bio-plates 0.2.0

checksums.yaml

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data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.rspec

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+--color

data/.travis.yml

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+language: ruby
+rvm:
+  - 2.1.0
+  - 2.2.0
+
+# - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+gem "bio", "~> 1.4"
+gem "thor"
+#   gem "activesupport", ">= 2.3.5"
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development, :test  do
+  gem "rspec", "~> 3.3"
+  gem "jeweler", "~> 2.0"
+  gem "bundler"
+  gem "rdoc", "~> 3.12"
+  gem "fakefs", "~> 0.6"
+  gem "simplecov", "~> 0.10"
+end

data/LICENSE.txt

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+Copyright (c) 2015 stveep
+
+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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+# bio-plates
+
+[![Build Status](https://secure.travis-ci.org/stveep/bioruby-plates.png)](http://travis-ci.org/stveep/bioruby-plates)
+
+Full description goes here
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+gem install bio-plates
+```
+
+## Usage
+Command line (currently only rearrangement of 96-well plates into a 384-well plate in quadrants):
+
+```sh
+gem install bio-plates
+
+bioplates example
+bioplates quadrants [--output=output.csv --newname='My Plate'] PLATE1.csv PLATE2.csv ...  # convert 4x96-well plate annotations to a 384-well plate
+```
+Example input [input.csv]:
+
+```csv
+Plate,Well,siRNA,Drug,Concentration
+Plate1,A1,PLK1,olaparib,0
+Plate1,A2,siCON,olaparib,1
+Plate1,A3,Allstar,olaparib,5
+Plate1,A4,Mock,olaparib,10
+Plate1,A5,BRCA1,olaparib,20
+Plate1,A6,TP53,olaparib,50
+Plate2,A1,PLK1,olaparib,0
+Plate2,A2,siCON,olaparib,1
+Plate2,A3,Allstar,olaparib,5
+Plate2,A4,Mock,olaparib,10
+Plate2,A5,ATR,olaparib,20
+Plate2,A6,ATM,olaparib,50
+Plate3,A1,PLK1,olaparib,0
+Plate3,A2,siCON,olaparib,1
+Plate3,A3,Allstar,olaparib,5
+Plate3,A4,Mock,olaparib,10
+Plate3,A5,PARP1,olaparib,20
+Plate3,A6,ARID1A,olaparib,50
+Plate4,A1,PLK1,olaparib,0
+Plate4,A2,siCON,olaparib,1
+Plate4,A3,Allstar,olaparib,5
+Plate4,A4,Mock,olaparib,10
+Plate4,A5,BRCA2,olaparib,20
+Plate4,A6,PALB2,olaparib,50
+```
+
+```sh
+bioplates quadrants --output=384.csv --newname="Screen Plate" input.csv
+```
+
+```csv
+Plate,Row,Column,sirna,drug,concentration,original_well,original_plate
+Screen Plate,A,01,PLK1,olaparib,0,A1,Plate1
+Screen Plate,A,02,PLK1,olaparib,0,A1,Plate2
+Screen Plate,A,03,siCON,olaparib,1,A2,Plate1
+Screen Plate,A,04,siCON,olaparib,1,A2,Plate2
+Screen Plate,A,05,Allstar,olaparib,5,A3,Plate1
+Screen Plate,A,06,Allstar,olaparib,5,A3,Plate2
