bio-plates 0.2.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- 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
ADDED
@@ -0,0 +1,7 @@
|
|
1
|
+
---
|
2
|
+
SHA1:
|
3
|
+
metadata.gz: e44d7a6b3cfc76994ef177d1c2c2797a34b86963
|
4
|
+
data.tar.gz: da64276088d9fb070d52137efde8e397da455bae
|
5
|
+
SHA512:
|
6
|
+
metadata.gz: b5a2b385d0776efee6e348dbede43caba9e781c3c7cc3a38bfd8fd2e457af634b924786796861d1c4f42416515d1d0af83271501dec954a2e13ff9638b8ff1e0
|
7
|
+
data.tar.gz: 4e88d259a43da26fc48346a8de5a8df88811fca00d3f5ad1fa09bb134c7985545a5cc884bd30213762e32055a87b996b5912dd529a314d12afbba743840c67b6
|
data/.document
ADDED
data/.rspec
ADDED
@@ -0,0 +1 @@
|
|
1
|
+
--color
|
data/.travis.yml
ADDED
data/Gemfile
ADDED
@@ -0,0 +1,16 @@
|
|
1
|
+
source "http://rubygems.org"
|
2
|
+
# Add dependencies required to use your gem here.
|
3
|
+
# Example:
|
4
|
+
gem "bio", "~> 1.4"
|
5
|
+
gem "thor"
|
6
|
+
# gem "activesupport", ">= 2.3.5"
|
7
|
+
# Add dependencies to develop your gem here.
|
8
|
+
# Include everything needed to run rake, tests, features, etc.
|
9
|
+
group :development, :test do
|
10
|
+
gem "rspec", "~> 3.3"
|
11
|
+
gem "jeweler", "~> 2.0"
|
12
|
+
gem "bundler"
|
13
|
+
gem "rdoc", "~> 3.12"
|
14
|
+
gem "fakefs", "~> 0.6"
|
15
|
+
gem "simplecov", "~> 0.10"
|
16
|
+
end
|
data/LICENSE.txt
ADDED
@@ -0,0 +1,20 @@
|
|
1
|
+
Copyright (c) 2015 stveep
|
2
|
+
|
3
|
+
Permission is hereby granted, free of charge, to any person obtaining
|
4
|
+
a copy of this software and associated documentation files (the
|
5
|
+
"Software"), to deal in the Software without restriction, including
|
6
|
+
without limitation the rights to use, copy, modify, merge, publish,
|
7
|
+
distribute, sublicense, and/or sell copies of the Software, and to
|
8
|
+
permit persons to whom the Software is furnished to do so, subject to
|
9
|
+
the following conditions:
|
10
|
+
|
11
|
+
The above copyright notice and this permission notice shall be
|
12
|
+
included in all copies or substantial portions of the Software.
|
13
|
+
|
14
|
+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
15
|
+
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
|
16
|
+
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
17
|
+
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
|
18
|
+
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
|
19
|
+
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
|
20
|
+
WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
data/README.md
ADDED
@@ -0,0 +1,146 @@
|
|
1
|
+
# bio-plates
|
2
|
+
|
3
|
+
[](http://travis-ci.org/stveep/bioruby-plates)
|
4
|
+
|
5
|
+
Full description goes here
|
6
|
+
|
7
|
+
Note: this software is under active development!
