing the feature
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set_feature(self, feature)
o feature Bio.SeqFeature object to be wrapped
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__process_feature(self)
Examine the feature to be wrapped, and set some of the Feature's properties accordingly
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Bio.SeqFeature
get_feature(self)
Returns the unwrapped Bio.SeqFeature object
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set_colour(self, colour)
Backwards compatible variant of set_color(self, color) using UK spelling.
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set_color(self, color)
object, an RGB tuple of floats, or an integer corresponding to colors in colors.txt
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various
__getattr__(self, name)
If the Feature class doesn't have the attribute called for, check in self._feature for it
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, parent=None, feature_id=None, feature=None, color=colors.lightgreen, label=0)
(Constructor)

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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

Overrides: object.__init__

set_feature(self, feature)

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o feature Bio.SeqFeature object to be wrapped

Defines the Bio.SeqFeature object to be wrapped

set_color(self, color)

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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