make_circos 0.0.1
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- checksums.yaml +7 -0
- data/.gitignore +22 -0
- data/Gemfile +4 -0
- data/LICENSE.txt +22 -0
- data/README.md +29 -0
- data/Rakefile +2 -0
- data/bin/fasta2kariotype.rb +21 -0
- data/bin/make_circos_configuration.rb +227 -0
- data/lib/make_circos/circos_conf_files/circos.conf +36 -0
- data/lib/make_circos/circos_conf_files/ideogram.conf +27 -0
- data/lib/make_circos/circos_conf_files/ticks.conf +41 -0
- data/lib/make_circos/version.rb +3 -0
- data/lib/make_circos.rb +5 -0
- data/make_circos.gemspec +23 -0
- metadata +87 -0
checksums.yaml
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---
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SHA1:
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metadata.gz: a295838ae019e0aaeb4de434b5ca0be5a075cc47
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data.tar.gz: 127f4a3eb96ef598ac27f69d6a45df0a2bb85e0e
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SHA512:
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metadata.gz: ae3ffd4ef777ca6164f33be4d6bc9fda2e6e81c9b02f61408e8fbd787a1b3551a6a6b053b6e4238c05d56b655d5586f0d99fe55e2c74fd670455073399cd9ea5
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data.tar.gz: b7731c4afe1442da8cdd184e41338b4ad4ce6d4fbed214aca3d0a395512ea81da34fd2eef0deb7e689c57dee28fc566638ded4bd0928c972fada1b75e15d674c
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data/.gitignore
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*.gem
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*.rbc
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.bundle
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.config
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.yardoc
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Gemfile.lock
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InstalledFiles
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_yardoc
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coverage
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doc/
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lib/bundler/man
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pkg
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rdoc
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spec/reports
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test/tmp
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test/version_tmp
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tmp
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*.bundle
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*.so
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*.o
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*.a
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mkmf.log
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data/Gemfile
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data/LICENSE.txt
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Copyright (c) 2015 TODO: Write your name
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MIT License
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.md
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# MakeCircos
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TODO: Write a gem description
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## Installation
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Add this line to your application's Gemfile:
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gem 'make_circos'
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And then execute:
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$ bundle
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Or install it yourself as:
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$ gem install make_circos
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## Usage
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TODO: Write usage instructions here
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## Contributing
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1. Fork it ( https://github.com/[my-github-username]/make_circos/fork )
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2. Create your feature branch (`git checkout -b my-new-feature`)
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3. Commit your changes (`git commit -am 'Add some feature'`)
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4. Push to the branch (`git push origin my-new-feature`)
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5. Create a new Pull Request
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data/Rakefile
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#! /usr/bin/env ruby
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all_seqs = []
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name = nil
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seq = ''
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File.open(ARGV[0]).each do |line|
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line.chomp!
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if line =~ /^>/
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all_seqs << [name, seq.length] if !name.nil?
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name = line.gsub('>', '')
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seq = ''
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else
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seq << line
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end
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end
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all_seqs << [name, seq.length]
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all_seqs.sort!{|s1, s2| s2.last <=> s1.last}
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all_seqs.each do |name, seq_length|
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puts "#{name}\t1\t#{seq_length}"
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end
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#! /usr/bin/env ruby
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ROOT_PATH=File.dirname(__FILE__)
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$: << File.expand_path(File.join(ROOT_PATH, "../lib/"))
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$: << File.expand_path(File.join(ROOT_PATH, "../lib/make_circos"))
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require 'fileutils'
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require 'optparse'
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#################################################################################################
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## INPUT PARSING
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#################################################################################################
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options = {}
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optparse = OptionParser.new do |opts|
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options[:karyotype_file] = nil
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opts.on( '-k', '--karyotype_file FILE', 'Input tabulated file' ) do |karyotype_file|
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options[:karyotype_file] = karyotype_file
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end
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options[:prefix_label] = ''
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opts.on( '-p', '--prefix_label STRING', 'Prefix to use with with labels' ) do |prefix|
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options[:prefix_label] = prefix
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end
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options[:output_folder] = Dir.pwd
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opts.on( '-o', '--output_folder PATH', 'Path to folder which circos files must be saved' ) do |output_folder|
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options[:output_folder] = output_folder
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end
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options[:system_coords] = 0
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opts.on( '-c', '--system_coords INTEGER', 'Base of coordinates used in karyotype_file') do |system_coords|
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options[:system_coords] = system_coords.to_i
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end
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options[:magnitude] = ['1', '1']
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opts.on( '-m', '--magnitude STRING', 'Units:multiplier' ) do |mag|
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options[:magnitude] = mag.split(':')
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end
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options[:track_length] = 0.06
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opts.on( '-l', '--track_length STRING', 'Length for each data track 0.2,0.4...' ) do |length|
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options[:track_length] = length.split(',').map{|i| i.to_f}
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end
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options[:histograms] = []
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opts.on( '-t', '--histograms PATHS', 'Paths to data, PATH1;PATH2...' ) do |hist|
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options[:histograms] = hist.split(',')
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end
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options[:visualization] = []
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opts.on( '-v', '--visualization_track STRING', 'h for histogram, m for heatmap, l for links, s for highlights E.g hmhm' ) do |vis|
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options[:visualization] = vis.split('')
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end
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options[:heatmap_limits] = nil
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opts.on( '-s', '--heatmap_limits STRING', 'Lower and upper limit for heatmps. Format lower,upper : 0,100' ) do |hl|
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options[:heatmap_limits] = hl.split(',')
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end
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# Set a banner, displayed at the top of the help screen.