|
8
|
+
|
9
|
+
## Installation
|
10
|
+
|
11
|
+
```sh
|
12
|
+
gem install bio-plates
|
13
|
+
```
|
14
|
+
|
15
|
+
## Usage
|
16
|
+
Command line (currently only rearrangement of 96-well plates into a 384-well plate in quadrants):
|
17
|
+
|
18
|
+
```sh
|
19
|
+
gem install bio-plates
|
20
|
+
|
21
|
+
bioplates example
|
22
|
+
bioplates quadrants [--output=output.csv --newname='My Plate'] PLATE1.csv PLATE2.csv ... # convert 4x96-well plate annotations to a 384-well plate
|
23
|
+
```
|
24
|
+
Example input [input.csv]:
|
25
|
+
|
26
|
+
```csv
|
27
|
+
Plate,Well,siRNA,Drug,Concentration
|
28
|
+
Plate1,A1,PLK1,olaparib,0
|
29
|
+
Plate1,A2,siCON,olaparib,1
|
30
|
+
Plate1,A3,Allstar,olaparib,5
|
31
|
+
Plate1,A4,Mock,olaparib,10
|
32
|
+
Plate1,A5,BRCA1,olaparib,20
|
33
|
+
Plate1,A6,TP53,olaparib,50
|
34
|
+
Plate2,A1,PLK1,olaparib,0
|
35
|
+
Plate2,A2,siCON,olaparib,1
|
36
|
+
Plate2,A3,Allstar,olaparib,5
|
37
|
+
Plate2,A4,Mock,olaparib,10
|
38
|
+
Plate2,A5,ATR,olaparib,20
|
39
|
+
Plate2,A6,ATM,olaparib,50
|
40
|
+
Plate3,A1,PLK1,olaparib,0
|
41
|
+
Plate3,A2,siCON,olaparib,1
|
42
|
+
Plate3,A3,Allstar,olaparib,5
|
43
|
+
Plate3,A4,Mock,olaparib,10
|
44
|
+
Plate3,A5,PARP1,olaparib,20
|
45
|
+
Plate3,A6,ARID1A,olaparib,50
|
46
|
+
Plate4,A1,PLK1,olaparib,0
|
47
|
+
Plate4,A2,siCON,olaparib,1
|
48
|
+
Plate4,A3,Allstar,olaparib,5
|
49
|
+
Plate4,A4,Mock,olaparib,10
|
50
|
+
Plate4,A5,BRCA2,olaparib,20
|
51
|
+
Plate4,A6,PALB2,olaparib,50
|
52
|
+
```
|
53
|
+
|
54
|
+
```sh
|
55
|
+
bioplates quadrants --output=384.csv --newname="Screen Plate" input.csv
|
56
|
+
```
|
57
|
+
|
58
|
+
```csv
|
59
|
+
Plate,Row,Column,sirna,drug,concentration,original_well,original_plate
|
60
|
+
Screen Plate,A,01,PLK1,olaparib,0,A1,Plate1
|
61
|
+
Screen Plate,A,02,PLK1,olaparib,0,A1,Plate2
|
62
|
+
Screen Plate,A,03,siCON,olaparib,1,A2,Plate1
|
63
|
+
Screen Plate,A,04,siCON,olaparib,1,A2,Plate2
|
64
|
+
Screen Plate,A,05,Allstar,olaparib,5,A3,Plate1
|
65
|
+
Screen Plate,A,06,Allstar,olaparib,5,A3,Plate2
|
66
|
+
Screen Plate,A,07,Mock,olaparib,10,A4,Plate1
|
67
|
+
Screen Plate,A,08,Mock,olaparib,10,A4,Plate2
|
68
|
+
Screen Plate,A,09,BRCA1,olaparib,20,A5,Plate1
|
69
|
+
Screen Plate,A,10,ATR,olaparib,20,A5,Plate2
|
70
|
+
Screen Plate,A,11,TP53,olaparib,50,A6,Plate1
|
71
|
+
Screen Plate,A,12,ATM,olaparib,50,A6,Plate2
|
72
|
+
Screen Plate,B,01,PLK1,olaparib,0,A1,Plate3
|
73
|
+
Screen Plate,B,02,PLK1,olaparib,0,A1,Plate4
|
74
|
+
Screen Plate,B,03,siCON,olaparib,1,A2,Plate3
|
75
|
+
Screen Plate,B,04,siCON,olaparib,1,A2,Plate4
|
76
|
+
Screen Plate,B,05,Allstar,olaparib,5,A3,Plate3
|
77
|
+
Screen Plate,B,06,Allstar,olaparib,5,A3,Plate4
|
78
|
+
Screen Plate,B,07,Mock,olaparib,10,A4,Plate3
|
79
|
+
Screen Plate,B,08,Mock,olaparib,10,A4,Plate4
|
80
|
+
Screen Plate,B,09,PARP1,olaparib,20,A5,Plate3
|
81
|
+
Screen Plate,B,10,BRCA2,olaparib,20,A5,Plate4
|
82
|
+
Screen Plate,B,11,ARID1A,olaparib,50,A6,Plate3
|
83
|
+
Screen Plate,B,12,PALB2,olaparib,50,A6,Plate4
|
84
|
+
```
|
85
|
+
|
86
|
+
In a script:
|
87
|
+
```ruby
|
88
|
+
require 'bio-plates'
|
89
|
+
BioPlates.read("plate.csv")
|
90
|
+
#=> => {"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"}>...
