bio-plates¶ ↑
Full description goes here
Note: this software is under active development!
Installation¶ ↑
gem install bio-plates
Usage¶ ↑
Command line (currently only rearrangement of 96-well plates into a 384-well plate in quadrants):
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]:
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
bioplates quadrants --output=384.csv --newname="Screen Plate" input.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:
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
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
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
Biogems.info¶ ↑
This Biogem is published at (biogems.info/index.html#bio-plates)
Copyright¶ ↑
Copyright © 2015 stveep. See LICENSE.txt for further details.