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#!/usr/bin/env ruby
#
# fastq2html.rb - HTML visualization of FASTQ sequences
#
# Usage:
#
# % ruby fastq2html.rb seq00.fastq > seq00.html
#
#
# Copyright:: Copyright (C) 2019 BioRuby Project
# Copyright (C) 2005 Mitsuteru C. Nakao <n@bioruby.org>
# License:: The Ruby License
#
#
require 'bio'
# thickness to color
def thickness2color(t)
c = "%02X" % ((t * 255.0).to_i)
c * 3
end
# Creates
def create_score2color_hashes
h_bg = {}
h_char = {}
cutoff_low = 0
cutoff_high = 50
range = cutoff_high - cutoff_low
sc_min = -5
sc_max = 100
(sc_min..sc_max).each do |i|
t = if i <= cutoff_low then
0.0
elsif i >= cutoff_high then
1.0
else
(i - cutoff_low).to_f / range
end
h_bg[i] = thickness2color(t)
h_char[i] = thickness2color((t > 0.3) ? 0.0 : 0.55)
end
h_bg.default = h_bg[cutoff_low]
h_char.default = h_char[cutoff_low]
[h_bg, h_char]
end
# Color code from quality score
SCORE2COLOR_BG, SCORE2COLOR_CHAR = create_score2color_hashes
# returns folded sequence with <br>.
def br(i, width = 80)
return "<br\n>" if i % width == 0
""
end
# returns sequence html doc
def display(naseq, scores)
html = '<p style="font-family: monospace">'
postfix = '</span>'
i = 0
naseq.each_char.with_index do |c, i|
sc = scores[i]
bgcol = SCORE2COLOR_BG[sc]
col = SCORE2COLOR_CHAR[sc]
prefix = %Q(<span style="color:\##{col}; background:\##{bgcol};">)
html += prefix + c + postfix
html += br(i += 1)
end
html + '</p>'
end
# returns colorized html doc
def fastq2html(definition, naseq, scores)
html = display(naseq, scores)
return ['<div>', "<div>>#{CGI.escapeHTML(definition)}</div>", html, '</div>']
end
title = 'Sequences with quality scores'
puts ['<html>',
'<header>', '<title>', title, '</title>', '</header>',
'<body>', '<h1>', title, '</h1>']
#main loop
ARGV.each do |filename|
Bio::FlatFile.open(filename) do |ff|
ff.each do |e|
puts fastq2html(e.definition, e.naseq, e.quality_scores)
end
end
end
puts ['</body>','</html>']
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