|
91
|
+
## See specs for examples
|
92
|
+
```
|
93
|
+
|
94
|
+
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)
|
95
|
+
Any number of further columns can be specified for annotations
|
96
|
+
Multiple plates can be specified in the same file, these are read into a Hash keyed by plate name
|
97
|
+
```csv
|
98
|
+
Plate,Well,Row,Column,siRNA,Conc
|
99
|
+
Plate1,,A,1,si1,5
|
100
|
+
Plate1,,A,2,si2,5
|
101
|
+
Plate1,,A,3,si3,5
|
102
|
+
Plate1,,A,4,si4,5
|
103
|
+
Plate1,,A,5,si5,5
|
104
|
+
Plate1,,A,6,si6,5
|
105
|
+
Plate1,,A,7,si7,5
|
106
|
+
Plate1,,A,8,si8,5
|
107
|
+
Plate1,,A,9,si9,5
|
108
|
+
Plate1,,A,10,si10,5
|
109
|
+
Plate1,,A,11,si11,5
|
110
|
+
Plate1,,A,12,si12,5
|
111
|
+
Plate1,,B,1,si1,5
|
112
|
+
Plate1,,B,1,si1,5
|
113
|
+
Plate1,,B,1,si1,5
|
114
|
+
Plate1,,B,1,si1,5
|
115
|
+
...
|
116
|
+
Plate2,A01,,,si1,15
|
117
|
+
Plate2,A02,,,si1,15
|
118
|
+
Plate2,A03,,,si1,15
|
119
|
+
```
|
120
|
+
|
121
|
+
The API doc is online. For more code examples see the test files in
|
122
|
+
the source tree.
|
123
|
+
|
124
|
+
## Project home page
|
125
|
+
|
126
|
+
Information on the source tree, documentation, examples, issues and
|
127
|
+
how to contribute, see
|
128
|
+
|
129
|
+
http://github.com/stveep/bioruby-plates
|
130
|
+
|
131
|
+
The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
|
132
|
+
|
133
|
+
## Cite
|
134
|
+
|
135
|
+
If you use this software, please cite one of
|
136
|
+
|
137
|
+
* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
|
138
|
+
* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
|
139
|
+
|
140
|
+
## Biogems.info
|
141
|
+
|
142
|
+
This Biogem is published at (http://biogems.info/index.html#bio-plates)
|
143
|
+
|
144
|
+
## Copyright
|
145
|
+
|
146
|
+
Copyright (c) 2015 stveep. See LICENSE.txt for further details.
|
data/README.rdoc
ADDED
@@ -0,0 +1,48 @@
|
|
1
|
+
= bio-plates
|
2
|
+
|
3
|
+
{<img
|
4
|
+
src="https://secure.travis-ci.org/stveep/bioruby-plates.png"
|
5
|
+
/>}[http://travis-ci.org/#!/stveep/bioruby-plates]
|
6
|
+
|
7
|
+
Full description goes here
|
8
|
+
|
9
|
+
Note: this software is under active development!
|
10
|
+
|
11
|
+
== Installation
|
12
|
+
|
13
|
+
gem install bio-plates
|
14
|
+
|
15
|
+
== Usage
|
16
|
+
|
17
|
+
== Developers
|
18
|
+
|
19
|
+
To use the library
|
20
|
+
|
21
|
+
require 'bio-plates'
|
22
|
+
|
23
|
+
The API doc is online. For more code examples see also the test files in
|
24
|
+
the source tree.
