make_circos 0.0.1

checksums.yaml

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+---
+SHA1:
+  metadata.gz: a295838ae019e0aaeb4de434b5ca0be5a075cc47
+  data.tar.gz: 127f4a3eb96ef598ac27f69d6a45df0a2bb85e0e
+SHA512:
+  metadata.gz: ae3ffd4ef777ca6164f33be4d6bc9fda2e6e81c9b02f61408e8fbd787a1b3551a6a6b053b6e4238c05d56b655d5586f0d99fe55e2c74fd670455073399cd9ea5
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data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+*.bundle
+*.so
+*.o
+*.a
+mkmf.log

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in make_circos.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2015 TODO: Write your name
+
+MIT License
+
+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.

data/README.md

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+# MakeCircos
+
+TODO: Write a gem description
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'make_circos'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install make_circos
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Contributing
+
+1. Fork it ( https://github.com/[my-github-username]/make_circos/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create a new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"
+

data/bin/fasta2kariotype.rb

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+#! /usr/bin/env ruby
+
+all_seqs = []
+name = nil
+seq = ''
+File.open(ARGV[0]).each do |line|
+	line.chomp!
+	if line =~ /^>/
+		all_seqs << [name, seq.length] if !name.nil?
+		name = line.gsub('>', '')
+		seq = ''
+	else
+		seq << line
+	end
+
+end
+all_seqs << [name, seq.length]
+all_seqs.sort!{|s1, s2| s2.last <=> s1.last}
+all_seqs.each do |name, seq_length|
+	puts "#{name}\t1\t#{seq_length}"
+end

