lazar-padel pa predictions fixed

2 files changed, 78 insertions, 62 deletions

diff --git a/scripts/pa-table.rb b/scripts/pa-table.rb
index d808fa1..e9c8902 100755
--- a/scripts/pa-table.rb
+++ b/scripts/pa-table.rb
@@ -1,98 +1,62 @@
 #!/usr/bin/env ruby
 
-puts '
-\definecolor{red}{rgb}{1,0,0}
-\definecolor{lightred}{rgb}{0.5,0,0}
-\definecolor{green}{rgb}{0,1,0}
-\definecolor{lightgreen}{rgb}{0,0.5,0}
-\definecolor{grey}{rgb}{0.5,0.5,0.5}
-\tiny
-\begin{longtable}{rcccccccccc}
-\caption{Summary of pyrrolizidine alkaloid predictions: red: mutagen, green: non-mutagen, grey: no prediction, dark red/green: low confidence} \\\\
-\label{tab:pa}
- & & \multicolumn{2}{c}{lazar} & \multicolumn{3}{c}{R} & \multicolumn{4}{c}{Tensorflow}\\\\
-'
-#header = ["ID","measured","lazar"]
-header = ["ID","Measured","MP2D","PaDEL"]
+header = ["ID","CID","Name","SMILES","Canonical SMILES","Measured","lazar-MP2D","lazar-MP2D-high-confidence","lazar-PaDEL","lazar-PaDEL-high-confidence"]
 tab = []
-=begin
+i = 0
 File.read("pyrrolizidine-alkaloids/180920_PA_complete_SMILES.csv").each_line do |l|
-  unless l.match("SMILES")
-    #tab << '\verb '+l.chomp.split(";")[2].sub('1: ','')#+'}'
-    tab << l.chomp.split(";")[0]
+  if i > 0
+    id,cid,name,smi = l.chomp.split(";")
+    name.sub!('1: ','')
+    tab << [id,cid,'"'+name+'"','"'+smi+'"']
   end
+  i += 1
 end
 i = 0
-=end
 File.read("pyrrolizidine-alkaloids/lazar/pa-mp2d-predictions.csv").each_line do |l|
-  unless l.match("SMILES")
-    id,smi,exp,mut,p0,p1,max_sim,nn = l.chomp.split(",")
-    row = id
-    if exp == "1"
-      row += ' & \cellcolor{red} '
-    elsif exp == "0"
-      row += ' & \cellcolor{green} '
-    else
-      row += ' & \cellcolor{grey} '
-    end
-    if mut == "1"
-      max_sim.to_f < 0.5 ? row += '& \cellcolor{lightred}  ' : row += '& \cellcolor{red}  '
-    elsif mut == "0"
-      max_sim.to_f < 0.5 ? row += '& \cellcolor{lightgreen}  ' : row += '& \cellcolor{green}  '
-    else #if mut.nil? or mut.empty?
-      row += '& \cellcolor{grey} '
-    end
-    tab << row
-    #i += 1
+  if i > 0
+    id,cansmi,exp,mut,p0,p1,max_sim,nn = l.chomp.split(",")
+    max_sim.to_f < 0.5? hc = "F" : hc = "T"
+    hc = "" if mut.empty?
+    tab[i-1] += ['"'+cansmi+'"',exp,mut,hc]
   end
+  i += 1
 end
 i=0
 File.read("pyrrolizidine-alkaloids/lazar/pa-padel-predictions.csv").each_line do |l|
-  smi,exp,mut,p0,p1,max_sim,nn = l.chomp.split(",")
-  #p mut
-  if mut == "1"
-    max_sim.to_f < 0.5 ? tab[i] += '& \cellcolor{lightred}  ' : tab[i] += '& \cellcolor{red}  '
-  elsif mut == "0"
-    max_sim.to_f < 0.5 ? tab[i] += '& \cellcolor{lightgreen}  ' : tab[i] += '& \cellcolor{green}  '
-  else #if mut.nil? or mut.empty?
-    tab[i] += '& \cellcolor{grey} '
-  end
+  #if i > 0
+    cansmi,exp,mut,p0,p1,max_sim,nn = l.chomp.split(",")
+    max_sim.to_f < 0.5? hc = "F" : hc = "T"
+    hc = "" if mut.empty?
+    tab[i] += [mut,hc]
+  #end
   i += 1
 end
 Dir["pyrrolizidine-alkaloids/R/PA.*.outcome.csv"].each do |r|
-  header << r.sub('pyrrolizidine-alkaloids/R/PA.','').sub('.outcome.csv','')
+  header << "R-"+r.sub('pyrrolizidine-alkaloids/R/PA.','').sub('.outcome.csv','')
   i = 0
   File.read(r).each_line do |l|
     if i > 0
       items = l.chomp.split(";")
       items.shift
       if items.uniq.include? "1"
-        tab[i-1] << ' & \cellcolor{red}'