|
25
|
+
|
26
|
+
== Project home page
|
27
|
+
|
28
|
+
Information on the source tree, documentation, issues and how to contribute, see
|
29
|
+
|
30
|
+
http://github.com/stveep/bioruby-plates
|
31
|
+
|
32
|
+
The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
|
33
|
+
|
34
|
+
== Cite
|
35
|
+
|
36
|
+
If you use this software, please cite one of
|
37
|
+
|
38
|
+
* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
|
39
|
+
* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
|
40
|
+
|
41
|
+
== Biogems.info
|
42
|
+
|
43
|
+
This Biogem is published at http://biogems.info/index.html#bio-plates
|
44
|
+
|
45
|
+
== Copyright
|
46
|
+
|
47
|
+
Copyright (c) 2015 stveep. See LICENSE.txt for further details.
|
48
|
+
|
data/Rakefile
ADDED
@@ -0,0 +1,53 @@
|
|
1
|
+
# encoding: utf-8
|
2
|
+
|
3
|
+
require 'rubygems'
|
4
|
+
require 'bundler'
|
5
|
+
begin
|
6
|
+
Bundler.setup(:default, :development)
|
7
|
+
rescue Bundler::BundlerError => e
|
8
|
+
$stderr.puts e.message
|
9
|
+
$stderr.puts "Run `bundle install` to install missing gems"
|
10
|
+
exit e.status_code
|
11
|
+
end
|
12
|
+
require 'rake'
|
13
|
+
|
14
|
+
require 'jeweler'
|
15
|
+
Jeweler::Tasks.new do |gem|
|
16
|
+
# gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
|
17
|
+
gem.name = "bio-plates"
|
18
|
+
gem.homepage = "http://github.com/stveep/bioruby-plates"
|
19
|
+
gem.license = "MIT"
|
20
|
+
gem.summary = %Q{Methods for handling multiwell plate annotations}
|
21
|
+
gem.description = %Q{Methods for handling multiwell plate annotations, includes ranges and quadrants}
|
22
|
+
gem.email = "spettitt@gmail.com"
|
23
|
+
gem.authors = ["Steve Pettitt"]
|
24
|
+
gem.version = "0.2.0"
|
25
|
+
gem.executables = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
|
26
|
+
gem.required_ruby_version = '>= 2.1.0'
|
27
|
+
# dependencies defined in Gemfile
|
28
|
+
end
|
29
|
+
Jeweler::RubygemsDotOrgTasks.new
|
30
|
+
|
31
|
+
require 'rspec/core'
|
32
|
+
require 'rspec/core/rake_task'
|
33
|
+
RSpec::Core::RakeTask.new(:spec) do |spec|
|
34
|
+
spec.pattern = FileList['spec/**/*_spec.rb']
|
35
|
+
end
|
36
|
+
|
37
|
+
desc "Code coverage detail"
|
38
|
+
task :simplecov do
|
39
|
+
ENV['COVERAGE'] = "true"
|
40
|
+
Rake::Task['spec'].execute
|
41
|
+
end
|
42
|
+
|
43
|
+
task :default => :spec
|
44
|
+
|
45
|
+
require 'rdoc/task'
|
46
|
+
Rake::RDocTask.new do |rdoc|
|
47
|
+
version = File.exist?('VERSION') ? File.read('VERSION') : ""
|
48
|
+
|
49
|
+
rdoc.rdoc_dir = 'rdoc'
|
50
|
+
rdoc.title = "bio-plates #{version}"
|
51
|
+
rdoc.rdoc_files.include('README*')
|
52
|
+
rdoc.rdoc_files.include('lib/**/*.rb')
|
53
|
+
end
|
data/bin/bioplates
ADDED
@@ -0,0 +1,54 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
require 'bio-plates'
|
3
|
+
require 'thor'
|
4
|
+
|
5
|
+
class BioPlatesCLI < Thor
|
6
|
+
desc "quadrants [--output=output.csv --newname='QuadrantPlate'] PLATE1.csv PLATE2.csv ...", "convert 4x96-well plate annotations to a 384-well plate"
|
7
|
+
option :output
|
8
|
+
option :newname
|
9
|
+
def quadrants(*plates)
|
10
|
+
# 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
|