+Screen Plate,A,07,Mock,olaparib,10,A4,Plate1
+Screen Plate,A,08,Mock,olaparib,10,A4,Plate2
+Screen Plate,A,09,BRCA1,olaparib,20,A5,Plate1
+Screen Plate,A,10,ATR,olaparib,20,A5,Plate2
+Screen Plate,A,11,TP53,olaparib,50,A6,Plate1
+Screen Plate,A,12,ATM,olaparib,50,A6,Plate2
+Screen Plate,B,01,PLK1,olaparib,0,A1,Plate3
+Screen Plate,B,02,PLK1,olaparib,0,A1,Plate4
+Screen Plate,B,03,siCON,olaparib,1,A2,Plate3
+Screen Plate,B,04,siCON,olaparib,1,A2,Plate4
+Screen Plate,B,05,Allstar,olaparib,5,A3,Plate3
+Screen Plate,B,06,Allstar,olaparib,5,A3,Plate4
+Screen Plate,B,07,Mock,olaparib,10,A4,Plate3
+Screen Plate,B,08,Mock,olaparib,10,A4,Plate4
+Screen Plate,B,09,PARP1,olaparib,20,A5,Plate3
+Screen Plate,B,10,BRCA2,olaparib,20,A5,Plate4
+Screen Plate,B,11,ARID1A,olaparib,50,A6,Plate3
+Screen Plate,B,12,PALB2,olaparib,50,A6,Plate4
+```
+
+In a script:
+```ruby
+require 'bio-plates'
+BioPlates.read("plate.csv")
+#=> => {"Plate1"=>#<BioPlates::Plate:0x007fbc3b0cb260 @name="Plate1", @wells=[#<BioPlates::Plate::Well:0x007fbc3b0cb1e8 @row="A", @column="01", @annotation={:plate=>"Plate1", :drug=>"si1", :conc=>"5"}>, #<BioPlates::Plate::Well:0x007fbc3b0cabf8 @row="A", @column="02", @annotation={:plate=>"Plate1", :drug=>"si2", :conc=>"5"}>, #<BioPlates::Plate::Well:0x007fbc3b0ca540 @row="A", @column="03", @annotation={:plate=>"Plate1", :drug=>"si3", :conc=>"5"}>, #<BioPlates::Plate::Well:0x007fbc3b0c9c30 @row="A", @column="04", @annotation={:plate=>"Plate1", :drug=>"si4", :conc=>"5"}>...
+## See specs for examples
+```
+
+Example CSV format. Must have a column headed Plate containing plate name, and either a well column Well (e.g. A01 or B4) or two further columns with Row and Column (A,3)
+Any number of further columns can be specified for annotations
+Multiple plates can be specified in the same file, these are read into a Hash keyed by plate name
+```csv
+  Plate,Well,Row,Column,siRNA,Conc
+  Plate1,,A,1,si1,5
+  Plate1,,A,2,si2,5
+  Plate1,,A,3,si3,5
+  Plate1,,A,4,si4,5
+  Plate1,,A,5,si5,5
+  Plate1,,A,6,si6,5
+  Plate1,,A,7,si7,5
+  Plate1,,A,8,si8,5
+  Plate1,,A,9,si9,5
+  Plate1,,A,10,si10,5
+  Plate1,,A,11,si11,5
+  Plate1,,A,12,si12,5
+  Plate1,,B,1,si1,5
+  Plate1,,B,1,si1,5
+  Plate1,,B,1,si1,5
+  Plate1,,B,1,si1,5
+  ...
+  Plate2,A01,,,si1,15
+  Plate2,A02,,,si1,15
+  Plate2,A03,,,si1,15
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/stveep/bioruby-plates
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+If you use this software, please cite one of
+
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at (http://biogems.info/index.html#bio-plates)
+
+## Copyright
+
+Copyright (c) 2015 stveep. See LICENSE.txt for further details.

