bio-plates 0.2.0

data/spec/bio-plates_spec.rb

@@ -0,0 +1,41 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "BioPlates" do
+  context "reading data from a supplied CSV file" do
+    it "reads data and checks for suitable headings" do
+      expect{BioPlates.read("spec/fixtures/4x96.csv")}.not_to raise_error
+      expect{BioPlates.read("spec/fixtures/rowname-error.csv")}.to raise_error(RuntimeError)
+    end
+
+    it "adds leading zeroes to Column strings" do
+      p = BioPlates.read("spec/fixtures/4x96.csv")
+      expect(p.first[1].wells.first.column).to eq "01"
+    end
+
+    it "converts Well to Row and Column if required" do
+      p = BioPlates.read("spec/fixtures/emptyrowcol.csv")
+      expect(p.first[1].wells.first.row).to eq "A"
+      expect(p.first[1].wells.first.column).to eq "01"
+    end
+
+  end
+
+  context "When fewer than four plates are supplied" do
+    p96 = BioPlates.read("spec/fixtures/4x96.csv")
+    twoplates = {"Plate1" => p96["Plate1"].dup,"Plate2" => p96["Plate2"].dup}
+    it "warns and re-uses previous plates" do
+      expect(BioPlates).to receive(:warn)
+      expect(BioPlates.quadrants(twoplates).wells.last.annotation[:drug]).to eq "si-last-p2"
+    end
+  end
+
+  context "When four 96-well plates are supplied" do
+    p96 = BioPlates.read("spec/fixtures/4x96.csv")
+    p384 = BioPlates.read("spec/fixtures/384.csv")
+    p384.first[1].wells.map(&:index!)
+    it "Forms a new 384-well BioPlates::Plate object with correct well annotations" do
+      expect(BioPlates.quadrants(p96).wells.map{|w| w.well}).to eq p384.first[1].wells.map{|w| w.well}
+    end
+  end
+
+end

data/spec/fixtures/384.csv

@@ -0,0 +1 @@
+Plate,Well,Row,Column,Drug,Conc,Junk,siRNA

data/spec/fixtures/4x96.csv

@@ -0,0 +1,385 @@
+Plate,Well,Row,Column,drug,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,2,si2,5
+Plate1,,B,3,si3,5
+Plate1,,B,4,si4,5
+Plate1,,B,5,si5,5
+Plate1,,B,6,si6,5
+Plate1,,B,7,si7,5
+Plate1,,B,8,si8,5
+Plate1,,B,9,si9,5
+Plate1,,B,10,si10,5
+Plate1,,B,11,si11,5
+Plate1,,B,12,si12,5
+Plate1,,C,1,si1,5
+Plate1,,C,2,si2,5
+Plate1,,C,3,si3,5
+Plate1,,C,4,si4,5
+Plate1,,C,5,si5,5
+Plate1,,C,6,si6,5
+Plate1,,C,7,si7,5
+Plate1,,C,8,si8,5
