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#!/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
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