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opts.banner = "Usage: table_header.rb -t tabulated_file \n\n"
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# This displays the help screen
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opts.on( '-h', '--help', 'Display this screen' ) do
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puts opts
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exit
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end
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end # End opts
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# parse options and remove from ARGV
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optparse.parse!
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#####################################################################################
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## MAIN
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####################################################################################
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if options[:karyotype_file].nil? || !File.exists?(options[:karyotype_file])
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Process.exit
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end
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FileUtils.mkdir('data') if !Dir.exists?('data')
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FileUtils.mkdir('etc') if !Dir.exists?('etc')
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paths = {}
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paths['data_folder'] = File.join(options[:output_folder], 'data')
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paths['etc_folder'] = File.join(options[:output_folder], 'etc')
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paths['templates'] = File.join(File.dirname(__FILE__), '..', 'lib', 'make_circos', 'circos_conf_files')
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## GENERATE KARYOTYPE FILE
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sequences= {}
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File.open(options[:karyotype_file]).each do |line|
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line.chomp!
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fields = line.split("\t")
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name = fields.shift + options[:prefix_label]
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sequences[name] = [fields.first, fields.last].map{|coord| coord.to_i - options[:system_coords]}
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end
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paths['karyotype_path'] = File.join(paths['data_folder'], options[:karyotype_file]+ '_kar')
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karyotype = File.open(paths['karyotype_path'], 'w')
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count = 1
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sequences.each do |sequence_name, coords|
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karyotype.puts "chr - #{sequence_name} #{sequence_name} #{coords.first} #{coords.last} chr#{count}" # the chr field is used to indicate taht color has de sequence
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count += 1
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end
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karyotype.close
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## GENERATE IDEOGRAM FILE
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ideogram_file_template = File.open(File.join(paths['templates'], 'ideogram.conf')).read
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paths['ideogram'] = File.join(paths['etc_folder'], 'ideogram.conf')
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File.open(paths['ideogram'], 'w') {|f| f.write(ideogram_file_template) }
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## GENERATE TICKS FILE
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ticks_file_template = File.open(File.join(paths['templates'], 'ticks.conf')).read
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ticks_file_template.gsub!('multiplier = mult', "multiplier = #{options[:magnitude].last}")
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paths['ticks'] = File.join(paths['etc_folder'], 'ticks.conf')
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File.open(paths['ticks'], 'w') {|f| f.write(ticks_file_template) }
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## GENERATE CONF FILE
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conf_file_template = File.open(File.join(paths['templates'], 'circos.conf')).read
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conf_file_template.gsub!("chromosomes_units = units", "chromosomes_units = #{options[:magnitude].first}") #magnitude of units to redeuce de number length
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conf_file_template.gsub!("karyotype = path", "karyotype = #{paths['karyotype_path']}") # karyotype file whith main axis coords
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conf_file_template.gsub!("<<include path_ideogram>>", "<<include #{paths['ideogram']}>>") #ideogram file configures main axis style
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conf_file_template.gsub!("<<include path_ticks>>", "<<include #{paths['ticks']}>>") #ticks file configures the scale style of main axis
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plot_section = ""
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if options[:histograms].length > 0
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plot_section << "<plots>\n" if options[:visualization].include?('h') || options[:visualization].include?('m')
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if options[:track_length].class != Array
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track_length = Array.new(options[:histograms].length, options[:track_length])
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else
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track_length = options[:track_length]
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end
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track_separation = 0.02
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histogram_template = '
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<plot>
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min = 0
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type = visualization_type
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file = DATA_PATH
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r1 = r1_lengthr
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r0 = r0_lengthr
