unipept 0.7.1 → 0.8.0

data/test/commands/test_peptfilter.rb

@@ -0,0 +1,170 @@
+require_relative '../../lib/commands'
+
+module Unipept
+  class PeptfilterTestCase < Unipept::TestCase
+    def test_length_filter
+      # min length
+      assert(Commands::Peptfilter.filter_length('AALER', 4, 10))
+      assert(Commands::Peptfilter.filter_length('AALER', 5, 10))
+      assert(!Commands::Peptfilter.filter_length('AALER', 6, 10))
+
+      # max length
+      assert(!Commands::Peptfilter.filter_length('AALER', 1, 4))
+      assert(Commands::Peptfilter.filter_length('AALER', 1, 5))
+      assert(Commands::Peptfilter.filter_length('AALER', 1, 6))
+    end
+
+    def test_lacks_filter
+      assert(Commands::Peptfilter.filter_lacks('AALER', ''.chars.to_a))
+      assert(Commands::Peptfilter.filter_lacks('AALER', 'BCD'.chars.to_a))
+      assert(!Commands::Peptfilter.filter_lacks('AALER', 'A'.chars.to_a))
+      assert(!Commands::Peptfilter.filter_lacks('AALER', 'AE'.chars.to_a))
+    end
+
+    def test_contains_filter
+      assert(Commands::Peptfilter.filter_contains('AALER', ''.chars.to_a))
+      assert(Commands::Peptfilter.filter_contains('AALER', 'A'.chars.to_a))
+      assert(Commands::Peptfilter.filter_contains('AALER', 'AE'.chars.to_a))
+      assert(!Commands::Peptfilter.filter_contains('AALER', 'BCD'.chars.to_a))
+      assert(!Commands::Peptfilter.filter_contains('AALER', 'AB'.chars.to_a))
+    end
+
+    def test_filter
+      assert(Commands::Peptfilter.filter('AALTER', 4, 10, 'BCD'.chars.to_a, 'AL'.chars.to_a))
+      assert(!Commands::Peptfilter.filter('AALTER', 7, 10, 'BCD.chars.to_a', 'AL'.chars.to_a))
+      assert(!Commands::Peptfilter.filter('AALTER', 4, 5, 'BCD'.chars.to_a, 'AL'.chars.to_a))
+      assert(!Commands::Peptfilter.filter('AALTER', 4, 10, 'ABC'.chars.to_a, 'AL'.chars.to_a))
+      assert(!Commands::Peptfilter.filter('AALTER', 4, 10, 'BCD'.chars.to_a, 'ALC'.chars.to_a))
+    end
+
+    def test_default_min_length_argument
+      out, _err = capture_io_with_input('A' * 6) do
+        Commands::Peptfilter.run(%w())
+      end
+      assert_equal('A' * 6, out.chomp)
+
+      out, _err = capture_io_with_input('A' * 5) do
+        Commands::Peptfilter.run(%w())
+      end
+      assert_equal('A' * 5, out.chomp)
+
+      out, _err = capture_io_with_input('A' * 4) do
+        Commands::Peptfilter.run(%w())
+      end
+      assert_equal('', out.chomp)
+    end
+
+    def test_default_max_length_argument
+      out, _err = capture_io_with_input('A' * 49) do
+        Commands::Peptfilter.run(%w())
+      end
+      assert_equal('A' * 49, out.chomp)
+
+      out, _err = capture_io_with_input('A' * 50) do
+        Commands::Peptfilter.run(%w())
+      end
+      assert_equal('A' * 50, out.chomp)
+
+      out, _err = capture_io_with_input('A' * 51) do
+        Commands::Peptfilter.run(%w())
+      end
+      assert_equal('', out.chomp)
