Rakefile instead of Makefile and scripts

4 files changed, 0 insertions, 73 deletions

diff --git a/scripts/carcinogenicity2csv.rb b/scripts/carcinogenicity2csv.rb
deleted file mode 100755
index bed0907..0000000
--- a/scripts/carcinogenicity2csv.rb
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/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
-
diff --git a/scripts/convert_pa.rb b/scripts/convert_pa.rb
deleted file mode 100755
index 779aded..0000000
--- a/scripts/convert_pa.rb
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env ruby
-require_relative '../../lazar/lib/lazar.rb'
-
-while STDIN.gets
-  tokens = $_.chomp.encode("UTF-8", {:invalid => :replace, :undef => :replace}).split(";")
-  begin
-    c = OpenTox::Compound.from_smiles tokens.last
-    puts "#{tokens[0]},#{c.smiles}"
-  rescue #=> e
-    STDERR.puts $_
-  end
-end
diff --git a/scripts/efsa2csv.rb b/scripts/efsa2csv.rb
deleted file mode 100755
index 48d4fb8..0000000
--- a/scripts/efsa2csv.rb
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env ruby
-require 'csv'
-require_relative '../../lazar/lib/lazar.rb'
-
-i = 0
-db = {}
-CSV.foreach(ARGV[0], :encoding => "UTF-8", :col_sep => "\t", :liberal_parsing => true) do |row|
-  #STDERR.puts i if i%100 == 0
-  if i > 0 and row[11] and !row[11].empty? and row[24].match(/Salmonella/i) and ( row[25].match("TA 98") or row[25].match("TA 100") ) and row[33]
-    begin
-      c = OpenTox::Compound.from_smiles(row[11].gsub('"','')).smiles
-    rescue
-      c = OpenTox::Compound.from_inchi(row[12]).smiles # some smiles (row[11]) contain non-parseable characters
-    end
-    db[c] ||= {}
-    db[c][:id] ||= "efsa_#{row[2]}"
-    if row[33].match(/Positiv/i)
-      db[c][:value] = 1 # at least one positive result in TA 98 or TA 100
-    elsif row[33].match(/Negativ/i)
-      db[c][:value] ||= 0
-    end
-  end
-  i += 1
-end
-
-db.each do |s,v|
-  puts [v[:id],s,v[:value]].join ","
-end
diff --git a/scripts/import-csv.rb b/scripts/import-csv.rb
deleted file mode 100755
index 255e342..0000000
--- a/scripts/import-csv.rb
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/usr/bin/env ruby
-require_relative '../../lazar/lib/lazar'
-include OpenTox
-
-dataset = Dataset.from_csv_file ARGV[0]
-puts dataset.id.to_s
-
-