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# 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
SymbolColor
IndexColor
RefSeqColor
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
from typing import List, Optional, Sequence
from . import seq
from .color import Color
from .seq import Alphabet
# TODO: Make as abstract
class ColorRule:
"""
Define an interface for coloring individual symbols based on their position
and identity. Subclasses should reimplement the symbol_color() method to
return a Color object based on the given parameters.
"""
def symbol_color(self, seq_index: int, symbol: str, rank: int) -> Optional[Color]:
raise NotImplementedError # pragma: no cover
class ColorScheme(ColorRule):
"""
Specify which color each symbol in a sequence logo should be.
A color scheme is primarily a container of color rules. These rules would
be along the lines of "hydrophobic residues are blue" or "indices 5-10 are
red" or "the wildtype sequence is black". When a color is requested for a
particular symbol, each rule is consulted in turn until one provides a
color. If no rule provides a color, the given default color will be used.
"""
def __init__(
self,
rules: List[ColorRule] = [],
title: str = "",
description: str = "",
default_color: str = "black",
alphabet: Alphabet = seq.generic_alphabet,
) -> None:
self.rules = rules
self.title = title
self.description = description
self.default_color = Color.from_string(default_color)
self.alphabet = alphabet
def symbol_color(self, seq_index: int, symbol: str, rank: int) -> Color:
if symbol not in self.alphabet:
raise KeyError("Colored symbol '%s' does not exist in alphabet." % symbol)
for rule in self.rules:
color = rule.symbol_color(seq_index, symbol, rank)
if color is not None:
return color
return self.default_color
class SymbolColor(ColorRule):
"""
Represent the given set of symbols (e.g. "DEHKR" for charged residues) with
a single color.
"""
def __init__(
self, symbols: str, color: str, description: Optional[str] = None
) -> None:
self.symbols = symbols
self.color = Color.from_string(color)
self.description = description
def symbol_color(self, seq_index: int, symbol: str, rank: int) -> Optional[Color]:
if symbol in self.symbols:
return self.color
return None
class IndexColor(ColorRule):
"""
Represent the given set of indices (e.g. range(10) for the first ten
residues) with a single color.
"""
def __init__(
self, indices: Sequence[int], color: str, description: Optional[str] = None
) -> None:
self.indices = indices
self.color = Color.from_string(color)
self.description = description
def symbol_color(self, seq_index: int, symbol: str, rank: int) -> Optional[Color]:
if seq_index in self.indices:
return self.color
return None
class RefSeqColor(ColorRule):
"""
Color the given reference sequence in its own color, so you can easily see
which positions match that sequence and which don't.
"""
def __init__(
self, ref_seq: str, color: str, description: Optional[str] = None
) -> None:
self.ref_seq = ref_seq
self.color = Color.from_string(color)
self.description = description
def symbol_color(self, seq_index: int, symbol: str, rank: int) -> Optional[Color]:
if symbol == self.ref_seq[seq_index]:
return self.color
return None
monochrome = ColorScheme([]) # This list intentionally left blank
# From makelogo
nucleotide = ColorScheme(
[
SymbolColor("G", "orange"),
SymbolColor("TU", "red"),
SymbolColor("C", "blue"),
SymbolColor("A", "green"),
],
)
base_pairing = ColorScheme(
[
SymbolColor("TAU", "darkorange", "Weak (2 Watson-Crick hydrogen bonds)"),
SymbolColor("GC", "blue", "Strong (3 Watson-Crick hydrogen bonds)"),
],
)
# From Crooks2004c-Proteins-SeqStr.pdf
hydrophobicity = ColorScheme(
[
SymbolColor("RKDENQ", "blue", "hydrophilic"),
SymbolColor("SGHTAP", "green", "neutral"),
SymbolColor("YVMCLFIW", "black", "hydrophobic"),
],
alphabet=seq.unambiguous_protein_alphabet,
)
# from makelogo
chemistry = ColorScheme(
[
SymbolColor("GSTYC", "green", "polar"),
SymbolColor("NQ", "purple", "neutral"),
SymbolColor("KRH", "blue", "basic"),
SymbolColor("DE", "red", "acidic"),
SymbolColor("PAWFLIMV", "black", "hydrophobic"),
],
alphabet=seq.unambiguous_protein_alphabet,
)
charge = ColorScheme(
[SymbolColor("KRH", "blue", "Positive"), SymbolColor("DE", "red", "Negative")],
alphabet=seq.unambiguous_protein_alphabet,
)
taylor = ColorScheme(
[
SymbolColor("A", "#CCFF00"),
SymbolColor("C", "#FFFF00"),
SymbolColor("D", "#FF0000"),
SymbolColor("E", "#FF0066"),
SymbolColor("F", "#00FF66"),
SymbolColor("G", "#FF9900"),
SymbolColor("H", "#0066FF"),
SymbolColor("I", "#66FF00"),
SymbolColor("K", "#6600FF"),
SymbolColor("L", "#33FF00"),
SymbolColor("M", "#00FF00"),
SymbolColor("N", "#CC00FF"),
SymbolColor("P", "#FFCC00"),
SymbolColor("Q", "#FF00CC"),
SymbolColor("R", "#0000FF"),
SymbolColor("S", "#FF3300"),
SymbolColor("T", "#FF6600"),
SymbolColor("V", "#99FF00"),
SymbolColor("W", "#00CCFF"),
SymbolColor("Y", "#00FFCC"),
],
title="Taylor",
description="W. Taylor, Protein Engineering, Vol 10 , 743-746 (1997)",
alphabet=seq.unambiguous_protein_alphabet,
)
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