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diff weblogolib/colorscheme.py @ 7:8d676bbd1f2d

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author davidmurphy
date Mon, 16 Jan 2012 07:03:36 -0500
parents c55bdc2fb9fa
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/weblogolib/colorscheme.py	Mon Jan 16 07:03:36 2012 -0500
@@ -0,0 +1,455 @@
+
+#  Copyright (c) 2003-2005 The Regents of the University of California.
+#  Copyright (c) 2005 Gavin E. Crooks
+
+#  This software is distributed under the MIT Open Source License.
+#  <http://www.opensource.org/licenses/mit-license.html>
+#
+#  Permission is hereby granted, free of charge, to any person obtaining a 
+#  copy of this software and associated documentation files (the "Software"),
+#  to deal in the Software without restriction, including without limitation
+#  the rights to use, copy, modify, merge, publish, distribute, sublicense,
+#  and/or sell copies of the Software, and to permit persons to whom the
+#  Software is furnished to do so, subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included
+#  in all copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
+#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 
+#  THE SOFTWARE.
+
+""" Popular color codings for nucleic and amino acids. 
+
+Classes:
+    ColorScheme -- A color scheme
+    ColorGroup  
+    
+    
+Generic
+    monochrome
+
+Nucleotides
+    nucleotide
+    base pairing
+
+Amino Acid
+    hydrophobicity
+    chemistry
+    charge
+    taylor
+
+Status : Beta - Needs documentation.
+
+"""
+# Good online references include bioruby and the JalView alignment editor.
+# Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), 
+# "The Jalview Java Alignment Editor," Bioinformatics, 12, 426-7
+# http://www.jalview.org
+
+import sys
+
+from corebio import seq
+from color import Color
+codon_alphabetU=['AAA', 'AAU', 'AAC', 'AAG', 'AUA', 'AUU', 'AUC', 'AUG', 'ACA', 'ACU', 'ACC', 'ACG', 'AGA', 'AGU', 'AGC', 'AGG', 'UAA', 'UAU', 'UAC', 'UAG', 'UUA', 'UUU', 'UUC', 'UUG', 'UCA', 'UCU', 'UCC', 'UCG', 'UGA', 'UGU', 'UGC', 'UGG', 'CAA', 'CAU', 'CAC', 'CAG', 'CUA', 'CUU', 'CUC', 'CUG', 'CCA', 'CCU', 'CCC', 'CCG', 'CGA', 'CGU', 'CGC', 'CGG', 'GAA', 'GAU', 'GAC', 'GAG', 'GUA', 'GUU', 'GUC', 'GUG', 'GCA', 'GCU', 'GCC', 'GCG', 'GGA', 'GGU', 'GGC', 'GGG']
+codon_alphabetT=['AAA', 'AAT', 'AAC', 'AAG', 'ATA', 'ATT', 'ATC', 'ATG', 'ACA', 'ACT', 'ACC', 'ACG', 'AGA', 'AGT', 'AGC', 'AGG', 'TAA', 'TAT', 'TAC', 'TAG', 'TTA', 'TTT', 'TTC', 'TTG', 'TCA', 'TCT', 'TCC', 'TCG', 'TGA', 'TGT', 'TGC', 'TGG', 'CAA', 'CAT', 'CAC', 'CAG', 'CTA', 'CTT', 'CTC', 'CTG', 'CCA', 'CCT', 'CCC', 'CCG', 'CGA', 'CGT', 'CGC', 'CGG', 'GAA', 'GAT', 'GAC', 'GAG', 'GTA', 'GTT', 'GTC', 'GTG', 'GCA', 'GCT', 'GCC', 'GCG', 'GGA', 'GGT', 'GGC', 'GGG']
+
+class ColorScheme(object):
+    """ A coloring of an alphabet.