data/bin/make_circos_configuration.rb

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+#! /usr/bin/env ruby
+
+ROOT_PATH=File.dirname(__FILE__)
+$: << File.expand_path(File.join(ROOT_PATH, "../lib/"))
+$: << File.expand_path(File.join(ROOT_PATH, "../lib/make_circos"))
+
+require 'fileutils'
+require 'optparse'
+
+#################################################################################################
+## INPUT PARSING
+#################################################################################################
+options = {}
+
+optparse = OptionParser.new do |opts|
+        options[:karyotype_file] = nil
+        opts.on( '-k', '--karyotype_file FILE', 'Input tabulated file' ) do |karyotype_file|
+            options[:karyotype_file] = karyotype_file
+        end
+
+        options[:prefix_label] = ''
+        opts.on( '-p', '--prefix_label STRING', 'Prefix to use with with labels' ) do |prefix|
+            options[:prefix_label] = prefix
+        end
+
+        options[:output_folder] = Dir.pwd
+        opts.on( '-o', '--output_folder PATH', 'Path to folder which circos files must be saved' ) do |output_folder|
+            options[:output_folder] = output_folder
+        end
+
+        options[:system_coords] = 0
+        opts.on( '-c', '--system_coords INTEGER', 'Base of coordinates used in karyotype_file') do |system_coords|
+            options[:system_coords] = system_coords.to_i
+        end
+
+		options[:magnitude] = ['1', '1']
+        opts.on( '-m', '--magnitude STRING', 'Units:multiplier' ) do |mag|
+            options[:magnitude] = mag.split(':')
+        end
+
+		options[:track_length] = 0.06
+        opts.on( '-l', '--track_length STRING', 'Length for each data track 0.2,0.4...' ) do |length|
+            options[:track_length] = length.split(',').map{|i| i.to_f}
+        end
+
+        options[:histograms] = []
+        opts.on( '-t', '--histograms PATHS', 'Paths to data, PATH1;PATH2...' ) do |hist|
+            options[:histograms] = hist.split(',')
+        end
+
+        options[:visualization] = []
+        opts.on( '-v', '--visualization_track STRING', 'h for histogram, m for heatmap, l for links, s for highlights E.g hmhm' ) do |vis|
+            options[:visualization] = vis.split('')
+        end
+
+        options[:heatmap_limits] = nil
+        opts.on( '-s', '--heatmap_limits STRING', 'Lower and upper limit for heatmps. Format lower,upper : 0,100' ) do |hl|
+            options[:heatmap_limits] = hl.split(',')
+        end
+
+
+        # Set a banner, displayed at the top of the help screen.
+        opts.banner = "Usage: table_header.rb -t tabulated_file \n\n"
+
+        # This displays the help screen
+        opts.on( '-h', '--help', 'Display this screen' ) do
+                puts opts
+                exit
+        end
+
+end # End opts
+
+# parse options and remove from ARGV
+optparse.parse!
+
+#####################################################################################
+## MAIN
+####################################################################################
+
+if options[:karyotype_file].nil? || !File.exists?(options[:karyotype_file])
+	Process.exit
+end
+
+FileUtils.mkdir('data') if !Dir.exists?('data')
+FileUtils.mkdir('etc') if !Dir.exists?('etc')
+
+paths = {}
+paths['data_folder'] = File.join(options[:output_folder], 'data')
+paths['etc_folder'] = File.join(options[:output_folder], 'etc')
+paths['templates'] = File.join(File.dirname(__FILE__), '..', 'lib', 'make_circos', 'circos_conf_files')
+
+## GENERATE KARYOTYPE FILE
+sequences= {}
+
+File.open(options[:karyotype_file]).each do |line|
+	line.chomp!
+	fields = line.split("\t")
+	name = fields.shift + options[:prefix_label]
+	sequences[name] = [fields.first, fields.last].map{|coord| coord.to_i - options[:system_coords]}
+end
+
+paths['karyotype_path'] = File.join(paths['data_folder'], options[:karyotype_file]+ '_kar')
+karyotype = File.open(paths['karyotype_path'], 'w')
+count = 1
+sequences.each do |sequence_name, coords|
+	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
+	count += 1
+end
+karyotype.close
+
+## GENERATE IDEOGRAM FILE
+ideogram_file_template = File.open(File.join(paths['templates'], 'ideogram.conf')).read
+paths['ideogram'] = File.join(paths['etc_folder'], 'ideogram.conf')
+File.open(paths['ideogram'], 'w') {|f| f.write(ideogram_file_template) }
+
+## GENERATE TICKS FILE
+ticks_file_template = File.open(File.join(paths['templates'], 'ticks.conf')).read
+ticks_file_template.gsub!('multiplier = mult', "multiplier = #{options[:magnitude].last}")
+paths['ticks'] = File.join(paths['etc_folder'], 'ticks.conf')
+File.open(paths['ticks'], 'w') {|f| f.write(ticks_file_template) }
+
+
+## GENERATE CONF FILE
+conf_file_template = File.open(File.join(paths['templates'], 'circos.conf')).read
+conf_file_template.gsub!("chromosomes_units = units", "chromosomes_units = #{options[:magnitude].first}") #magnitude of units to redeuce de number length
+conf_file_template.gsub!("karyotype = path", "karyotype = #{paths['karyotype_path']}") # karyotype file whith main axis coords
+conf_file_template.gsub!("<<include path_ideogram>>", "<<include #{paths['ideogram']}>>") #ideogram file configures main axis style
+conf_file_template.gsub!("<<include path_ticks>>", "<<include #{paths['ticks']}>>") #ticks file configures the scale style of main axis
+plot_section = ""
+if options[:histograms].length > 0
+	plot_section << "<plots>\n" if options[:visualization].include?('h') || options[:visualization].include?('m')
+	if options[:track_length].class != Array
+		track_length = Array.new(options[:histograms].length, options[:track_length])
+	else
+		track_length = options[:track_length]
+	end
+	track_separation = 0.02
+	histogram_template = '
+<plot>
+min = 0
+type = visualization_type
+file = DATA_PATH
+r1   = r1_lengthr
+r0   = r0_lengthr
+fill_color = vdgrey
+extend_bin = no
+<backgrounds>
+	# Show the backgrounds only for ideograms that have data
+	<background>
+	color =  BACKGROUND_COLOR #vvlgrey
+	</background>
+
+</backgrounds>
+</plot>
+'
+	last_r = 1
+	options[:histograms].each_with_index do |data_path, i|
+		if options[:visualization][i] == 'h' || options[:visualization][i] == 'm'
+			if i == 0 
+				r1 = 1 - track_separation 
+			else
+				r1 = last_r - track_separation
+			end
+			r0 = r1 - track_length[i]
+			last_r = r0
+			data_file_path = File.join(paths['data_folder'], File.basename(data_path))
+			FileUtils.cp(data_path, data_file_path)
+			custom_track = histogram_template.gsub('DATA_PATH', data_file_path)
+			if options[:visualization][i] == 'h'
+				visualization_type = 'histogram'
+			elsif options[:visualization][i] == 'm'
+				#visualization_type = "heatmap\ncolor  = spectral-11-div\n"
+				visualization_type = "heatmap\ncolor  = ylorrd-5-seq-rev\n"
+				visualization_type << "min*=#{options[:heatmap_limits].first}\nmax=#{options[:heatmap_limits].last}\n" if options[:heatmap_limits].class == Array
+			end
+			custom_track.gsub!('visualization_type', visualization_type)
+			custom_track.gsub!('r1_length', r1.to_s)
+			custom_track.gsub!('r0_length', r0.to_s)
+			if i % 2 == 0
+				custom_track.gsub!('BACKGROUND_COLOR', '240,240,240')
+			else
+				custom_track.gsub!('BACKGROUND_COLOR', '227,227,227')
+			end
+			plot_section << custom_track
+		end
+	end
+    plot_section << "</plots>\n" if options[:visualization].include?('h') || options[:visualization].include?('m')
+
+	plot_section << "\n<links>"
+	link_template= '
+<link>
+file          = DATA_PATH
+radius        = radius_lengthr
+bezier_radius = 0.1r
+thickness     = 4
+</link>
+'
+	options[:histograms].each_with_index do |data_path, i|
+		next if options[:visualization][i] != 'l'
+	    data_file_path = File.join(paths['data_folder'], File.basename(data_path))
+	    FileUtils.cp(data_path, data_file_path)
+        custom_track = link_template.gsub('DATA_PATH', data_file_path)
+		last_r = last_r - 0.02
+        custom_track.gsub!('radius_length', last_r.to_s)
+		plot_section << custom_track
+	end
+	plot_section << "</links>"
+	if options[:visualization].include?('s') 
+	    plot_section << "\n\n<highlights>" 
+
+	    options[:histograms].each_with_index do |data_path, i|
+	            next if options[:visualization][i] != 's'
+	            data_file_path = File.join(paths['data_folder'], File.basename(data_path))
+	            FileUtils.cp(data_path, data_file_path)
+		high= "\n<highlight>\nfile=" +  data_file_path
+		high << "\nstroke_thickness = 1\nstroke_color = black\n</highlight>\n"
+	            plot_section << high
+	    end
+	    plot_section << "</highlights>"
+	end
+end
+
+conf_file_template.gsub!("plot_section", plot_section)
+paths['conf'] = File.join(paths['etc_folder'], 'circos.conf')
+File.open(paths['conf'], 'w') {|f| f.write(conf_file_template) }
+
+

