bio-plates 0.2.0
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- checksums.yaml +7 -0
- data/.document +5 -0
- data/.rspec +1 -0
- data/.travis.yml +12 -0
- data/Gemfile +16 -0
- data/LICENSE.txt +20 -0
- data/README.md +146 -0
- data/README.rdoc +48 -0
- data/Rakefile +53 -0
- data/bin/bioplates +54 -0
- data/lib/bio-plates.rb +12 -0
- data/lib/bio-plates/plates.rb +159 -0
- data/spec/bio-plates_spec.rb +41 -0
- data/spec/fixtures/384.csv +1 -0
- data/spec/fixtures/4x96.csv +385 -0
- data/spec/fixtures/anno96.csv +385 -0
- data/spec/fixtures/emptyrowcol.csv +3 -0
- data/spec/fixtures/rowname-error.csv +1 -0
- data/spec/plate_spec.rb +66 -0
- data/spec/spec_helper.rb +32 -0
- data/spec/tmp/output.txt +97 -0
- metadata +180 -0
checksums.yaml
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SHA1:
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metadata.gz: e44d7a6b3cfc76994ef177d1c2c2797a34b86963
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data.tar.gz: da64276088d9fb070d52137efde8e397da455bae
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metadata.gz: b5a2b385d0776efee6e348dbede43caba9e781c3c7cc3a38bfd8fd2e457af634b924786796861d1c4f42416515d1d0af83271501dec954a2e13ff9638b8ff1e0
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data.tar.gz: 4e88d259a43da26fc48346a8de5a8df88811fca00d3f5ad1fa09bb134c7985545a5cc884bd30213762e32055a87b996b5912dd529a314d12afbba743840c67b6
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data/.document
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data/.rspec
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--color
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data/.travis.yml
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data/Gemfile
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source "http://rubygems.org"
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# Add dependencies required to use your gem here.
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# Example:
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gem "bio", "~> 1.4"
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gem "thor"
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# gem "activesupport", ">= 2.3.5"
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# Add dependencies to develop your gem here.
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# Include everything needed to run rake, tests, features, etc.
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group :development, :test do
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gem "rspec", "~> 3.3"
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gem "jeweler", "~> 2.0"
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gem "bundler"
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gem "rdoc", "~> 3.12"
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gem "fakefs", "~> 0.6"
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gem "simplecov", "~> 0.10"
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end
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data/LICENSE.txt
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Copyright (c) 2015 stveep
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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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# bio-plates
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[![Build Status](https://secure.travis-ci.org/stveep/bioruby-plates.png)](http://travis-ci.org/stveep/bioruby-plates)
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Full description goes here
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Note: this software is under active development!
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## Installation
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```sh
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gem install bio-plates
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```
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## Usage
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Command line (currently only rearrangement of 96-well plates into a 384-well plate in quadrants):
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```sh
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gem install bio-plates
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bioplates example
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bioplates quadrants [--output=output.csv --newname='My Plate'] PLATE1.csv PLATE2.csv ... # convert 4x96-well plate annotations to a 384-well plate
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```
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Example input [input.csv]:
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```csv
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Plate,Well,siRNA,Drug,Concentration
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Plate1,A1,PLK1,olaparib,0
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Plate1,A2,siCON,olaparib,1
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Plate1,A3,Allstar,olaparib,5
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Plate1,A4,Mock,olaparib,10
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Plate1,A5,BRCA1,olaparib,20
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Plate1,A6,TP53,olaparib,50
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Plate2,A1,PLK1,olaparib,0
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Plate2,A2,siCON,olaparib,1
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Plate2,A3,Allstar,olaparib,5
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Plate2,A4,Mock,olaparib,10
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Plate2,A5,ATR,olaparib,20
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Plate2,A6,ATM,olaparib,50
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Plate3,A1,PLK1,olaparib,0
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Plate3,A2,siCON,olaparib,1
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Plate3,A3,Allstar,olaparib,5
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Plate3,A4,Mock,olaparib,10
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Plate3,A5,PARP1,olaparib,20
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Plate3,A6,ARID1A,olaparib,50
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Plate4,A1,PLK1,olaparib,0
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Plate4,A2,siCON,olaparib,1
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Plate4,A3,Allstar,olaparib,5
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Plate4,A4,Mock,olaparib,10
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Plate4,A5,BRCA2,olaparib,20
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Plate4,A6,PALB2,olaparib,50
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```
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```sh
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bioplates quadrants --output=384.csv --newname="Screen Plate" input.csv
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```
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```csv
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Plate,Row,Column,sirna,drug,concentration,original_well,original_plate
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Screen Plate,A,01,PLK1,olaparib,0,A1,Plate1
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Screen Plate,A,02,PLK1,olaparib,0,A1,Plate2