+    
+    title : string            -- A human readable description
+    defualt_color : Color           --
+    groups : list of color groups 
+    alphabet : string               -- The set of colored symbols
+    color -- A map between a symbol and a Coloring
+    
+
+    """
+    
+    def __init__(self, 
+                groups = [], 
+                title = "", 
+                description = "",
+                default_color = "black", 
+                alphabet = seq.generic_alphabet) :
+        """  """
+        self.title= title
+        self.description = description
+        self.default_color = Color.from_string(default_color)
+        self.groups = groups
+        self.alphabet = alphabet
+        #print >> sys.stderr, groups
+	altype="codons"
+	#print >> sys.stderr,altype
+	#if(alphabet==codon_alphabet):
+	  #print >> sys.stderr,"haleyulia it works"
+
+        color = {}
+        #print >> sys.stderr, groups
+        if(alphabet!=codon_alphabetT and alphabet!=codon_alphabetU):
+	  for cg in groups :
+	      #print >> sys.stderr, cg
+	      for s in cg.symbols :
+		  color[s] = cg.color
+		  #print >> sys.stderr, s
+		  #print >> sys.stderr, cg
+		  if s not in alphabet :
+		      raise KeyError("Colored symbol does not exist in alphabet.")
+	else:
+	  for cg in groups :
+	      #print >> sys.stderr, cg
+	    color[cg.symbols] = cg.color
+	    #print >> sys.stderr, cg.symbols
+        self._color = color
+
+    def color(self, symbol) :
+        if symbol in self._color :
+            return self._color[symbol]
+        return self.default_color
+        
+class ColorGroup(object) :
+    """Associate a group of symbols with a color"""
+    def __init__(self, symbols, color, description=None) :
+        self.symbols = symbols              
+        self.color =  Color.from_string(color)
+        self.description = description
+
+
+         
+monochrome = ColorScheme([]) # This list intentionally left blank
+               
+# From makelogo
+nucleotide = ColorScheme([
+    ColorGroup("G", "orange"),
+    ColorGroup("TU", "red"),
+    ColorGroup("C",  "blue"),
+    ColorGroup("A",  "green") 
+    ]) 
+
+base_pairing = ColorScheme([
+    ColorGroup("TAU",  "darkorange", "Weak (2 Watson-Crick hydrogen bonds)"),
+    ColorGroup("GC",    "blue", "Strong (3 Watson-Crick hydrogen bonds)")],
+    )
+
+
+hydrophobicity = ColorScheme([
+    ColorGroup( "RKDENQ",   "black", "hydrophobic"),
+    ColorGroup( "SGHTAP",   "green", "neutral"  ),
+    ColorGroup( "YVMCLFIW", "blue",  "hydrophilic") ],
+    alphabet = seq.unambiguous_protein_alphabet
+    )
+
+# from makelogo
+chemistry = ColorScheme([
+  ColorGroup( "GSTYC",  "green",   "polar"),