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fill_color = vdgrey
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extend_bin = no
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<backgrounds>
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# Show the backgrounds only for ideograms that have data
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<background>
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color = BACKGROUND_COLOR #vvlgrey
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</background>
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</backgrounds>
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</plot>
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'
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last_r = 1
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options[:histograms].each_with_index do |data_path, i|
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if options[:visualization][i] == 'h' || options[:visualization][i] == 'm'
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if i == 0
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r1 = 1 - track_separation
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else
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r1 = last_r - track_separation
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end
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r0 = r1 - track_length[i]
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last_r = r0
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data_file_path = File.join(paths['data_folder'], File.basename(data_path))
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FileUtils.cp(data_path, data_file_path)
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custom_track = histogram_template.gsub('DATA_PATH', data_file_path)
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if options[:visualization][i] == 'h'
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visualization_type = 'histogram'
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elsif options[:visualization][i] == 'm'
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#visualization_type = "heatmap\ncolor = spectral-11-div\n"
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visualization_type = "heatmap\ncolor = ylorrd-5-seq-rev\n"
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visualization_type << "min*=#{options[:heatmap_limits].first}\nmax=#{options[:heatmap_limits].last}\n" if options[:heatmap_limits].class == Array
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end
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custom_track.gsub!('visualization_type', visualization_type)
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custom_track.gsub!('r1_length', r1.to_s)
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custom_track.gsub!('r0_length', r0.to_s)
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if i % 2 == 0
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custom_track.gsub!('BACKGROUND_COLOR', '240,240,240')
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else
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custom_track.gsub!('BACKGROUND_COLOR', '227,227,227')
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end
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plot_section << custom_track
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end
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end
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plot_section << "</plots>\n" if options[:visualization].include?('h') || options[:visualization].include?('m')
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plot_section << "\n<links>"
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link_template= '
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<link>
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file = DATA_PATH
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radius = radius_lengthr
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bezier_radius = 0.1r
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thickness = 4
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</link>
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'
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options[:histograms].each_with_index do |data_path, i|
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next if options[:visualization][i] != 'l'
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data_file_path = File.join(paths['data_folder'], File.basename(data_path))
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FileUtils.cp(data_path, data_file_path)
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custom_track = link_template.gsub('DATA_PATH', data_file_path)
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last_r = last_r - 0.02
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custom_track.gsub!('radius_length', last_r.to_s)
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plot_section << custom_track
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end
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plot_section << "</links>"
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if options[:visualization].include?('s')
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plot_section << "\n\n<highlights>"
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options[:histograms].each_with_index do |data_path, i|
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next if options[:visualization][i] != 's'
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data_file_path = File.join(paths['data_folder'], File.basename(data_path))
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FileUtils.cp(data_path, data_file_path)
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high= "\n<highlight>\nfile=" + data_file_path
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216
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high << "\nstroke_thickness = 1\nstroke_color = black\n</highlight>\n"
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plot_section << high
|
218
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end
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plot_section << "</highlights>"
|
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+
end
|
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end
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conf_file_template.gsub!("plot_section", plot_section)
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paths['conf'] = File.join(paths['etc_folder'], 'circos.conf')
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File.open(paths['conf'], 'w') {|f| f.write(conf_file_template) }