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Screen Plate,A,03,siCON,olaparib,1,A2,Plate1
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Screen Plate,A,04,siCON,olaparib,1,A2,Plate2
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Screen Plate,A,05,Allstar,olaparib,5,A3,Plate1
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Screen Plate,A,06,Allstar,olaparib,5,A3,Plate2
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Screen Plate,A,07,Mock,olaparib,10,A4,Plate1
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Screen Plate,A,08,Mock,olaparib,10,A4,Plate2
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Screen Plate,A,09,BRCA1,olaparib,20,A5,Plate1
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Screen Plate,A,10,ATR,olaparib,20,A5,Plate2
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Screen Plate,A,11,TP53,olaparib,50,A6,Plate1
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Screen Plate,A,12,ATM,olaparib,50,A6,Plate2
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Screen Plate,B,01,PLK1,olaparib,0,A1,Plate3
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Screen Plate,B,02,PLK1,olaparib,0,A1,Plate4
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Screen Plate,B,03,siCON,olaparib,1,A2,Plate3
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Screen Plate,B,04,siCON,olaparib,1,A2,Plate4
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Screen Plate,B,05,Allstar,olaparib,5,A3,Plate3
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Screen Plate,B,06,Allstar,olaparib,5,A3,Plate4
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Screen Plate,B,07,Mock,olaparib,10,A4,Plate3
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Screen Plate,B,08,Mock,olaparib,10,A4,Plate4
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Screen Plate,B,09,PARP1,olaparib,20,A5,Plate3
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Screen Plate,B,10,BRCA2,olaparib,20,A5,Plate4
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Screen Plate,B,11,ARID1A,olaparib,50,A6,Plate3
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Screen Plate,B,12,PALB2,olaparib,50,A6,Plate4
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```
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In a script:
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```ruby
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require 'bio-plates'
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BioPlates.read("plate.csv")
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#=> => {"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"}>...
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## See specs for examples
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```
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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)
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Any number of further columns can be specified for annotations
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Multiple plates can be specified in the same file, these are read into a Hash keyed by plate name
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```csv
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Plate,Well,Row,Column,siRNA,Conc
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Plate1,,A,1,si1,5
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Plate1,,A,2,si2,5
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Plate1,,A,3,si3,5
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Plate1,,A,4,si4,5
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Plate1,,A,5,si5,5
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Plate1,,A,6,si6,5
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Plate1,,A,7,si7,5
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Plate1,,A,8,si8,5
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Plate1,,A,9,si9,5
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Plate1,,A,10,si10,5
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Plate1,,A,11,si11,5
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Plate1,,A,12,si12,5
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Plate1,,B,1,si1,5
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Plate1,,B,1,si1,5
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Plate1,,B,1,si1,5
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Plate1,,B,1,si1,5
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...
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Plate2,A01,,,si1,15
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Plate2,A02,,,si1,15
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Plate2,A03,,,si1,15
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```
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The API doc is online. For more code examples see the test files in
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the source tree.
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## Project home page
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Information on the source tree, documentation, examples, issues and
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how to contribute, see
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http://github.com/stveep/bioruby-plates
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The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
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## Cite
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If you use this software, please cite one of
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* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
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* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
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## Biogems.info
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This Biogem is published at (http://biogems.info/index.html#bio-plates)
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## Copyright
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Copyright (c) 2015 stveep. See LICENSE.txt for further details.
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data/README.rdoc
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= bio-plates
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{<img
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src="https://secure.travis-ci.org/stveep/bioruby-plates.png"
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/>}[http://travis-ci.org/#!/stveep/bioruby-plates]
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Full description goes here
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Note: this software is under active development!
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== Installation
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gem install bio-plates
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== Usage
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== Developers
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To use the library
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require 'bio-plates'
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The API doc is online. For more code examples see also the test files in
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the source tree.
