unique neighbor sets

1 files changed, 25 insertions, 0 deletions

diff --git a/scripts/carcinogenicity2csv.rb b/scripts/carcinogenicity2csv.rb
new file mode 100755
index 0000000..9501bdc
--- /dev/null
+++ b/scripts/carcinogenicity2csv.rb
@@ -0,0 +1,25 @@
+#!/usr/bin/env ruby
+require_relative '../../lazar/lib/lazar.rb'
+
+i = 0
+activities = []
+File.readlines(ARGV[0]).each do |line|
+  if i > 2
+    tokens = line.split ","
+    p line if tokens[1].empty?
+    activities << [tokens[1],tokens[3]]
+  end
+  i += 1
+end
+
+puts "SMILES,Activity"
+activities.each_slice(100) do |slice| # get SMILES in chunks
+  sids = slice.collect{|e| e[0]}
+  smiles = `curl https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/#{sids.join(",")}/property/CanonicalSMILES/TXT`.split("\n")
+  abort("Could not get SMILES for all SIDs from PubChem") unless sids.size == smiles.size
+  smiles.each_with_index do |smi,i|
+    act = slice[i]
+    puts [smi.chomp,act[1]].join(",")
+  end
+end
+