Source Code for Module Bio.Graphics.GenomeDiagram._Feature

  1  # Copyright 2003-2008 by Leighton Pritchard.  All rights reserved. 
  2  # This code is part of the Biopython distribution and governed by its 
  3  # license.  Please see the LICENSE file that should have been included 
  4  # as part of this package. 
  5  # 
  6  # Contact:       Leighton Pritchard, Scottish Crop Research Institute, 
  7  #                Invergowrie, Dundee, Scotland, DD2 5DA, UK 
  8  #                L.Pritchard@scri.ac.uk 
  9  ################################################################################ 
 10   
 11  """ Feature module 
 12   
 13      Provides: 
 14   
 15      o Feature - class to wrap Bio.SeqFeature objects with drawing information 
 16   
 17      For drawing capabilities, this module uses reportlab to define colors: 
 18   
 19      http://www.reportlab.com 
 20   
 21      For dealing with biological information, the package uses BioPython: 
 22   
 23      http://www.biopython.org 
 24  """ 
 25   
 26  # ReportLab imports 
 27  from reportlab.lib import colors 
 28   
 29  # GenomeDiagram imports 
 30  from _Colors import ColorTranslator 
 31   
 32   
 33 -class Feature(object): 
 34      """ Class to wrap Bio.SeqFeature objects for GenomeDiagram 
 35   
 36          Provides: 
 37   
 38          Methods: 
 39   
 40          o __init__(self, parent=None, feature_id=None, feature=None, 
 41                   color=colors.lightgreen) Called when the feature is 
 42                   instantiated 
 43   
 44          o set_feature(self, feature) Wrap the passed feature 
 45   
 46          o get_feature(self) Return the unwrapped Bio.SeqFeature object 
 47   
 48          o set_color(self, color) Set the color in which the feature will 
 49                  be drawn (accepts multiple formats: reportlab color.Color() 
 50                  tuple and color.name, or integer representing Artemis color 
 51   
 52          o get_color(self) Returns color.Color tuple of the feature's color 
 53   
 54          o __getattr__(self, name) Catches attribute requests and passes them to 
 55                  the wrapped Bio.SeqFeature object 
 56   
 57          Attributes: 
 58   
 59          o parent    FeatureSet, container for the object 
 60   
 61          o id        Unique id 
 62   
 63          o color    color.Color, color to draw the feature 
 64   
 65          o hide      Boolean for whether the feature will be drawn or not 
 66   
 67          o sigil     String denoting the type of sigil to use for the feature. 
 68                      Currently either "BOX" or "ARROW" are supported. 
 69   
 70          o arrowhead_length  Float denoting length of the arrow head to be drawn, 
 71                              relative to the bounding box height.  The arrow shaft 
 72                              takes up the remainder of the bounding box's length. 
 73   
 74          o arrowshaft_height  Float denoting length of the representative arrow 
 75                               shaft to be drawn, relative to the bounding box height. 
 76                               The arrow head takes the full height of the bound box. 
 77   
 78          o name_qualifiers   List of Strings, describes the qualifiers that may 
 79                      contain feature names in the wrapped Bio.SeqFeature object 
 80   
 81          o label     Boolean, 1 if the label should be shown 
 82   
 83          o label_font    String describing the font to use for the feature label 
 84   
 85          o label_size    Int describing the feature label font size 
 86   
 87          o label_color  color.Color describing the feature label color 
 88   
 89          o label_angle   Float describing the angle through which to rotate the 
 90                      feature label in degrees (default = 45, linear only) 
 91   
 92          o label_position    String, 'start', 'end' or 'middle' denoting where 
 93                      to place the feature label (linear only) 
 94   
 95          o locations     List of tuples of (start, end) ints describing where the 
 96                      feature and any subfeatures start and end 
 97   
 98          o type      String denoting the feature type 
 99   
100          o name      String denoting the feature name 
101   
102          o strand    Int describing the strand on which the feature is found 
103   
104      """ 
105 -    def __init__(self, parent=None, feature_id=None, feature=None, 
106                   color=colors.lightgreen, label=0, border=None, colour=None): 
107          """ __init__(self, parent=None, feature_id=None, feature=None, 
108                   color=colors.lightgreen, label=0) 
109   
110              o parent    FeatureSet containing the feature 
111   
112              o feature_id    Unique id for the feature 
113   
114              o feature   Bio.SeqFeature object to be wrapped 
115   
116              o color    color.Color Color to draw the feature (overridden 
117                         by backwards compatible argument with UK spelling, 
118                         colour).  Either argument is overridden if 'color' 