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== Project home page
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Information on the source tree, documentation, issues and how to contribute, see
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http://github.com/stveep/bioruby-plates
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The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
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== Cite
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If you use this software, please cite one of
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* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
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* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
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|
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== Biogems.info
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This Biogem is published at http://biogems.info/index.html#bio-plates
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== Copyright
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Copyright (c) 2015 stveep. See LICENSE.txt for further details.
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data/Rakefile
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# encoding: utf-8
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require 'rubygems'
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require 'bundler'
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begin
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Bundler.setup(:default, :development)
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rescue Bundler::BundlerError => e
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$stderr.puts e.message
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$stderr.puts "Run `bundle install` to install missing gems"
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exit e.status_code
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end
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require 'rake'
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require 'jeweler'
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Jeweler::Tasks.new do |gem|
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# gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
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gem.name = "bio-plates"
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gem.homepage = "http://github.com/stveep/bioruby-plates"
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gem.license = "MIT"
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gem.summary = %Q{Methods for handling multiwell plate annotations}
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gem.description = %Q{Methods for handling multiwell plate annotations, includes ranges and quadrants}
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gem.email = "spettitt@gmail.com"
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gem.authors = ["Steve Pettitt"]
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gem.version = "0.2.0"
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gem.executables = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
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gem.required_ruby_version = '>= 2.1.0'
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# dependencies defined in Gemfile
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end
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Jeweler::RubygemsDotOrgTasks.new
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require 'rspec/core'
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require 'rspec/core/rake_task'
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RSpec::Core::RakeTask.new(:spec) do |spec|
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spec.pattern = FileList['spec/**/*_spec.rb']
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end
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desc "Code coverage detail"
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task :simplecov do
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ENV['COVERAGE'] = "true"
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Rake::Task['spec'].execute
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end
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task :default => :spec
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require 'rdoc/task'
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Rake::RDocTask.new do |rdoc|
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version = File.exist?('VERSION') ? File.read('VERSION') : ""
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rdoc.rdoc_dir = 'rdoc'
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rdoc.title = "bio-plates #{version}"
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rdoc.rdoc_files.include('README*')
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rdoc.rdoc_files.include('lib/**/*.rb')
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end
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data/bin/bioplates
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#!/usr/bin/env ruby
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require 'bio-plates'
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require 'thor'
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class BioPlatesCLI < Thor
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desc "quadrants [--output=output.csv --newname='QuadrantPlate'] PLATE1.csv PLATE2.csv ...", "convert 4x96-well plate annotations to a 384-well plate"
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option :output
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option :newname
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def quadrants(*plates)
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|
+
# read files and merge
|
11
|
+
plate_array = []
|
12
|
+
plates.each do |plate|
|
13
|
+
# TODO: check/warn if any plate names are the same
|
14
|
+
BioPlates.read(plate).each{|k,v| plate_array << v}
|
15
|
+
end
|
16
|
+
output = options[:output] || "output.csv"
|
17
|
+
newname = options[:newname] || "QuadrantPlate"
|
18
|
+
BioPlates.quadrants(plate_array, newname).dump(output)
|
19
|
+
end
|
20
|
+
|
21
|
+
desc "example", "Show example plate config"
|
22
|
+
def example
|
23
|
+
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)"
|
24
|
+
puts "Any number of further columns can be specified for annotations"
|
25
|
+
print "
|
26
|
+
Plate,Well,Row,Column,siRNA,Conc
|
27
|
+
Plate1,,A,1,si1,5
|
28
|
+
Plate1,,A,2,si2,5
|
29
|
+
Plate1,,A,3,si3,5
|
30
|
+
Plate1,,A,4,si4,5
|
31
|
+
Plate1,,A,5,si5,5
|
32
|
+
Plate1,,A,6,si6,5
|
33
|
+
Plate1,,A,7,si7,5
|
34
|
+
Plate1,,A,8,si8,5
|
35
|
+
Plate1,,A,9,si9,5
|
36
|
+
Plate1,,A,10,si10,5
|
37
|
+
Plate1,,A,11,si11,5
|
38
|
+
Plate1,,A,12,si12,5
|
39
|
+
Plate1,,B,1,si1,5
|
40
|
+
Plate1,,B,1,si1,5
|
41
|
+
Plate1,,B,1,si1,5
|
42
|
+
Plate1,,B,1,si1,5
|
43
|
+
...