+    end
+
+    def test_with_min_argument
+      out, _err = capture_io_with_input('A' * 6) do
+        Commands::Peptfilter.run(%w(--minlen 7))
+      end
+      assert_equal('', out.chomp)
+
+      out, _err = capture_io_with_input('A' * 4) do
+        Commands::Peptfilter.run(%w(--minlen 3))
+      end
+      assert_equal('A' * 4, out.chomp)
+    end
+
+    def test_with_max_argument
+      out, _err = capture_io_with_input('A' * 45) do
+        Commands::Peptfilter.run(%w(--maxlen 40))
+      end
+      assert_equal('', out.chomp)
+
+      out, _err = capture_io_with_input('A' * 55) do
+        Commands::Peptfilter.run(%w(--maxlen 60))
+      end
+      assert_equal('A' * 55, out.chomp)
+    end
+
+    def test_with_lacks_argument
+      out, _err = capture_io_with_input('A' * 10) do
+        Commands::Peptfilter.run(%w(--lacks B))
+      end
+      assert_equal('A' * 10, out.chomp)
+
+      out, _err = capture_io_with_input('A' * 10) do
+        Commands::Peptfilter.run(%w(-l B))
+      end
+      assert_equal('A' * 10, out.chomp)
+
+      out, _err = capture_io_with_input('A' * 10) do
+        Commands::Peptfilter.run(%w(--lacks A))
+      end
+      assert_equal('', out.chomp)
+
+      out, _err = capture_io_with_input('A' * 10) do
+        Commands::Peptfilter.run(%w(-l A))
+      end
+      assert_equal('', out.chomp)
+    end
+
+    def test_with_contains_argument
+      out, _err = capture_io_with_input('A' * 10) do
+        Commands::Peptfilter.run(%w(--contains A))
+      end
+      assert_equal('A' * 10, out.chomp)
+
+      out, _err = capture_io_with_input('A' * 10) do
+        Commands::Peptfilter.run(%w(-c A))
+      end
+      assert_equal('A' * 10, out.chomp)
+
+      out, _err = capture_io_with_input('A' * 10) do
+        Commands::Peptfilter.run(%w(--contains B))
+      end
+      assert_equal('', out.chomp)
+
+      out, _err = capture_io_with_input('A' * 10) do
+        Commands::Peptfilter.run(%w(-c B))
+      end
+      assert_equal('', out.chomp)
+    end
+
+    def test_fasta_input
+      out, _err = capture_io_with_input('>') do
+        Commands::Peptfilter.run(%w())
+      end
+      assert_equal('>', out.chomp)
+
+      out, _err = capture_io_with_input(['>', 'A', 'AALTER', '>']) do
+        Commands::Peptfilter.run(%w())
+      end
+      assert_equal(">\nAALTER\n>", out.chomp)
+    end
+
+    def test_normal_input
+      out, _err = capture_io_with_input(['A', 'A' * 11, 'AAAAB', 'BBBBB', 'CCCCC', 'CCCCCA']) do
+        Commands::Peptfilter.run(%w(--minlen 4 --maxlen 10 --lacks B --contains A))
+      end
+      assert_equal('CCCCCA', out.chomp)
+    end
+
+    def test_help
+      out, _err = capture_io_while do
+        assert_raises SystemExit do
+          Commands::Peptfilter.run(%w(-h))
+        end
+      end
+      assert(out.include? 'show help for this command')
+    end
+  end
+end