|
226
|
+
|
227
|
+
|
@@ -0,0 +1,36 @@
|
|
1
|
+
|
2
|
+
# Chromosome name, size and color definition
|
3
|
+
karyotype = path
|
4
|
+
|
5
|
+
# The <ideogram> block defines the position, size, labels and other
|
6
|
+
# properties of the segments on which data are drawn. These segments
|
7
|
+
# are usually chromosomes, but can be any integer axis.
|
8
|
+
|
9
|
+
# The chromosomes_unit value is used as a unit (suffix "u") to shorten
|
10
|
+
# values in other parts of the configuration file. Some parameters,
|
11
|
+
# such as ideogram and tick spacing, accept "u" suffixes, so instead of
|
12
|
+
#
|
13
|
+
# spacing = 10000000
|
14
|
+
#
|
15
|
+
# you can write
|
16
|
+
#
|
17
|
+
# spacing = 10u
|
18
|
+
#
|
19
|
+
# See ticks.conf for examples.
|
20
|
+
|
21
|
+
chromosomes_units = units
|
22
|
+
|
23
|
+
plot_section
|
24
|
+
|
25
|
+
<<include path_ideogram>>
|
26
|
+
|
27
|
+
<<include path_ticks>>
|
28
|
+
|
29
|
+
<image>
|
30
|
+
<<include etc/image.conf>>
|
31
|
+
</image>
|
32
|
+
|
33
|
+
<<include etc/colors_fonts_patterns.conf>>
|
34
|
+
|
35
|
+
<<include etc/housekeeping.conf>>
|
36
|
+
|
@@ -0,0 +1,27 @@
|
|
1
|
+
|
2
|
+
<ideogram>
|
3
|
+
|
4
|
+
<spacing>
|
5
|
+
default = 0.005r
|
6
|
+
break = 5r
|
7
|
+
</spacing>
|
8
|
+
|
9
|
+
# Ideogram position, fill and outline
|
10
|
+
radius = 0.90r
|
11
|
+
thickness = 20p
|
12
|
+
fill = yes
|
13
|
+
stroke_color = dgrey
|
14
|
+
stroke_thickness = 2p
|
15
|
+
|
16
|
+
# Minimum definition for ideogram labels.
|
17
|
+
|
18
|
+
show_label = yes
|
19
|
+
# see etc/fonts.conf for list of font names
|
20
|
+
label_font = default
|
21
|
+
label_radius = dims(image,radius) - 60p
|
22
|
+
label_size = 30
|
23
|
+
label_parallel = yes
|
24
|
+
|
25
|
+
</ideogram>
|
26
|
+
|
27
|
+
|
@@ -0,0 +1,41 @@
|
|
1
|
+
show_ticks = yes
|
2
|
+
show_tick_labels = yes
|
3
|
+
|
4
|
+
<ticks>
|
5
|
+
radius = 1r
|
6
|
+
color = black
|
7
|
+
thickness = 2p
|
8
|
+
|
9
|
+
# the tick label is derived by multiplying the tick position
|
10
|
+
# by 'multiplier' and casting it in 'format':
|
11
|
+
#
|
12
|
+
# sprintf(format,position*multiplier)
|
13
|
+
#
|
14
|
+
|
15
|
+
multiplier = mult
|
16
|
+
|
17
|
+
# %d - integer
|
18
|
+
# %f - float
|
19
|
+
# %.1f - float with one decimal
|
20
|
+
# %.2f - float with two decimals
|
21
|
+
#
|
22
|
+
# for other formats, see http://perldoc.perl.org/functions/sprintf.html
|
23
|
+
|
24
|
+
format = %d
|
25
|
+
|
26
|
+
<tick>
|
27
|
+
spacing = 5u
|
28
|
+
size = 10p
|
29
|
+
</tick>
|
30
|
+
|
31
|
+
<tick>
|
32
|
+
spacing = 25u
|
33
|
+
size = 15p
|
34
|
+
show_label = yes
|
35
|
+
label_size = 20p
|
36
|
+
label_offset = 10p
|
37
|
+
format = %d
|
38
|
+
</tick>
|
39
|
+
|
40
|
+
</ticks>
|
41
|
+
|
data/lib/make_circos.rb
ADDED
data/make_circos.gemspec
ADDED
@@ -0,0 +1,23 @@
|
|
1
|
+
# coding: utf-8
|
2
|
+
lib = File.expand_path('../lib', __FILE__)
|
3
|
+
$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
|
4
|
+
require 'make_circos/version'
|
5
|
+
|
6
|
+
Gem::Specification.new do |spec|
|
7
|
+
spec.name = "make_circos"
|
8
|
+
spec.version = MakeCircos::VERSION
|
9
|
+
spec.authors = ["Pedro Seoane Zonjic"]
|
10
|
+
spec.email = ["seoanezonjic@uma.es"]
|
11
|
+