|
44
|
+
Plate2,A01,,,si1,15
|
45
|
+
Plate2,A02,,,si1,15
|
46
|
+
Plate2,A03,,,si1,15"
|
47
|
+
|
48
|
+
|
49
|
+
end
|
50
|
+
|
51
|
+
|
52
|
+
end
|
53
|
+
|
54
|
+
BioPlatesCLI.start(ARGV)
|
data/lib/bio-plates.rb
ADDED
@@ -0,0 +1,12 @@
|
|
1
|
+
# Please require your code below, respecting the naming conventions in the
|
2
|
+
# bioruby directory tree.
|
3
|
+
#
|
4
|
+
# For example, say you have a plugin named bio-plugin, the only uncommented
|
5
|
+
# line in this file would be
|
6
|
+
#
|
7
|
+
# require 'bio/bio-plugin/plugin'
|
8
|
+
#
|
9
|
+
# In this file only require other files. Avoid other source code.
|
10
|
+
|
11
|
+
require 'bio-plates/plates.rb'
|
12
|
+
|
@@ -0,0 +1,159 @@
|
|
1
|
+
class BioPlates
|
2
|
+
require 'csv'
|
3
|
+
def self.read(file)
|
4
|
+
plates = Hash.new{|h,k| h[k] = BioPlates::Plate.new(k)}
|
5
|
+
csv = CSV.read(File.open(file), headers: true, header_converters: :symbol)
|
6
|
+
unless csv.headers.include? :well || ((csv.headers.include? :row) && (csv.headers.include? :column))
|
7
|
+
raise "Column headers must include either Well, or Row and Column"
|
8
|
+
end
|
9
|
+
csv.each do |row|
|
10
|
+
plates[row[:plate]].wells << BioPlates::Plate::Well.new(row)
|
11
|
+
end
|
12
|
+
plates.map{|k,v| v.add_leading_zeroes!}
|
13
|
+
# Return a hash of Plate Objects for all the plates in the CSV
|
14
|
+
#plates.each.map!{|k,v| v.name = k}
|
15
|
+
plates
|
16
|
+
end
|
17
|
+
|
18
|
+
# form quadrants from four plate Objects
|
19
|
+
def self.quadrants(plates,newname="QuadrantPlate")
|
20
|
+
if plates.is_a? Hash
|
21
|
+
plates = plates.sort.to_h.values
|
22
|
+
end
|
23
|
+
unless plates.length == 4
|
24
|
+
warn "Number of plates supplied should be four; truncating/reusing"
|
25
|
+
if plates.length > 4
|
26
|
+
plates = plates[0..3]
|
27
|
+
elsif plates.length < 4
|
28
|
+
i = 0
|
29
|
+
until plates.length == 4 do
|
30
|
+
duplicate = plates[i].dup
|
31
|
+
duplicate.wells = duplicate.wells.map(&:dup)
|
32
|
+
plates << duplicate
|
33
|
+
# Keep incrementing as long as there are still supplied plates, else reset
|
34
|
+
i < plates.length ? i += 1 : i = 0
|
35
|
+
end
|
36
|
+
end
|
37
|
+
end
|
38
|
+
newplate = BioPlates::Plate.new(newname)
|
39
|
+
plates.each.with_index do |plateobj, plateno|
|
40
|
+
plateno = plateno + 1
|
41
|
+
modplate = plateobj.dup
|
42
|
+
modplate.wells.map!{|x| x.quadrantize!(plateno)}
|
43
|
+
modplate.add_leading_zeroes!
|
44
|
+
modplate.wells.map(&:index!)
|
45
|
+
newplate.wells = newplate.wells + modplate.wells
|
46
|
+
end
|
47
|
+
newplate.wells = newplate.wells.sort_by{|w| w.well}
|
48
|
+
newplate
|
49
|
+
end
|
50
|
+
|
51
|
+
end
|
52
|
+
|
53
|
+
|
54
|
+
|
55
|
+
|
56
|
+
class BioPlates::Plate
|
57
|
+
attr_accessor :wells, :name, :rows, :columns
|
58
|
+
|
59
|
+
def initialize(name="")
|
60
|
+
@name = name
|
61
|
+
@wells = []
|
62
|
+
end
|
63
|
+
|
64
|
+
def each
|
65
|
+
@wells.each
|
66
|
+
end
|
67
|
+
|
68
|
+
def rows
|
69
|
+
@rows = Hash.new{|h,k| h[k] = []}
|
70
|
+
@wells.each{|well| @rows[well.row] << well}
|
71
|
+
@rows
|
72
|
+
end
|
73
|
+
|
74
|
+
def columns
|
75
|
+
@columns = Hash.new{|h,k| h[k] = []}
|
76
|
+
@wells.each{|well| @columns[well.column] << well}
|
77
|
+
@columns
|
78
|
+
end
|
79
|
+
|
80
|
+
# Add leading zeroes to column strings
|
81
|
+
def add_leading_zeroes!