data/README.rdoc

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+= bio-plates
+
+{<img
+src="https://secure.travis-ci.org/stveep/bioruby-plates.png"
+/>}[http://travis-ci.org/#!/stveep/bioruby-plates]
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+        gem install bio-plates
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require 'bio-plates'
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+        
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/stveep/bioruby-plates
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+== Cite
+
+  If you use this software, please cite one of
+ 
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+== Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-plates
+
+== Copyright
+
+Copyright (c) 2015 stveep. See LICENSE.txt for further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
+  gem.name = "bio-plates"
+  gem.homepage = "http://github.com/stveep/bioruby-plates"
+  gem.license = "MIT"
+  gem.summary = %Q{Methods for handling multiwell plate annotations}
+  gem.description = %Q{Methods for handling multiwell plate annotations, includes ranges and quadrants}
+  gem.email = "spettitt@gmail.com"
+  gem.authors = ["Steve Pettitt"]
+  gem.version = "0.2.0"
+  gem.executables = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
+  gem.required_ruby_version = '>= 2.1.0'
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+desc "Code coverage detail"
+task :simplecov do
+  ENV['COVERAGE'] = "true"
+  Rake::Task['spec'].execute
+end
+
+task :default => :spec
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-plates #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/bin/bioplates

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+#!/usr/bin/env ruby
+require 'bio-plates'
+require 'thor'
+
+class BioPlatesCLI < Thor
+  desc "quadrants [--output=output.csv --newname='QuadrantPlate'] PLATE1.csv PLATE2.csv ...", "convert 4x96-well plate annotations to a 384-well plate"
+  option :output
+  option :newname
+  def quadrants(*plates)
+    # read files and merge
+    plate_array = []
+    plates.each do |plate|
+      # TODO: check/warn if any plate names are the same
+      BioPlates.read(plate).each{|k,v| plate_array << v}
+    end
+    output = options[:output] || "output.csv"
+    newname = options[:newname] || "QuadrantPlate"
+    BioPlates.quadrants(plate_array, newname).dump(output)
+  end
+
+  desc "example", "Show example plate config"
+  def example
+  puts "Input as comma-separated values, must have a column headed Plate containing plate name, and either a well column Well (e.g. A01 or B4) or two further columns with Row and Column (A,3)"
+  puts "Any number of further columns can be specified for annotations"
+  print "
+  Plate,Well,Row,Column,siRNA,Conc
+  Plate1,,A,1,si1,5
+  Plate1,,A,2,si2,5
+  Plate1,,A,3,si3,5
+  Plate1,,A,4,si4,5
+  Plate1,,A,5,si5,5
+  Plate1,,A,6,si6,5
+  Plate1,,A,7,si7,5
+  Plate1,,A,8,si8,5
+  Plate1,,A,9,si9,5
+  Plate1,,A,10,si10,5
+  Plate1,,A,11,si11,5
+  Plate1,,A,12,si12,5
+  Plate1,,B,1,si1,5
+  Plate1,,B,1,si1,5
+  Plate1,,B,1,si1,5
+  Plate1,,B,1,si1,5
+  ...
+  Plate2,A01,,,si1,15
+  Plate2,A02,,,si1,15
+  Plate2,A03,,,si1,15"
+
+
+  end
+
+
+end
+
+BioPlatesCLI.start(ARGV)

data/lib/bio-plates.rb

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+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be 
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require 'bio-plates/plates.rb'
+