+Plate1,,C,9,si9,5
+Plate1,,C,10,si10,5
+Plate1,,C,11,si11,5
+Plate1,,C,12,si12,5
+Plate1,,D,1,si1,5
+Plate1,,D,2,si2,5
+Plate1,,D,3,si3,5
+Plate1,,D,4,si4,5
+Plate1,,D,5,si5,5
+Plate1,,D,6,si6,5
+Plate1,,D,7,si7,5
+Plate1,,D,8,si8,5
+Plate1,,D,9,si9,5
+Plate1,,D,10,si10,5
+Plate1,,D,11,si11,5
+Plate1,,D,12,si12,5
+Plate1,,E,1,si1,5
+Plate1,,E,2,si2,5
+Plate1,,E,3,si3,5
+Plate1,,E,4,si4,5
+Plate1,,E,5,si5,5
+Plate1,,E,6,si6,5
+Plate1,,E,7,si7,5
+Plate1,,E,8,si8,5
+Plate1,,E,9,si9,5
+Plate1,,E,10,si10,5
+Plate1,,E,11,si11,5
+Plate1,,E,12,si12,5
+Plate1,,F,1,si1,5
+Plate1,,F,2,si2,5
+Plate1,,F,3,si3,5
+Plate1,,F,4,si4,5
+Plate1,,F,5,si5,5
+Plate1,,F,6,si6,5
+Plate1,,F,7,si7,5
+Plate1,,F,8,si8,5
+Plate1,,F,9,si9,5
+Plate1,,F,10,si10,5
+Plate1,,F,11,si11,5
+Plate1,,F,12,si12,5
+Plate1,,G,1,si1,5
+Plate1,,G,2,si2,5
+Plate1,,G,3,si3,5
+Plate1,,G,4,si4,5
+Plate1,,G,5,si5,5
+Plate1,,G,6,si6,5
+Plate1,,G,7,si7,5
+Plate1,,G,8,si8,5
+Plate1,,G,9,si9,5
+Plate1,,G,10,si10,5
+Plate1,,G,11,si11,5
+Plate1,,G,12,si12,5
+Plate1,,H,1,si1,5
+Plate1,,H,2,si2,5
+Plate1,,H,3,si3,5
+Plate1,,H,4,si4,5
+Plate1,,H,5,si5,5
+Plate1,,H,6,si6,5
+Plate1,,H,7,si7,5
+Plate1,,H,8,si8,5
+Plate1,,H,9,si9,5
+Plate1,,H,10,si10,5
+Plate1,,H,11,si11,5
+Plate1,,H,12,si12,5
+Plate2,,A,1,si1,5
+Plate2,,A,2,si2,5
+Plate2,,A,3,si3,5
+Plate2,,A,4,si4,5
+Plate2,,A,5,si5,5
+Plate2,,A,6,si6,5
+Plate2,,A,7,si7,5
+Plate2,,A,8,si8,5
+Plate2,,A,9,si9,5
+Plate2,,A,10,si10,5
+Plate2,,A,11,si11,5
+Plate2,,A,12,si12,5
+Plate2,,B,1,si1,5
+Plate2,,B,2,si2,5
+Plate2,,B,3,si3,5
+Plate2,,B,4,si4,5
+Plate2,,B,5,si5,5
+Plate2,,B,6,si6,5
+Plate2,,B,7,si7,5
+Plate2,,B,8,si8,5
+Plate2,,B,9,si9,5
+Plate2,,B,10,si10,5
+Plate2,,B,11,si11,5
+Plate2,,B,12,si12,5
+Plate2,,C,1,si1,5
+Plate2,,C,2,si2,5
+Plate2,,C,3,si3,5
+Plate2,,C,4,si4,5
+Plate2,,C,5,si5,5
+Plate2,,C,6,si6,5
+Plate2,,C,7,si7,5
+Plate2,,C,8,si8,5
+Plate2,,C,9,si9,5
+Plate2,,C,10,si10,5
+Plate2,,C,11,si11,5
+Plate2,,C,12,si12,5
+Plate2,,D,1,si1,5
+Plate2,,D,2,si2,5
+Plate2,,D,3,si3,5
+Plate2,,D,4,si4,5
+Plate2,,D,5,si5,5
+Plate2,,D,6,si6,5
+Plate2,,D,7,si7,5
+Plate2,,D,8,si8,5
+Plate2,,D,9,si9,5
+Plate2,,D,10,si10,5
+Plate2,,D,11,si11,5
+Plate2,,D,12,si12,5
+Plate2,,E,1,si1,5