data/test/commands/test_prot2pept.rb

@@ -0,0 +1,82 @@
+require_relative '../../lib/commands'
+
+module Unipept
+  class Prot2peptTestCase < Unipept::TestCase
+    def test_normal_input
+      out, _err = capture_io_with_input('AALTERAALTERPAALTER') do
+        Commands::Prot2pept.run(%w())
+      end
+      assert_equal("AALTER\nAALTERPAALTER", out.chomp)
+
+      out, _err = capture_io_with_input('KRKPR') do
+        Commands::Prot2pept.run(%w())
+      end
+      assert_equal("K\nR\nKPR", out.chomp)
+
+      out, _err = capture_io_with_input(%w(AALTERAALTERPAALTER AALTERAA)) do
+        Commands::Prot2pept.run(%w())
+      end
+      assert_equal("AALTER\nAALTERPAALTER\nAALTER\nAA", out.chomp)
+    end
+
+    def test_fasta_input
+      out, _err = capture_io_with_input(">AKA\nAALTERAALTERPAALTER") do
+        Commands::Prot2pept.run(%w())
+      end
+      assert_equal(">AKA\nAALTER\nAALTERPAALTER", out.chomp)
+
+      out, _err = capture_io_with_input(">AKA\nAAL\nT\nERAALTER\nP\nAALTER") do
+        Commands::Prot2pept.run(%w())
+      end
+      assert_equal(">AKA\nAALTER\nAALTERPAALTER", out.chomp)
+
+      out, _err = capture_io_with_input(">AKA\nAAL\nT\n>\nERAALTER\nP\nAALTER") do
+        Commands::Prot2pept.run(%w())
+      end
+      assert_equal(">AKA\nAALT\n>\nER\nAALTERPAALTER", out.chomp)
+    end
+
+    def test_default_pattern
+      default_out, _err = capture_io_with_input('AALTERAALTERPAALTER') do
+        Commands::Prot2pept.run(%w())
+      end
+      assert_equal("AALTER\nAALTERPAALTER", default_out.chomp)
+
+      pattern_out, _err = capture_io_with_input('AALTERAALTERPAALTER') do
+        Commands::Prot2pept.run(['-p', '([KR])([^P])'])
+      end
+      assert_equal(default_out, pattern_out)
+
+      pattern_out, _err = capture_io_with_input('AALTERAALTERPAALTER') do
+        Commands::Prot2pept.run(['--pattern', '([KR])([^P])'])
+      end
+      assert_equal(default_out, pattern_out)
+    end
+
+    def test_pattern
+      out, _err = capture_io_with_input('AALTERAALTERPAALTER') do
+        Commands::Prot2pept.run(%w())
+      end
+      assert_equal("AALTER\nAALTERPAALTER", out.chomp)
+
+      out, _err = capture_io_with_input('AALTERAALTERPAALTER') do
+        Commands::Prot2pept.run(%w(-p ([KR])([^A])))
+      end
+      assert_equal("AALTERAALTER\nPAALTER", out.chomp)
+
+      out, _err = capture_io_with_input('AALTERAALTERPAALTER') do
+        Commands::Prot2pept.run(%w(--pattern ([KR])([^A])))
+      end
+      assert_equal("AALTERAALTER\nPAALTER", out.chomp)
+    end
+
+    def test_help
+      out, _err = capture_io_while do
+        assert_raises SystemExit do
+          Commands::Prot2pept.run(%w(-h))
+        end
+      end
+      assert(out.include? 'show help for this command')
+    end
+  end
+end

data/test/commands/test_unipept.rb

@@ -0,0 +1,37 @@
+require_relative '../../lib/commands'
+
+module Unipept
+  class UnipeptTestCase < Unipept::TestCase
+    def test_help
+      out, _err = capture_io_while do
+        assert_raises SystemExit do
+          Commands::Unipept.run(%w(-h))
+        end
+      end
+      assert(out.include? 'show help for this command')
+
+      out, _err = capture_io_while do
+        assert_raises SystemExit do
+          Commands::Unipept.run(%w(--help))
+        end
+      end
+      assert(out.include? 'show help for this command')
+    end
+
+    def test_no_valid_subcommand
+      _out, err = capture_io_while do
+        assert_raises SystemExit do
+          Commands::Unipept.run(%w())
+        end
+      end
+      assert(err.include? 'show help for this command')
+    end
+
+    def test_version
+      out, _err = capture_io_while do
+        Commands::Unipept.run(%w(-v))
+      end
+      assert_equal(VERSION, out.chomp)
+    end
+  end
+end