+        tab[i-1] << 1
       elsif items.uniq.include? "0"
-        tab[i-1] << ' & \cellcolor{green}'
+        tab[i-1] << 0
       end
     end
     i += 1
   end
 end
 Dir["pyrrolizidine-alkaloids/tensorflow/pred.*.v3-ext-Padel-2D.csv"].each do |r|
-  header << r.sub('pyrrolizidine-alkaloids/tensorflow/pred.','').sub('.v3-ext-Padel-2D.csv','').sub("lr2","LR-scikit").sub("lr","LR-sgd").sub("rf","RF").sub("nn","NN")
+  header << "TF-"+r.sub('pyrrolizidine-alkaloids/tensorflow/pred.','').sub('.v3-ext-Padel-2D.csv','').sub("lr2","LR-scikit").sub("lr","LR-sgd").sub("rf","RF").sub("nn","NN")
   i = 0
   File.read(r).each_line do |l|
     if i > 0
       id,pred = l.chomp.split(",")
-      pred.to_f > 0.5 ? tab[i-1] << ' & \cellcolor{red}' : tab[i-1] << ' & \cellcolor{green}'
+      pred.to_f > 0.5 ? tab[i-1] << 1 : tab[i-1] << 0
     end
     i += 1
   end
 end
-#tab.collect!{|t| t + '\cellcolor{grey}  \\\\'}
-puts header.join(" & ")+" \\\\"
-puts '\hline'
-puts '\renewcommand{\arraystretch}{0.075}'
-tab.collect!{|t| t + ''}
-print tab.join(" \\\\ \n")
-puts ' \\\\
-\end{longtable}
-\normalsize
-'
+puts header.join(",")
+puts tab.collect{|r| r.join(",")}.join("\n")
diff --git a/scripts/pa-tex-table.rb b/scripts/pa-tex-table.rb
new file mode 100755
index 0000000..06f7b26
--- /dev/null
+++ b/scripts/pa-tex-table.rb
@@ -0,0 +1,52 @@
+#!/usr/bin/env ruby
+
+puts '
+\definecolor{red}{rgb}{1,0,0}
+\definecolor{lightred}{rgb}{0.5,0,0}
+\definecolor{green}{rgb}{0,1,0}
+\definecolor{lightgreen}{rgb}{0,0.5,0}
+\definecolor{grey}{rgb}{0.5,0.5,0.5}
+\tiny
+\begin{longtable}{rcccccccccc}
+\caption{Summary of pyrrolizidine alkaloid predictions: red: mutagen, green: non-mutagen, grey: no prediction, dark red/green: low confidence} \\\\
+\label{tab:pa}
+   & & \multicolumn{2}{c}{lazar} & \multicolumn{3}{c}{R} & \multicolumn{4}{c}{Tensorflow}\\\\
+ID & Measured & MP2D & PaDEL & DL & RF & SVM & LR-sgd & LR-scikit & NN & RF \\\\
+\hline
+\renewcommand{\arraystretch}{0.075}
+'
+File.read(ARGV[0]).each_line do |l|
+  unless l.match("SMILES")
+    id,cid,name,smi,cansmi,exp,lazar_MP2D,lazar_MP2D_high_confidence,lazar_PaDEL,lazar_PaDEL_high_confidence,r_DL,r_RF,r_SVM,tf_lr_sgd,tf_lr_scikit,tf_NN,tf_RF = l.chomp.split(",")
+    row = id
+    if exp == "1"
+      row += ' & \cellcolor{red}'
+    elsif exp == "0"
+      row += ' & \cellcolor{green}'
+    else
+      row += ' & \cellcolor{grey}'
+    end
+    if lazar_MP2D == "1"
+      lazar_MP2D_high_confidence == "F" ? row += ' & \cellcolor{lightred}' : row += ' & \cellcolor{red}'
+    elsif lazar_MP2D == "0"
+      lazar_MP2D_high_confidence == "F" ? row += ' & \cellcolor{lightgreen}' : row += ' & \cellcolor{green}'
+    else 
+      row += '& \cellcolor{grey} '
+    end
+    if lazar_PaDEL == "1"
+      lazar_PaDEL_high_confidence == "F" ? row += ' & \cellcolor{lightred}' : row += ' & \cellcolor{red}'
+    elsif lazar_PaDEL == "0"
+      lazar_PaDEL_high_confidence == "F" ? row += ' & \cellcolor{lightgreen}' : row += ' & \cellcolor{green}'
+    else 
+      row += ' & \cellcolor{grey}'
+    end
+    [r_DL,r_RF,r_SVM,tf_lr_sgd,tf_lr_scikit,tf_NN,tf_RF].each do |mut|
+      mut == "1" ? row += ' & \cellcolor{red}' : row += ' & \cellcolor{green}'
+    end
+    puts row + ' \\\\'
+  end
+end
+puts '
+\end{longtable}
+\normalsize
+'