+Plate2,,E,2,si2,5
+Plate2,,E,3,si3,5
+Plate2,,E,4,si4,5
+Plate2,,E,5,si5,5
+Plate2,,E,6,si6,5
+Plate2,,E,7,si7,5
+Plate2,,E,8,si8,5
+Plate2,,E,9,si9,5
+Plate2,,E,10,si10,5
+Plate2,,E,11,si11,5
+Plate2,,E,12,si12,5
+Plate2,,F,1,si1,5
+Plate2,,F,2,si2,5
+Plate2,,F,3,si3,5
+Plate2,,F,4,si4,5
+Plate2,,F,5,si5,5
+Plate2,,F,6,si6,5
+Plate2,,F,7,si7,5
+Plate2,,F,8,si8,5
+Plate2,,F,9,si9,5
+Plate2,,F,10,si10,5
+Plate2,,F,11,si11,5
+Plate2,,F,12,si12,5
+Plate2,,G,1,si1,5
+Plate2,,G,2,si2,5
+Plate2,,G,3,si3,5
+Plate2,,G,4,si4,5
+Plate2,,G,5,si5,5
+Plate2,,G,6,si6,5
+Plate2,,G,7,si7,5
+Plate2,,G,8,si8,5
+Plate2,,G,9,si9,5
+Plate2,,G,10,si10,5
+Plate2,,G,11,si11,5
+Plate2,,G,12,si12,5
+Plate2,,H,1,si1,5
+Plate2,,H,2,si2,5
+Plate2,,H,3,si3,5
+Plate2,,H,4,si4,5
+Plate2,,H,5,si5,5
+Plate2,,H,6,si6,5
+Plate2,,H,7,si7,5
+Plate2,,H,8,si8,5
+Plate2,,H,9,si9,5
+Plate2,,H,10,si10,5
+Plate2,,H,11,si11,5
+Plate2,,H,12,si-last-p2,5
+Plate3,,A,1,si1,5
+Plate3,,A,2,si2,5
+Plate3,,A,3,si3,5
+Plate3,,A,4,si4,5
+Plate3,,A,5,si5,5
+Plate3,,A,6,si6,5
+Plate3,,A,7,si7,5
+Plate3,,A,8,si8,5
+Plate3,,A,9,si9,5
+Plate3,,A,10,si10,5
+Plate3,,A,11,si11,5
+Plate3,,A,12,si12,5
+Plate3,,B,1,si1,5
+Plate3,,B,2,si2,5
+Plate3,,B,3,si3,5
+Plate3,,B,4,si4,5
+Plate3,,B,5,si5,5
+Plate3,,B,6,si6,5
+Plate3,,B,7,si7,5
+Plate3,,B,8,si8,5
+Plate3,,B,9,si9,5
+Plate3,,B,10,si10,5
+Plate3,,B,11,si11,5
+Plate3,,B,12,si12,5
+Plate3,,C,1,si1,5
+Plate3,,C,2,si2,5
+Plate3,,C,3,si3,5
+Plate3,,C,4,si4,5
+Plate3,,C,5,si5,5
+Plate3,,C,6,si6,5
+Plate3,,C,7,si7,5
+Plate3,,C,8,si8,5
+Plate3,,C,9,si9,5
+Plate3,,C,10,si10,5
+Plate3,,C,11,si11,5
+Plate3,,C,12,si12,5
+Plate3,,D,1,si1,5
+Plate3,,D,2,si2,5
+Plate3,,D,3,si3,5
+Plate3,,D,4,si4,5
+Plate3,,D,5,si5,5
+Plate3,,D,6,si6,5
+Plate3,,D,7,si7,5
+Plate3,,D,8,si8,5
+Plate3,,D,9,si9,5
+Plate3,,D,10,si10,5
+Plate3,,D,11,si11,5
+Plate3,,D,12,si12,5
+Plate3,,E,1,si1,5
+Plate3,,E,2,si2,5
+Plate3,,E,3,si3,5
+Plate3,,E,4,si4,5
+Plate3,,E,5,si5,5
+Plate3,,E,6,si6,5
+Plate3,,E,7,si7,5
+Plate3,,E,8,si8,5
+Plate3,,E,9,si9,5
+Plate3,,E,10,si10,5
+Plate3,,E,11,si11,5
+Plate3,,E,12,si12,5
+Plate3,,F,1,si1,5
+Plate3,,F,2,si2,5
+Plate3,,F,3,si3,5
+Plate3,,F,4,si4,5
+Plate3,,F,5,si5,5
+Plate3,,F,6,si6,5