|
82
|
+
max = self.wells.dup.sort_by!{|x| x.column.to_s.length}.pop.column.to_s.length
|
83
|
+
self.wells.map!{|x| y = ""; (max - x.column.to_s.length).times{y << "0"} ; x.column = y + x.column.to_s; x }
|
84
|
+
self
|
85
|
+
end
|
86
|
+
|
87
|
+
def dump(file="output.csv",head=true,format="csv")
|
88
|
+
#Column titles required:
|
89
|
+
columns = Hash.new{|h,k| h[k] = 1}
|
90
|
+
self.wells.each do |well|
|
91
|
+
well.annotation.each{|k,v| columns[k] += 1}
|
92
|
+
end
|
93
|
+
columns.delete(:plate) # Remove original plate annotation
|
94
|
+
CSV.open(file,"wb") do |csv|
|
95
|
+
if head
|
96
|
+
csv << ["Plate","Row","Column"] + columns.keys
|
97
|
+
head = false
|
98
|
+
end
|
99
|
+
self.wells.each do |well|
|
100
|
+
line = [self.name,well.row,well.column]
|
101
|
+
columns.keys.each do |col_title|
|
102
|
+
if well.annotation.keys.include?(col_title)
|
103
|
+
line << well.annotation[col_title]
|
104
|
+
else
|
105
|
+
# Any wells without value for an annotation get a zero
|
106
|
+
line << 0
|
107
|
+
end
|
108
|
+
end
|
109
|
+
csv << line
|
110
|
+
end
|
111
|
+
end
|
112
|
+
|
113
|
+
end
|
114
|
+
|
115
|
+
end
|
116
|
+
|
117
|
+
class BioPlates::Plate::Well
|
118
|
+
attr_accessor :row, :column, :annotation, :well
|
119
|
+
@@regexp = /(?<row>[A-Za-z]+)(?<column>\d+)/
|
120
|
+
# Better not to hard code these...
|
121
|
+
@@nrow = 8
|
122
|
+
@@ncol = 12
|
123
|
+
def initialize(hash)
|
124
|
+
|
125
|
+
if hash[:row] && hash[:column]
|
126
|
+
@row = hash[:row]
|
127
|
+
@column = hash[:column].to_s
|
128
|
+
else
|
129
|
+
# Split the well annotation if row & col not given separately
|
130
|
+
m = hash[:well].match(@@regexp)
|
131
|
+
@well = hash[:well]
|
132
|
+
@row = m[:row]
|
133
|
+
@column = m[:column]
|
134
|
+
end
|
135
|
+
# NB annotation includes the original well annotation
|
136
|
+
@annotation = hash.delete_if{|k,f| [:row, :column, :well].include? k}.to_h
|
137
|
+
end
|
138
|
+
|
139
|
+
def index!
|
140
|
+
@well = @row.upcase.to_s + @column
|
141
|
+
end
|
142
|
+
|
143
|
+
def quadrantize!(plate)
|
144
|
+
self.index! unless @well
|
145
|
+
@annotation[:original_well] = @well
|
146
|
+
@annotation[:original_plate] = @annotation[:plate]
|
147
|
+
@annotation.delete(:plate) # Remove so no conflict with new plate
|
148
|
+
(plate == 2 || plate == 4) ? inc = 1 : inc = 0
|
149
|
+
(plate == 3 || plate == 4) ? rowinc = 1 : rowinc = 0
|
150
|
+
@column = (@column.to_i + [*0..@@ncol][@column.to_i-1]+inc).to_s
|
151
|
+
@row = (@row.ord + [*0..@@nrow][@row.upcase.ord-65]+rowinc).chr # 65 = ASCII "A"
|
152
|
+
self
|
153
|
+
end
|
154
|
+
|
155
|
+
def quadrantize(plate)
|
156
|
+
dup = self.dup
|
157
|
+
dup.quadrantize!(plate)
|
158
|
+
end
|
159
|
+
end
|