+  ColorGroup( "NQ",      "purple", "neutral"), 
+  ColorGroup( "KRH",     "blue",   "basic"),
+  ColorGroup( "DE",      "red",    "acidic"),
+  ColorGroup("PAWFLIMV", "black",  "hydrophobic") ],
+  alphabet = seq.unambiguous_protein_alphabet
+  ) 
+  
+
+codonsU = ColorScheme([
+ColorGroup( 'CAT', '#00FFFF'),
+ColorGroup( 'CAU', '#00FFFF'),
+ColorGroup( 'CAC', '#00FFFF'),
+
+ColorGroup( 'AAA', '#00FFFF'),
+ColorGroup( 'AAG', '#00FFFF'),
+
+ColorGroup( 'CGT', '#00FFFF'),
+ColorGroup( 'CGU', '#00FFFF'),
+ColorGroup( 'CGC', '#00FFFF'),
+ColorGroup( 'CGA', '#00FFFF'),
+ColorGroup( 'CGG', '#00FFFF'),
+ColorGroup( 'AGA', '#00FFFF'),
+ColorGroup( 'AGG', '#00FFFF'),
+
+
+ColorGroup( 'GAT', '#FF0000'),
+ColorGroup( 'GAU', '#FF0000'),
+ColorGroup( 'GAC', '#FF0000'),
+
+ColorGroup( 'GAA', '#FF0000'),
+ColorGroup( 'GAG', '#FF0000'),
+
+
+ColorGroup( 'TCT', '#00FF00'),
+ColorGroup( 'UCU', '#00FF00'),
+ColorGroup( 'TCC', '#00FF00'),
+ColorGroup( 'UCC', '#00FF00'),
+ColorGroup( 'TCA', '#00FF00'),
+ColorGroup( 'UCA', '#00FF00'),
+ColorGroup( 'TCG', '#00FF00'),
+ColorGroup( 'UCG', '#00FF00'),
+ColorGroup( 'AGT', '#00FF00'),
+ColorGroup( 'AGU', '#00FF00'),
+ColorGroup( 'AGC', '#00FF00'),
+
+ColorGroup( 'ACT', '#00FF00'),
+ColorGroup( 'ACU', '#00FF00'),
+ColorGroup( 'ACC', '#00FF00'),
+ColorGroup( 'ACA', '#00FF00'),
+ColorGroup( 'ACG', '#00FF00'),
+
+ColorGroup( 'CAA', '#00FF00'),
+ColorGroup( 'CAG', '#00FF00'),
+
+ColorGroup( 'AAT', '#00FF00'),
+ColorGroup( 'AAU', '#00FF00'),
+ColorGroup( 'AAC', '#00FF00'),
+
+
+ColorGroup( 'GCT', '#5555FF'),
+ColorGroup( 'GCU', '#5555FF'),
+ColorGroup( 'GCC', '#5555FF'),
+ColorGroup( 'GCA', '#5555FF'),
+ColorGroup( 'GCG', '#5555FF'),
+
+ColorGroup( 'GTT', '#5555FF'),
+ColorGroup( 'GUU', '#5555FF'),
+ColorGroup( 'GTC', '#5555FF'),
+ColorGroup( 'GUC', '#5555FF'),
+ColorGroup( 'GTA', '#5555FF'),
+ColorGroup( 'GUA', '#5555FF'),
+ColorGroup( 'GTG', '#5555FF'),
+ColorGroup( 'GUG', '#5555FF'),
+
+ColorGroup( 'CTT', '#5555FF'),
+ColorGroup( 'CUU', '#5555FF'),
+ColorGroup( 'CTC', '#5555FF'),
+ColorGroup( 'CUC', '#5555FF'),
+ColorGroup( 'CTA', '#5555FF'),
+ColorGroup( 'CUA', '#5555FF'),
+ColorGroup( 'CTG', '#5555FF'),
+ColorGroup( 'CUG', '#5555FF'),
+ColorGroup( 'TTA', '#5555FF'),
+ColorGroup( 'UUA', '#5555FF'),
+ColorGroup( 'TTG', '#5555FF'),
+ColorGroup( 'UUG', '#5555FF'),
+
+ColorGroup( 'ATT', '#5555FF'),
+ColorGroup( 'AUU', '#5555FF'),
+ColorGroup( 'ATC', '#5555FF'),
+ColorGroup( 'AUC', '#5555FF'),
+ColorGroup( 'ATA', '#5555FF'),
+ColorGroup( 'AUA', '#5555FF'),
+
+ColorGroup( 'ATG', '#5555FF'),
+ColorGroup( 'AUG', '#5555FF'),
+
+
+ColorGroup( 'TTT', '#FF00FF'),
+ColorGroup( 'UUU', '#FF00FF'),