+Plate3,,F,7,si7,5
+Plate3,,F,8,si8,5
+Plate3,,F,9,si9,5
+Plate3,,F,10,si10,5
+Plate3,,F,11,si11,5
+Plate3,,F,12,si12,5
+Plate3,,G,1,si1,5
+Plate3,,G,2,si2,5
+Plate3,,G,3,si3,5
+Plate3,,G,4,si4,5
+Plate3,,G,5,si5,5
+Plate3,,G,6,si6,5
+Plate3,,G,7,si7,5
+Plate3,,G,8,si8,5
+Plate3,,G,9,si9,5
+Plate3,,G,10,si10,5
+Plate3,,G,11,si11,5
+Plate3,,G,12,si12,5
+Plate3,,H,1,si1,5
+Plate3,,H,2,si2,5
+Plate3,,H,3,si3,5
+Plate3,,H,4,si4,5
+Plate3,,H,5,si5,5
+Plate3,,H,6,si6,5
+Plate3,,H,7,si7,5
+Plate3,,H,8,si8,5
+Plate3,,H,9,si9,5
+Plate3,,H,10,si10,5
+Plate3,,H,11,si11,5
+Plate3,,H,12,si12,5
+Plate4,,A,1,si1,5
+Plate4,,A,2,si2,5
+Plate4,,A,3,si3,5
+Plate4,,A,4,si4,5
+Plate4,,A,5,si5,5
+Plate4,,A,6,si6,5
+Plate4,,A,7,si7,5
+Plate4,,A,8,si8,5
+Plate4,,A,9,si9,5
+Plate4,,A,10,si10,5
+Plate4,,A,11,si11,5
+Plate4,,A,12,si12,5
+Plate4,,B,1,si1,5
+Plate4,,B,2,si2,5
+Plate4,,B,3,si3,5
+Plate4,,B,4,si4,5
+Plate4,,B,5,si5,5
+Plate4,,B,6,si6,5
+Plate4,,B,7,si7,5
+Plate4,,B,8,si8,5
+Plate4,,B,9,si9,5
+Plate4,,B,10,si10,5
+Plate4,,B,11,si11,5
+Plate4,,B,12,si12,5
+Plate4,,C,1,si1,5
+Plate4,,C,2,si2,5
+Plate4,,C,3,si3,5
+Plate4,,C,4,si4,5
+Plate4,,C,5,si5,5
+Plate4,,C,6,si6,5
+Plate4,,C,7,si7,5
+Plate4,,C,8,si8,5
+Plate4,,C,9,si9,5
+Plate4,,C,10,si10,5
+Plate4,,C,11,si11,5
+Plate4,,C,12,si12,5
+Plate4,,D,1,si1,5
+Plate4,,D,2,si2,5
+Plate4,,D,3,si3,5
+Plate4,,D,4,si4,5
+Plate4,,D,5,si5,5
+Plate4,,D,6,si6,5
+Plate4,,D,7,si7,5
+Plate4,,D,8,si8,5
+Plate4,,D,9,si9,5
+Plate4,,D,10,si10,5
+Plate4,,D,11,si11,5
+Plate4,,D,12,si12,5
+Plate4,,E,1,si1,5
+Plate4,,E,2,si2,5
+Plate4,,E,3,si3,5
+Plate4,,E,4,si4,5
+Plate4,,E,5,si5,5
+Plate4,,E,6,si6,5
+Plate4,,E,7,si7,5
+Plate4,,E,8,si8,5
+Plate4,,E,9,si9,5
+Plate4,,E,10,si10,5
+Plate4,,E,11,si11,5
+Plate4,,E,12,si12,5
+Plate4,,F,1,si1,5
+Plate4,,F,2,si2,5
+Plate4,,F,3,si3,5
+Plate4,,F,4,si4,5
+Plate4,,F,5,si5,5
+Plate4,,F,6,si6,5
+Plate4,,F,7,si7,5
+Plate4,,F,8,si8,5
+Plate4,,F,9,si9,5
+Plate4,,F,10,si10,5
+Plate4,,F,11,si11,5
+Plate4,,F,12,si12,5
+Plate4,,G,1,si1,5
+Plate4,,G,2,si2,5
+Plate4,,G,3,si3,5
+Plate4,,G,4,si4,5
+Plate4,,G,5,si5,5
+Plate4,,G,6,si6,5
+Plate4,,G,7,si7,5
+Plate4,,G,8,si8,5
+Plate4,,G,9,si9,5
+Plate4,,G,10,si10,5
+Plate4,,G,11,si11,5