spec.summary = %q{Gem helper to ahndle the CIRCOS suite}
|
12
|
+
spec.description = %q{Helper that generate preconfigured conf files of the CIRCOS suite.}
|
13
|
+
spec.homepage = ""
|
14
|
+
spec.license = "MIT"
|
15
|
+
|
16
|
+
spec.files = `git ls-files -z`.split("\x0")
|
17
|
+
spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
|
18
|
+
spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
|
19
|
+
spec.require_paths = ["lib"]
|
20
|
+
|
21
|
+
spec.add_development_dependency "bundler", "~> 1.6"
|
22
|
+
spec.add_development_dependency "rake"
|
23
|
+
end
|
metadata
ADDED
@@ -0,0 +1,87 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: make_circos
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.0.1
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- Pedro Seoane Zonjic
|
8
|
+
autorequire:
|
9
|
+
bindir: bin
|
10
|
+
cert_chain: []
|
11
|
+
date: 2018-01-17 00:00:00.000000000 Z
|
12
|
+
dependencies:
|
13
|
+
- !ruby/object:Gem::Dependency
|
14
|
+
name: bundler
|
15
|
+
requirement: !ruby/object:Gem::Requirement
|
16
|
+
requirements:
|
17
|
+
- - "~>"
|
18
|
+
- !ruby/object:Gem::Version
|
19
|
+
version: '1.6'
|
20
|
+
type: :development
|
21
|
+
prerelease: false
|
22
|
+
version_requirements: !ruby/object:Gem::Requirement
|
23
|
+
requirements:
|
24
|
+
- - "~>"
|
25
|
+
- !ruby/object:Gem::Version
|
26
|
+
version: '1.6'
|
27
|
+
- !ruby/object:Gem::Dependency
|
28
|
+
name: rake
|
29
|
+
requirement: !ruby/object:Gem::Requirement
|
30
|
+
requirements:
|
31
|
+
- - ">="
|
32
|
+
- !ruby/object:Gem::Version
|
33
|
+
version: '0'
|
34
|
+
type: :development
|
35
|
+
prerelease: false
|
36
|
+
version_requirements: !ruby/object:Gem::Requirement
|
37
|
+
requirements:
|
38
|
+
- - ">="
|
39
|
+
- !ruby/object:Gem::Version
|
40
|
+
version: '0'
|
41
|
+
description: Helper that generate preconfigured conf files of the CIRCOS suite.
|
42
|
+
email:
|
43
|
+
- seoanezonjic@uma.es
|
44
|
+
executables:
|
45
|
+
- fasta2kariotype.rb
|
46
|
+
- make_circos_configuration.rb
|
47
|
+
extensions: []
|
48
|
+
extra_rdoc_files: []
|
49
|
+
files:
|
50
|
+
- ".gitignore"
|
51
|
+
- Gemfile
|
52
|
+
- LICENSE.txt
|
53
|
+
- README.md
|
54
|
+
- Rakefile
|
55
|
+
- bin/fasta2kariotype.rb
|
56
|
+
- bin/make_circos_configuration.rb
|
57
|
+
- lib/make_circos.rb
|
58
|
+
- lib/make_circos/circos_conf_files/circos.conf
|
59
|
+
- lib/make_circos/circos_conf_files/ideogram.conf
|
60
|
+
- lib/make_circos/circos_conf_files/ticks.conf
|
61
|
+
- lib/make_circos/version.rb
|
62
|
+
- make_circos.gemspec
|
63
|
+
homepage: ''
|
64
|
+
licenses:
|
65
|
+
- MIT
|
66
|
+
metadata: {}
|
67
|
+
post_install_message:
|
68
|
+
rdoc_options: []
|
69
|
+
require_paths:
|
70
|
+
- lib
|
71
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
72
|
+
requirements:
|
73
|
+
- - ">="
|
74
|
+
- !ruby/object:Gem::Version
|
75
|
+
version: '0'
|
76
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
77
|
+
requirements:
|
78
|
+
- - ">="
|
79
|
+
- !ruby/object:Gem::Version
|
80
|
+
version: '0'
|
81
|
+
requirements: []
|
82
|
+
rubyforge_project:
|
83
|
+
rubygems_version: 2.6.14
|
84
|
+
signing_key:
|
85
|
+
specification_version: 4
|
86
|
+
summary: Gem helper to ahndle the CIRCOS suite
|
87
|
+
test_files: []
|