+ColorGroup( 'TTC', '#FF00FF'),
+ColorGroup( 'UUC', '#FF00FF'),
+
+ColorGroup( 'TAT', '#FF00FF'),
+ColorGroup( 'UAU', '#FF00FF'),
+ColorGroup( 'TAC', '#FF00FF'),
+ColorGroup( 'UAC', '#FF00FF'),
+
+ColorGroup( 'TGG', '#FF00FF'),
+ColorGroup( 'UGG', '#FF00FF'),
+
+
+ColorGroup( 'GGT', '#996600'),
+ColorGroup( 'GGU', '#996600'),
+ColorGroup( 'GGC', '#996600'),
+ColorGroup( 'GGA', '#996600'),
+ColorGroup( 'GGG', '#996600'),
+
+ColorGroup( 'CCT', '#996600'),
+ColorGroup( 'CCU', '#996600'),
+ColorGroup( 'CCC', '#996600'),
+ColorGroup( 'CCA', '#996600'),
+ColorGroup( 'CCG', '#996600'),
+
+
+ColorGroup( 'TGT', '#FFFF00'),
+ColorGroup( 'UGU', '#FFFF00'),
+ColorGroup( 'TGC', '#FFFF00'),
+ColorGroup( 'UGC', '#FFFF00'),
+
+ColorGroup( 'TAA', '#000000'),
+ColorGroup( 'UAA', '#000000'),
+ColorGroup( 'TAG', '#000000'),
+ColorGroup( 'UAG', '#000000'),
+ColorGroup( 'TGA', '#000000'),  
+ColorGroup( 'UGA', '#000000')],
+  alphabet = codon_alphabetU
+  )
+codonsT = ColorScheme([
+ColorGroup( 'CAT', '#00FFFF'),
+ColorGroup( 'CAU', '#00FFFF'),
+ColorGroup( 'CAC', '#00FFFF'),
+
+ColorGroup( 'AAA', '#00FFFF'),
+ColorGroup( 'AAG', '#00FFFF'),
+
+ColorGroup( 'CGT', '#00FFFF'),
+ColorGroup( 'CGU', '#00FFFF'),
+ColorGroup( 'CGC', '#00FFFF'),
+ColorGroup( 'CGA', '#00FFFF'),
+ColorGroup( 'CGG', '#00FFFF'),
+ColorGroup( 'AGA', '#00FFFF'),
+ColorGroup( 'AGG', '#00FFFF'),
+
+
+ColorGroup( 'GAT', '#FF0000'),
+ColorGroup( 'GAU', '#FF0000'),
+ColorGroup( 'GAC', '#FF0000'),
+
+ColorGroup( 'GAA', '#FF0000'),
+ColorGroup( 'GAG', '#FF0000'),
+
+
+ColorGroup( 'TCT', '#00FF00'),
+ColorGroup( 'UCU', '#00FF00'),
+ColorGroup( 'TCC', '#00FF00'),
+ColorGroup( 'UCC', '#00FF00'),
+ColorGroup( 'TCA', '#00FF00'),
+ColorGroup( 'UCA', '#00FF00'),
+ColorGroup( 'TCG', '#00FF00'),
+ColorGroup( 'UCG', '#00FF00'),
+ColorGroup( 'AGT', '#00FF00'),
+ColorGroup( 'AGU', '#00FF00'),
+ColorGroup( 'AGC', '#00FF00'),
+
+ColorGroup( 'ACT', '#00FF00'),
+ColorGroup( 'ACU', '#00FF00'),
+ColorGroup( 'ACC', '#00FF00'),
+ColorGroup( 'ACA', '#00FF00'),
+ColorGroup( 'ACG', '#00FF00'),
+
+ColorGroup( 'CAA', '#00FF00'),
+ColorGroup( 'CAG', '#00FF00'),
+
+ColorGroup( 'AAT', '#00FF00'),
+ColorGroup( 'AAU', '#00FF00'),
+ColorGroup( 'AAC', '#00FF00'),
+
+
+ColorGroup( 'GCT', '#5555FF'),
+ColorGroup( 'GCU', '#5555FF'),
+ColorGroup( 'GCC', '#5555FF'),
+ColorGroup( 'GCA', '#5555FF'),
+ColorGroup( 'GCG', '#5555FF'),
+
+ColorGroup( 'GTT', '#5555FF'),
+ColorGroup( 'GUU', '#5555FF'),
+ColorGroup( 'GTC', '#5555FF'),
+ColorGroup( 'GUC', '#5555FF'),
+ColorGroup( 'GTA', '#5555FF'),
+ColorGroup( 'GUA', '#5555FF'),
+ColorGroup( 'GTG', '#5555FF'),
+ColorGroup( 'GUG', '#5555FF'),
+
+ColorGroup( 'CTT', '#5555FF'),