+Plate4,,G,12,si12,5
+Plate4,,H,1,si1,5
+Plate4,,H,2,si2,5
+Plate4,,H,3,si3,5
+Plate4,,H,4,si4,5
+Plate4,,H,5,si5,5
+Plate4,,H,6,si6,5
+Plate4,,H,7,si7,5
+Plate4,,H,8,si8,5
+Plate4,,H,9,si9,5
+Plate4,,H,10,si10,5
+Plate4,,H,11,si11,5
+Plate4,,H,12,si12,5

data/spec/fixtures/anno96.csv

@@ -0,0 +1,385 @@
+Row,Column,Plate,gene,Well
+A,1,1,FUBP1,A01
+A,2,1,FUBP1,A02
+A,3,1,FUBP1,A03
+A,4,1,FUBP1,A04
+A,5,1,FUBP1,A05
+A,6,1,FUBP1,A06
+A,7,1,FUBP1,A07
+A,8,1,FUBP1,A08
+A,9,1,FUBP1,A09
+A,10,1,FUBP1,A10
+A,11,1,FUBP1,A11
+A,12,1,FUBP1,A12
+B,1,1,PDHA1,B01
+B,2,1,PDHA1,B02
+B,3,1,PDHA1,B03
+B,4,1,PDHA1,B04
+B,5,1,PDHA1,B05
+B,6,1,PDHA1,B06
+B,7,1,PDHA1,B07
+B,8,1,PDHA1,B08
+B,9,1,PDHA1,B09
+B,10,1,PDHA1,B10
+B,11,1,PDHA1,B11
+B,12,1,PDHA1,B12
+C,1,1,RBBP7,C01
+C,2,1,RBBP7,C02
+C,3,1,RBBP7,C03
+C,4,1,RBBP7,C04
+C,5,1,RBBP7,C05
+C,6,1,RBBP7,C06
+C,7,1,RBBP7,C07
+C,8,1,RBBP7,C08
+C,9,1,RBBP7,C09
+C,10,1,RBBP7,C10
+C,11,1,RBBP7,C11
+C,12,1,RBBP7,C12
+D,1,1,MGEA5,D01
+D,2,1,MGEA5,D02
+D,3,1,MGEA5,D03
+D,4,1,MGEA5,D04
+D,5,1,MGEA5,D05
+D,6,1,MGEA5,D06
+D,7,1,MGEA5,D07
+D,8,1,MGEA5,D08
+D,9,1,MGEA5,D09
+D,10,1,MGEA5,D10
+D,11,1,MGEA5,D11
+D,12,1,MGEA5,D12
+E,1,1,TLE4,E01
+E,2,1,TLE4,E02
+E,3,1,TLE4,E03
+E,4,1,TLE4,E04
+E,5,1,TLE4,E05
+E,6,1,TLE4,E06
+E,7,1,TLE4,E07
+E,8,1,TLE4,E08
+E,9,1,TLE4,E09
+E,10,1,TLE4,E10
+E,11,1,TLE4,E11
+E,12,1,TLE4,E12
+F,1,1,HIP1,F01
+F,2,1,HIP1,F02
+F,3,1,HIP1,F03
+F,4,1,HIP1,F04
+F,5,1,HIP1,F05
+F,6,1,HIP1,F06
+F,7,1,HIP1,F07
+F,8,1,HIP1,F08
+F,9,1,HIP1,F09
+F,10,1,HIP1,F10
+F,11,1,HIP1,F11
+F,12,1,HIP1,F12
+G,1,1,KLF6,G01
+G,2,1,KLF6,G02
+G,3,1,KLF6,G03
+G,4,1,KLF6,G04
+G,5,1,KLF6,G05
+G,6,1,KLF6,G06
+G,7,1,KLF6,G07
+G,8,1,KLF6,G08
+G,9,1,KLF6,G09
+G,10,1,KLF6,G10
+G,11,1,KLF6,G11
+G,12,1,KLF6,G12
+H,1,1,DENND5B,H01
+H,2,1,DENND5B,H02
+H,3,1,DENND5B,H03
+H,4,1,DENND5B,H04
+H,5,1,DENND5B,H05
+H,6,1,DENND5B,H06
+H,7,1,DENND5B,H07
+H,8,1,DENND5B,H08
+H,9,1,DENND5B,H09
+H,10,1,DENND5B,H10
+H,11,1,DENND5B,H11
+H,12,1,DENND5B,H12
+A,1,2,siCON1,A01
+A,2,2,siCON1,A02
+A,3,2,siCON1,A03
+A,4,2,siCON1,A04
+A,5,2,siCON1,A05
+A,6,2,siCON1,A06
+A,7,2,siCON1,A07
+A,8,2,siCON1,A08
+A,9,2,siCON1,A09
+A,10,2,siCON1,A10
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