data/lib/bio-plates/plates.rb

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+class BioPlates
+  require 'csv'
+  def self.read(file)
+    plates = Hash.new{|h,k| h[k] = BioPlates::Plate.new(k)}
+    csv = CSV.read(File.open(file), headers: true, header_converters: :symbol)
+    unless csv.headers.include? :well || ((csv.headers.include? :row) && (csv.headers.include? :column))
+      raise "Column headers must include either Well, or Row and Column"
+    end
+    csv.each do |row|
+      plates[row[:plate]].wells << BioPlates::Plate::Well.new(row)
+    end
+    plates.map{|k,v| v.add_leading_zeroes!}
+    # Return a hash of Plate Objects for all the plates in the CSV
+    #plates.each.map!{|k,v| v.name = k}
+    plates
+  end
+
+  # form quadrants from four plate Objects
+  def self.quadrants(plates,newname="QuadrantPlate")
+    if plates.is_a? Hash
+      plates = plates.sort.to_h.values
+    end
+    unless plates.length == 4
+      warn "Number of plates supplied should be four; truncating/reusing"
+      if plates.length > 4
+        plates = plates[0..3]
+      elsif plates.length < 4
+        i = 0
+        until plates.length == 4 do
+          duplicate = plates[i].dup
+          duplicate.wells = duplicate.wells.map(&:dup)
+          plates << duplicate
+	  # Keep incrementing as long as there are still supplied plates, else reset
+          i < plates.length ? i += 1 : i = 0
+        end
+      end
+    end
+    newplate = BioPlates::Plate.new(newname)
+    plates.each.with_index do |plateobj, plateno|
+      plateno = plateno + 1
+      modplate = plateobj.dup
+      modplate.wells.map!{|x| x.quadrantize!(plateno)}
+      modplate.add_leading_zeroes!
+      modplate.wells.map(&:index!)
+      newplate.wells = newplate.wells + modplate.wells
+    end
+    newplate.wells = newplate.wells.sort_by{|w| w.well}
+    newplate
+  end
+
+end
+
+
+
+
+class BioPlates::Plate
+  attr_accessor :wells, :name, :rows, :columns
+
+  def initialize(name="")
+    @name = name
+    @wells = []
+  end
+
+  def each
+    @wells.each
+  end
+
+  def rows
+    @rows = Hash.new{|h,k| h[k] = []}
+    @wells.each{|well| @rows[well.row] << well}
+    @rows
+  end
+
+  def columns
+    @columns = Hash.new{|h,k| h[k] = []}
+    @wells.each{|well| @columns[well.column] << well}
+    @columns
+  end
+
+  # Add leading zeroes to column strings
+  def add_leading_zeroes!
+    max = self.wells.dup.sort_by!{|x| x.column.to_s.length}.pop.column.to_s.length
+    self.wells.map!{|x| y = ""; (max - x.column.to_s.length).times{y << "0"} ; x.column = y + x.column.to_s; x }
+    self
+  end
+
+  def dump(file="output.csv",head=true,format="csv")
+    #Column titles required:
+    columns = Hash.new{|h,k| h[k] = 1}
+    self.wells.each do |well|
+      well.annotation.each{|k,v| columns[k] += 1}
+    end
+    columns.delete(:plate) # Remove original plate annotation
+    CSV.open(file,"wb") do |csv|
+      if head
+        csv << ["Plate","Row","Column"] + columns.keys
+        head = false
+      end
+      self.wells.each do |well|
+        line = [self.name,well.row,well.column]
+        columns.keys.each do |col_title|
+          if well.annotation.keys.include?(col_title)
+            line << well.annotation[col_title]
+          else
+	    # Any wells without value for an annotation get a zero
+            line << 0
+          end
+        end
+      csv << line
+      end
+    end
+
+  end
+
+end
+
+class BioPlates::Plate::Well
+  attr_accessor :row, :column, :annotation, :well
+  @@regexp = /(?<row>[A-Za-z]+)(?<column>\d+)/
+  # Better not to hard code these...
+  @@nrow = 8
+  @@ncol = 12
+  def initialize(hash)
+
+    if hash[:row] && hash[:column]
+      @row = hash[:row]
+      @column = hash[:column].to_s
+    else
+      # Split the well annotation if row & col not given separately
+      m = hash[:well].match(@@regexp)
+      @well = hash[:well]
+      @row = m[:row]
+      @column = m[:column]
+    end
+    # NB annotation includes the original well annotation
+    @annotation = hash.delete_if{|k,f| [:row, :column, :well].include? k}.to_h
+  end
+
+  def index!
+    @well = @row.upcase.to_s + @column
+  end
+
+  def quadrantize!(plate)
+    self.index! unless @well
+    @annotation[:original_well] = @well
+    @annotation[:original_plate] = @annotation[:plate]
+    @annotation.delete(:plate) # Remove so no conflict with new plate
+    (plate == 2 || plate == 4) ? inc = 1 : inc = 0
+    (plate == 3 || plate == 4) ? rowinc = 1 : rowinc = 0
+    @column = (@column.to_i + [*0..@@ncol][@column.to_i-1]+inc).to_s
+    @row = (@row.ord + [*0..@@nrow][@row.upcase.ord-65]+rowinc).chr # 65 = ASCII "A"
+    self
+  end
+
+  def quadrantize(plate)
+    dup = self.dup
+    dup.quadrantize!(plate)
+  end
+end