+ColorGroup( 'CUU', '#5555FF'),
+ColorGroup( 'CTC', '#5555FF'),
+ColorGroup( 'CUC', '#5555FF'),
+ColorGroup( 'CTA', '#5555FF'),
+ColorGroup( 'CUA', '#5555FF'),
+ColorGroup( 'CTG', '#5555FF'),
+ColorGroup( 'CUG', '#5555FF'),
+ColorGroup( 'TTA', '#5555FF'),
+ColorGroup( 'UUA', '#5555FF'),
+ColorGroup( 'TTG', '#5555FF'),
+ColorGroup( 'UUG', '#5555FF'),
+
+ColorGroup( 'ATT', '#5555FF'),
+ColorGroup( 'AUU', '#5555FF'),
+ColorGroup( 'ATC', '#5555FF'),
+ColorGroup( 'AUC', '#5555FF'),
+ColorGroup( 'ATA', '#5555FF'),
+ColorGroup( 'AUA', '#5555FF'),
+
+ColorGroup( 'ATG', '#5555FF'),
+ColorGroup( 'AUG', '#5555FF'),
+
+
+ColorGroup( 'TTT', '#FF00FF'),
+ColorGroup( 'UUU', '#FF00FF'),
+ColorGroup( 'TTC', '#FF00FF'),
+ColorGroup( 'UUC', '#FF00FF'),
+
+ColorGroup( 'TAT', '#FF00FF'),
+ColorGroup( 'UAU', '#FF00FF'),
+ColorGroup( 'TAC', '#FF00FF'),
+ColorGroup( 'UAC', '#FF00FF'),
+
+ColorGroup( 'TGG', '#FF00FF'),
+ColorGroup( 'UGG', '#FF00FF'),
+
+
+ColorGroup( 'GGT', '#996600'),
+ColorGroup( 'GGU', '#996600'),
+ColorGroup( 'GGC', '#996600'),
+ColorGroup( 'GGA', '#996600'),
+ColorGroup( 'GGG', '#996600'),
+
+ColorGroup( 'CCT', '#996600'),
+ColorGroup( 'CCU', '#996600'),
+ColorGroup( 'CCC', '#996600'),
+ColorGroup( 'CCA', '#996600'),
+ColorGroup( 'CCG', '#996600'),
+
+
+ColorGroup( 'TGT', '#FFFF00'),
+ColorGroup( 'UGU', '#FFFF00'),
+ColorGroup( 'TGC', '#FFFF00'),
+ColorGroup( 'UGC', '#FFFF00'),
+
+ColorGroup( 'TAA', '#000000'),
+ColorGroup( 'UAA', '#000000'),
+ColorGroup( 'TAG', '#000000'),
+ColorGroup( 'UAG', '#000000'),
+ColorGroup( 'TGA', '#000000'),  
+ColorGroup( 'UGA', '#000000')],
+  alphabet = codon_alphabetT
+  )
+
+
+
+
+charge = ColorScheme([
+    ColorGroup("KRH", "blue", "Positive" ),
+    ColorGroup( "DE", "red", "Negative") ],
+    alphabet = seq.unambiguous_protein_alphabet
+    )
+
+
+taylor = ColorScheme([
+    ColorGroup( 'A', '#CCFF00' ),
+    ColorGroup( 'C', '#FFFF00' ),
+    ColorGroup( 'D', '#FF0000'),
+    ColorGroup( 'E', '#FF0066' ),
+    ColorGroup( 'F', '#00FF66'),
+    ColorGroup( 'G', '#FF9900'),
+    ColorGroup( 'H', '#0066FF'),
+    ColorGroup( 'I', '#66FF00'),
+    ColorGroup( 'K', '#6600FF'),
+    ColorGroup( 'L', '#33FF00'),
+    ColorGroup( 'M', '#00FF00'),
+    ColorGroup( 'N', '#CC00FF'),
+    ColorGroup( 'P', '#FFCC00'),
+    ColorGroup( 'Q', '#FF00CC'),
+    ColorGroup( 'R', '#0000FF'),
+    ColorGroup( 'S', '#FF3300'),
+    ColorGroup( 'T', '#FF6600'),
+    ColorGroup( 'V', '#99FF00'),
+    ColorGroup( 'W', '#00CCFF'),
+    ColorGroup( 'Y', '#00FFCC')],
+    title = "Taylor",
+    description = "W. Taylor, Protein Engineering, Vol 10 , 743-746 (1997)",
+    alphabet = seq.unambiguous_protein_alphabet
+    )
+    
+
+