Package weblogolib :: Module colorscheme

# Source Code for Module weblogolib.colorscheme

      1
      2  #  Copyright (c) 2003-2005 The Regents of the University of California.
      3  #  Copyright (c) 2005 Gavin E. Crooks
      4
      5  #  This software is distributed under the MIT Open Source License.
      6  #  <http://www.opensource.org/licenses/mit-license.html>
      7  #
      8  #  Permission is hereby granted, free of charge, to any person obtaining a
      9  #  copy of this software and associated documentation files (the "Software"),
     10  #  to deal in the Software without restriction, including without limitation
     11  #  the rights to use, copy, modify, merge, publish, distribute, sublicense,
     12  #  and/or sell copies of the Software, and to permit persons to whom the
     13  #  Software is furnished to do so, subject to the following conditions:
     14  #
     15  #  The above copyright notice and this permission notice shall be included
     16  #  in all copies or substantial portions of the Software.
     17  #
     18  #  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
     19  #  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
     20  #  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
     21  #  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
     22  #  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
     23  #  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
     24  #  THE SOFTWARE.
     25
     26  """ Popular color codings for nucleic and amino acids.
     27
     28  Classes:
     29      ColorScheme -- A color scheme
     30      ColorGroup
     31
     32
     33  Generic
     34      monochrome
     35
     36  Nucleotides
     37      nucleotide
     38      base pairing
     39
     40  Amino Acid
     41      hydrophobicity
     42      chemistry
     43      charge
     44      taylor
     45
     46  Status : Beta - Needs documentation.
     47
     48  """
     49  # Good online references include bioruby and the JalView alignment editor.
     50  # Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004),
     51  # "The Jalview Java Alignment Editor," Bioinformatics, 12, 426-7
     52  # http://www.jalview.org
     53
     54
     55  from corebio import seq
     56  from color import Color
     57
     58 -class ColorScheme(object):
     59      """ A coloring of an alphabet.
     60
     61      title : string            -- A human readable description
     62      defualt_color : Color           --
     63      groups : list of color groups
     64      alphabet : string               -- The set of colored symbols
     65      color -- A map between a symbol and a Coloring
     66
     67
     68      """
     69
     70 -    def __init__(self,
     71                  groups = [],
     72                  title = "",
     73                  description = "",
     74                  default_color = "black",
     75                  alphabet = seq.generic_alphabet) :
     76          """  """
     77          self.title= title
     78          self.description = description
     79          self.default_color = Color.from_string(default_color)
     80          self.groups = groups
     81          self.alphabet = alphabet
     82
     83          color = {}
     84          for cg in groups :
     85              for s in cg.symbols :
     86                  color[s] = cg.color
     87                  if s not in alphabet :
     88                      raise KeyError("Colored symbol does not exist in alphabet.")
     89          self._color = color
     90
     91 -    def color(self, symbol) :
     92          if symbol in self._color :
     93              return self._color[symbol]
     94          return self.default_color
     95
     96 -class ColorGroup(object) :
     97      """Associate a group of symbols with a color"""
     98 -    def __init__(self, symbols, color, description=None) :
     99          self.symbols = symbols
    100          self.color =  Color.from_string(color)
    101          self.description = description
    102
    103
    104
    105  monochrome = ColorScheme([]) # This list intentionally left blank
    106
    107  # From makelogo
    108  nucleotide = ColorScheme([
    109      ColorGroup("G", "orange"),
    110      ColorGroup("TU", "red"),
    111      ColorGroup("C",  "blue"),
    112      ColorGroup("A",  "green")
    113      ])
    114
    115  base_pairing = ColorScheme([
    116      ColorGroup("TAU",  "darkorange", "Weak (2 Watson-Crick hydrogen bonds)"),
    117      ColorGroup("GC",    "blue", "Strong (3 Watson-Crick hydrogen bonds)")],
    118      )
    119
    120  # From Crooks2004c-Proteins-SeqStr.pdf
    121  hydrophobicity = ColorScheme([
    122      ColorGroup( "RKDENQ",   "black", "hydrophilic"),
    123      ColorGroup( "SGHTAP",   "green", "neutral"  ),
    124      ColorGroup( "YVMCLFIW", "blue",  "hydrophobic") ],
    125      alphabet = seq.unambiguous_protein_alphabet
    126      )
    127
    128  # from makelogo
    129  chemistry = ColorScheme([
    130    ColorGroup( "GSTYC",  "green",   "polar"),
    131    ColorGroup( "NQ",      "purple", "neutral"),
    132    ColorGroup( "KRH",     "blue",   "basic"),
    133    ColorGroup( "DE",      "red",    "acidic"),
    134    ColorGroup("PAWFLIMV", "black",  "hydrophobic") ],
    135    alphabet = seq.unambiguous_protein_alphabet
    136    )
    137
    138  charge = ColorScheme([
    139      ColorGroup("KRH", "blue", "Positive" ),
    140      ColorGroup( "DE", "red", "Negative") ],
    141      alphabet = seq.unambiguous_protein_alphabet
    142      )
    143
    144
    145  taylor = ColorScheme([
    146      ColorGroup( 'A', '#CCFF00' ),
    147      ColorGroup( 'C', '#FFFF00' ),
    148      ColorGroup( 'D', '#FF0000'),
    149      ColorGroup( 'E', '#FF0066' ),
    150      ColorGroup( 'F', '#00FF66'),
    151      ColorGroup( 'G', '#FF9900'),
    152      ColorGroup( 'H', '#0066FF'),
    153      ColorGroup( 'I', '#66FF00'),
    154      ColorGroup( 'K', '#6600FF'),
    155      ColorGroup( 'L', '#33FF00'),
    156      ColorGroup( 'M', '#00FF00'),
    157      ColorGroup( 'N', '#CC00FF'),
    158      ColorGroup( 'P', '#FFCC00'),
    159      ColorGroup( 'Q', '#FF00CC'),
    160      ColorGroup( 'R', '#0000FF'),
    161      ColorGroup( 'S', '#FF3300'),
    162      ColorGroup( 'T', '#FF6600'),
    163      ColorGroup( 'V', '#99FF00'),
    164      ColorGroup( 'W', '#00CCFF'),
    165      ColorGroup( 'Y', '#00FFCC')],
    166      title = "Taylor",
    167      description = "W. Taylor, Protein Engineering, Vol 10 , 743-746 (1997)",
    168      alphabet = seq.unambiguous_protein_alphabet
    169      )
    170