119                         is found in feature qualifiers 
120   
121              o border   color.Color Color to draw the feature border, use 
122                         None for the same as the fill color, False for no border. 
123   
124              o label     Boolean, 1 if the label should be shown 
125          """ 
126          #Let the UK spelling (colour) override the USA spelling (color) 
127          if colour is not None: 
128              color = colour 
129   
130          self._colortranslator = ColorTranslator() 
131   
132          # Initialise attributes 
133          self.parent = parent 
134          self.id = feature_id 
135          self.color = color            # default color to draw the feature 
136          self.border = border 
137          self._feature = None            # Bio.SeqFeature object to wrap 
138          self.hide = 0                   # show by default 
139          self.sigil = 'BOX' 
140          self.arrowhead_length = 0.5 # 50% of the box height 
141          self.arrowshaft_height = 0.4 # 40% of the box height 
142          self.name_qualifiers = ['gene', 'label', 'name', 'locus_tag', 'product'] 
143          self.label = label 
144          self.label_font = 'Helvetica' 
145          self.label_size = 6 
146          self.label_color = colors.black 
147          self.label_angle = 45 
148          self.label_position = 'start' 
149   
150          if feature is not None: 
151              self.set_feature(feature) 
152   
153 -    def set_feature(self, feature): 
154          """ set_feature(self, feature) 
155   
156              o feature   Bio.SeqFeature object to be wrapped 
157   
158              Defines the Bio.SeqFeature object to be wrapped 
159          """ 
160          self._feature = feature 
161          self.__process_feature() 
162   
163 -    def __process_feature(self): 
164          """ __process_feature(self) 
165   
166              Examine the feature to be wrapped, and set some of the Feature's 
167              properties accordingly 
168          """ 
169          self.locations = [] 
170          bounds = [] 
171          if self._feature.sub_features == []: 
172              start = self._feature.location.nofuzzy_start 
173              end = self._feature.location.nofuzzy_end 
174              #if start > end and self.strand == -1: 
175              #    start, end = end, start 
176              self.locations.append((start, end)) 
177              bounds += [start, end] 
178          else: 
179              for subfeature in self._feature.sub_features: 
180                  start = subfeature.location.nofuzzy_start 
181                  end = subfeature.location.nofuzzy_end 
182                  #if start > end and self.strand == -1: 
183                  #    start, end = end, start 
184                  self.locations.append((start, end)) 
185                  bounds += [start, end] 
186          self.type = str(self._feature.type)                     # Feature type 
187          #TODO - Strand can vary with subfeatures (e.g. mixed strand tRNA) 
188          if self._feature.strand is None: 
189              #This is the SeqFeature default (None), but the drawing code 
190              #only expects 0, +1 or -1. 
191              self.strand = 0 
192          else: 
193              self.strand = int(self._feature.strand)                 # Feature strand 
194          if 'color' in self._feature.qualifiers:                # Artemis color (if present) 
195              self.color = self._colortranslator.artemis_color( 
196                                           self._feature.qualifiers['color'][0]) 
197          self.name = self.type 
198          for qualifier in self.name_qualifiers: 
199              if qualifier in self._feature.qualifiers: 
200                  self.name = self._feature.qualifiers[qualifier][0] 
201                  break 
202          #Note will be 0 to N for origin wrapping feature on genome of length N 
203          self.start, self.end = min(bounds), max(bounds) 
204   
205 -    def get_feature(self): 
206          """ get_feature(self) -> Bio.SeqFeature 
207   
208              Returns the unwrapped Bio.SeqFeature object 
209          """ 
210          return self._feature 
211   
212 -    def set_colour(self, colour): 
213          """Backwards compatible variant of set_color(self, color) using UK spelling.""" 
214          color = self._colortranslator.translate(colour) 
215          self.color = color 
216   
217 -    def set_color(self, color): 
218          """ set_color(self, color) 
219   
220              o color    The color to draw the feature - either a colors.Color 
221                         object, an RGB tuple of floats, or an integer 
222                         corresponding to colors in colors.txt 
223   
224              Set the color in which the feature will be drawn 
225          """ 
226          #TODO - Make this into the set method for a color property? 
227          color = self._colortranslator.translate(color) 
228          self.color = color 
229   
230 -    def __getattr__(self, name): 
231          """ __getattr__(self, name) -> various 
232   
233              If the Feature class doesn't have the attribute called for, 
234              check in self._feature for it 
235          """ 
236          return getattr(self._feature, name) # try to get the attribute from the feature 
237   
238   
239  ################################################################################ 
240  # RUN AS SCRIPT 
241  ################################################################################ 
242   
243  if __name__ == '__main__': 
244   
245      # Test code 
246      gdf = Feature() 
247