re-init

2 files changed, 49 insertions, 0 deletions

diff --git a/scripts/bbp2blood-brain-barrier.rb b/scripts/bbp2blood-brain-barrier.rb
new file mode 100644
index 0000000..aab8872
--- /dev/null
+++ b/scripts/bbp2blood-brain-barrier.rb
@@ -0,0 +1,18 @@
+require_relative '../../lazar/lib/lazar'
+include OpenTox
+
+CSV.open("../classification/blood-brain-barrier.csv", "wb") do |csv|
+  CSV.read("../classification/bbp2.smi",{:col_sep => "\t"}).each do |line|
+    smi = line.first
+    act = line[-2]
+    p smi, act
+    if act =~ /p/i
+      csv << [smi, "penetrating"]
+    elsif act =~ /n/i
+      csv << [smi, "nonpenetrating"]
+    else
+      p "unknown act '#{act}'"
+    end
+  end
+end
+
diff --git a/scripts/modena2lazar.rb b/scripts/modena2lazar.rb
new file mode 100644
index 0000000..801106b
--- /dev/null
+++ b/scripts/modena2lazar.rb
@@ -0,0 +1,31 @@
+require_relative '../../lazar/lib/lazar'
+include OpenTox
+
+descriptors = ["Material","Coating","Primary size 1st Dimension [nm]","Primary size 2nd Dimension [nm]","Aspect ratio","Surface area [m2/g]","Zeta potential [mV]","Size in situ  [nm]"]
+
+conditions = ["Assay","Treatment time","Cell type","Serum concentration","Dispersion protocol"]
+endpoints = ["EC25 (ug/ml)","EC50 (ug/ml)","slope EC50 (ug/ml)","EC25 (mm2/ml)","EC50 (mm2/ml)","slope EC50 (surface area)","EC25 (10E12 particles/ml)","EC50 (10E12 particles/ml)","slope EC50 (number)"] 
+
+descriptor_csv = CSV.open("../regression/MODENA-descriptors.csv", "wb")
+#endpoint_csvs 
+#endpoins.each do |e| 
+
+#descriptor_csv << ["ID"]+descriptors
+input = CSV.read("../src/MODENA-EC50_EC25.csv")
+header = input.shift
+descriptor_indices = descriptors.collect{|d| header.index d}
+condition_indices = conditions.collect{|c| header.index c}
+condition_parameters = []
+condition_counts = {}
+input.each do |line|
+  id = line[0]+"_"+line[1].gsub(" ","_")
+  #descriptor_csv << [id]+descriptor_indices.collect{|i| line[i]}
+  conds = condition_indices.collect{|i| line[i]}
+  condition_parameters << conds
+  condition_counts[conds] ||= 0
+  condition_counts[conds] += 1
+end
+#descriptor_csv.close
+p condition_parameters.size
+p condition_parameters.uniq.size
+p condition_counts.sort{|a,b| b.last <=> a.last}