data/test/commands/test_uniprot.rb

@@ -0,0 +1,136 @@
+require_relative '../../lib/commands'
+
+module Unipept
+  class UniprotTestCase < Unipept::TestCase
+    def test_argument_input
+      out, _err = capture_io_while do
+        Commands::Uniprot.run(%w(Q6GZX3))
+      end
+      assert_equal(1, out.split(/\n/).length)
+
+      out, _err = capture_io_while do
+        Commands::Uniprot.run(%w(Q6GZX3 Q6GZX4))
+      end
+      assert_equal(2, out.split(/\n/).length)
+
+      out, _err = capture_io_while do
+        Commands::Uniprot.run(%w(-f fasta Q6GZX3 Q6GZX4))
+      end
+      assert_equal(2, out.count('>'))
+
+      out, _err = capture_io_while do
+        Commands::Uniprot.run(%w(--format fasta Q6GZX3 Q6GZX4))
+      end
+      assert_equal(2, out.count('>'))
+    end
+
+    def test_stdin_input
+      out, _err = capture_io_with_input('Q6GZX3') do
+        Commands::Uniprot.run(%w())
+      end
+      assert_equal(1, out.split(/\n/).length)
+
+      out, _err = capture_io_with_input(%w(Q6GZX3 Q6GZX4)) do
+        Commands::Uniprot.run(%w())
+      end
+      assert_equal(2, out.split(/\n/).length)
+
+      out, _err = capture_io_with_input(%w(Q6GZX3 Q6GZX4)) do
+        Commands::Uniprot.run(%w(-f fasta))
+      end
+      assert_equal(2, out.count('>'))
+
+      out, _err = capture_io_with_input(%w(Q6GZX3 Q6GZX4)) do
+        Commands::Uniprot.run(%w(--format fasta))
+      end
+      assert_equal(2, out.count('>'))
+    end
+
+    def test_argument_input_priority
+      out, _err = capture_io_with_input('Q6GZX3') do
+        Commands::Uniprot.run(%w(Q6GZX3 Q6GZX4))
+      end
+      assert_equal(2, out.split(/\n/).length)
+
+      out, _err = capture_io_with_input(%w(Q6GZX3 Q6GZX4)) do
+        Commands::Uniprot.run(%w(Q6GZX3))
+      end
+      assert_equal(1, out.split(/\n/).length)
+    end
+
+    def test_invalid_format
+      out, err = capture_io_while do
+        assert_raises SystemExit do
+          Commands::Uniprot.run(%w(--format xxx))
+        end
+      end
+      assert_equal('', out)
+      assert(err.include? 'xxx is not a valid output format')
+    end
+
+    def test_default_format
+      out_default, _err = capture_io_while do
+        Commands::Uniprot.run(%w(Q6GZX3))
+      end
+      assert_equal(1, out_default.split(/\n/).length)
+
+      out_sequence, _err = capture_io_while do
+        Commands::Uniprot.run(%w(-f sequence Q6GZX3))
+      end
+      assert_equal(out_default, out_sequence)
+
+      out_sequence, _err = capture_io_while do
+        Commands::Uniprot.run(%w(--format sequence Q6GZX3))
+      end
+      assert_equal(out_default, out_sequence)
+    end
+
+    def test_format_options
+      # fasta txt xml rdf gff sequence
+      out, err = capture_io_while do
+        Commands::Uniprot.run(%w(-f fasta Q6GZX3))
+      end
+      assert(!out.empty?)
+      assert(err.empty?)
+
+      out, err = capture_io_while do
+        Commands::Uniprot.run(%w(-f txt Q6GZX3))
+      end
+      assert(!out.empty?)
+      assert(err.empty?)
+
+      out, err = capture_io_while do
+        Commands::Uniprot.run(%w(-f xml Q6GZX3))
+      end
+      assert(!out.empty?)
+      assert(err.empty?)
+
+      out, err = capture_io_while do
+        Commands::Uniprot.run(%w(-f rdf Q6GZX3))
+      end
+      assert(!out.empty?)
+      assert(err.empty?)
+
+      out, err = capture_io_while do
+        Commands::Uniprot.run(%w(-f gff Q6GZX3))
+      end
+      assert(!out.empty?)
+      assert(err.empty?)
+
+      out, err = capture_io_while do
+        Commands::Uniprot.run(%w(-f sequence Q6GZX3))
+      end
+      assert(!out.empty?)
+      assert(err.empty?)
+    end
+
+    def test_help
+      out, _err = capture_io_while do
+        assert_raises SystemExit do
+          Commands::Uniprot.run(%w(-h))
+        end
+      end
+      assert(out.include? 'show help for this command')
+    end
+  end
+end