module Bio::ColorScheme
bio/util/color_scheme.rb - Popular color codings for nucleic and amino acids
- Author
-
Trevor Wennblom <trevor@corevx.com>
- Copyright
-
Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
- License
-
The Ruby License
Description¶ ↑
The Bio::ColorScheme
module contains classes that return popular color codings for nucleic and amino acids in RGB hex format suitable for HTML code.
The current schemes supported are:
-
Buried - Buried index
-
Helix - Helix propensity
-
Hydropathy - Hydrophobicity
-
Nucleotide - Nucelotide color coding
-
Strand - Strand propensity
-
Taylor - Taylor color coding
-
Turn - Turn propensity
-
Zappo - Zappo color coding
Planned color schemes include:
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BLOSUM62
-
ClustalX
-
Percentage Identity (PID)
Color schemes BLOSUM62, ClustalX, and Percentage Identity are all dependent on the alignment consensus.
This data is currently referenced from 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 www.jalview.org
Currently the score data for things such as hydropathy, helix, turn, etc. are contained here but should be moved to bio/data/aa once a good reference is found for these values.
Usage¶ ↑
require 'bio' seq = 'gattaca' scheme = Bio::ColorScheme::Zappo postfix = '</span>' html = '' seq.each_byte do |c| color = scheme[c.chr] prefix = %Q(<span style="background:\##{color};">) html += prefix + c.chr + postfix end puts html
Accessing colors¶ ↑
puts Bio::ColorScheme::Buried['A'] # 00DC22 puts Bio::ColorScheme::Buried[:c] # 00BF3F puts Bio::ColorScheme::Buried[nil] # nil puts Bio::ColorScheme::Buried['-'] # FFFFFF puts Bio::ColorScheme::Buried[7] # FFFFFF puts Bio::ColorScheme::Buried['junk'] # FFFFFF puts Bio::ColorScheme::Buried['t'] # 00CC32
Constants
- NA