data/lib/make_circos/circos_conf_files/circos.conf

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+
+# Chromosome name, size and color definition
+karyotype = path
+
+# The <ideogram> block defines the position, size, labels and other
+# properties of the segments on which data are drawn. These segments
+# are usually chromosomes, but can be any integer axis.
+
+# The chromosomes_unit value is used as a unit (suffix "u") to shorten
+# values in other parts of the configuration file. Some parameters,
+# such as ideogram and tick spacing, accept "u" suffixes, so instead of
+#
+# spacing = 10000000
+#
+# you can write
+#
+# spacing = 10u
+#
+# See ticks.conf for examples.
+
+chromosomes_units = units
+
+plot_section
+
+<<include path_ideogram>>
+
+<<include path_ticks>>
+
+<image>
+<<include etc/image.conf>>                
+</image>
+
+<<include etc/colors_fonts_patterns.conf>> 
+
+<<include etc/housekeeping.conf>> 
+

data/lib/make_circos/circos_conf_files/ideogram.conf

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+
+<ideogram>
+
+<spacing>
+default = 0.005r
+break   = 5r 
+</spacing>
+
+# Ideogram position, fill and outline
+radius           = 0.90r
+thickness        = 20p
+fill             = yes
+stroke_color     = dgrey
+stroke_thickness = 2p
+
+# Minimum definition for ideogram labels.
+
+show_label       = yes
+# see etc/fonts.conf for list of font names
+label_font       = default 
+label_radius     = dims(image,radius) - 60p
+label_size       = 30
+label_parallel   = yes
+
+</ideogram>
+
+

data/lib/make_circos/circos_conf_files/ticks.conf

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+show_ticks          = yes
+show_tick_labels    = yes
+
+<ticks>
+radius           = 1r
+color            = black
+thickness        = 2p
+
+# the tick label is derived by multiplying the tick position
+# by 'multiplier' and casting it in 'format':
+#
+# sprintf(format,position*multiplier)
+#
+
+multiplier = mult
+
+# %d   - integer
+# %f   - float
+# %.1f - float with one decimal
+# %.2f - float with two decimals
+#
+# for other formats, see http://perldoc.perl.org/functions/sprintf.html
+
+format           = %d
+
+<tick>
+spacing        = 5u
+size           = 10p
+</tick>
+
+<tick>
+spacing        = 25u
+size           = 15p
+show_label     = yes
+label_size     = 20p
+label_offset   = 10p
+format         = %d
+</tick>
+
+</ticks>
+

data/lib/make_circos/version.rb

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+module MakeCircos
+  VERSION = "0.0.1"
+end

data/lib/make_circos.rb

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+require "make_circos/version"
+
+module MakeCircos
+  # Your code goes here...
+end

data/make_circos.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'make_circos/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "make_circos"
+  spec.version       = MakeCircos::VERSION
+  spec.authors       = ["Pedro Seoane Zonjic"]
+  spec.email         = ["seoanezonjic@uma.es"]
+  spec.summary       = %q{Gem helper to ahndle the CIRCOS suite}
+  spec.description   = %q{Helper that generate preconfigured conf files of the CIRCOS suite.}
+  spec.homepage      = ""
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.6"
+  spec.add_development_dependency "rake"
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: make_circos
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Pedro Seoane Zonjic
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2018-01-17 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Helper that generate preconfigured conf files of the CIRCOS suite.
+email:
+- seoanezonjic@uma.es
+executables:
+- fasta2kariotype.rb
+- make_circos_configuration.rb
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/fasta2kariotype.rb
+- bin/make_circos_configuration.rb
+- lib/make_circos.rb
+- lib/make_circos/circos_conf_files/circos.conf
+- lib/make_circos/circos_conf_files/ideogram.conf
+- lib/make_circos/circos_conf_files/ticks.conf
+- lib/make_circos/version.rb
+- make_circos.gemspec
+homepage: ''
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.6.14
+signing_key: 
+specification_version: 4
+summary: Gem helper to ahndle the CIRCOS suite
+test_files: []