https://github.com/protocolbuffers/protobuf/pull/235

--- /src/google/protobuf/compiler/command_line_interface.cc
+++ /src/google/protobuf/compiler/command_line_interface.cc
@@ -938,6 +938,28 @@
   }
 
   if (mode_ == MODE_ENCODE || mode_ == MODE_DECODE) {
+    bool success = false;
+    int in_fd = STDIN_FILENO;
+    int out_fd = STDOUT_FILENO;
+
+    if (!protobuf_in_path_.empty()) {
+      in_fd = open(protobuf_in_path_.c_str(), O_RDONLY);
+      if (in_fd == -1) {
+        std::cerr << protobuf_in_path_ << ": error: failed to open file." << std::endl;
+        return 1;
+      }
+    }
+    if (!protobuf_out_path_.empty()) {
+      out_fd = open(protobuf_out_path_.c_str(),
+                    O_WRONLY | O_CREAT | O_TRUNC,
+                    0644);
+      if (out_fd == -1) {
+        std::cerr << protobuf_out_path_ << ": error: failed to open file." << std::endl;
+        close(in_fd);
+        return 1;
+      }
+    }
+
     if (codec_type_.empty()) {
       // HACK:  Define an EmptyMessage type to use for decoding.
       DescriptorPool pool;
@@ -946,13 +968,20 @@
       file.add_message_type()->set_name("EmptyMessage");
       GOOGLE_CHECK(pool.BuildFile(file) != NULL);
       codec_type_ = "EmptyMessage";
-      if (!EncodeOrDecode(&pool)) {
-        return 1;
-      }
+      success = EncodeOrDecode(&pool, in_fd, out_fd);
     } else {
-      if (!EncodeOrDecode(descriptor_pool.get())) {
-        return 1;
-      }
+      success = EncodeOrDecode(descriptor_pool.get(), in_fd, out_fd);
+    }
+
+    if (in_fd != STDIN_FILENO) {
+      close(in_fd);
+    }
+    if (out_fd != STDOUT_FILENO) {
+      close(out_fd);
+    }
+
+    if (!success) {
+      return 1;
     }
   }
 
@@ -990,6 +1019,11 @@
   for (int i = 0; i < proto_path_.size(); i++) {
     source_tree->MapPath(proto_path_[i].first, proto_path_[i].second);
   }
+  if (mode_ == MODE_COMPILE &&
+      (!protobuf_in_path_.empty() || !protobuf_out_path_.empty())) {
+    std::cerr << "--protobuf_in and --protobuf_out are only valid with "
+         << "decode operations. Ignoring.";
+  }
 
   // Map input files to virtual paths if possible.
   if (!MakeInputsBeProtoPathRelative(source_tree, fallback_database)) {
@@ -1650,6 +1684,12 @@
 
     codec_type_ = value;
 
+  } else if (name == "--protobuf_in") {
+    protobuf_in_path_ = value;
+
+  } else if (name == "--protobuf_out") {
+    protobuf_out_path_ = value;
+
   } else if (name == "--error_format") {
     if (value == "gcc") {
       error_format_ = ERROR_FORMAT_GCC;
@@ -1786,29 +1826,50 @@
          "  -h, --help                  Show this text and exit.\n"
          "  --encode=MESSAGE_TYPE       Read a text-format message of the "
          "given type\n"
-         "                              from standard input and write it in "
-         "binary\n"
-         "                              to standard output.  The message type "
-         "must\n"
+         "                              and write it in binary.  The message "
+         "type must\n"
          "                              be defined in PROTO_FILES or their "
          "imports.\n"
+         "                              The input/output protobuf files are "
+         "specified\n"
+         "                              using the --protobuf_in and "
+         "--protobuf_out\n"
+         "                              command line flags.\n"
          "  --decode=MESSAGE_TYPE       Read a binary message of the given "
-         "type from\n"
-         "                              standard input and write it in text "
-         "format\n"
-         "                              to standard output.  The message type "
-         "must\n"
-         "                              be defined in PROTO_FILES or their "
-         "imports.\n"
+         "type and\n"
+         "                              write it in text format.  The message "
+         "type\n"
+         "                              must be defined in PROTO_FILES or "
+         "their imports.\n"
+         "                              The input/output protobuf files are "
+         "specified\n"
+         "                              using the --protobuf_in and "
+         "--protobuf_out\n"
+         "                              command line flags.\n"
          "  --decode_raw                Read an arbitrary protocol message "
-         "from\n"
-         "                              standard input and write the raw "
-         "tag/value\n"
-         "                              pairs in text format to standard "
-         "output.  No\n"
+         "and write\n"
+         "                              the raw tag/value pairs in text format."
+         "  No\n"
          "                              PROTO_FILES should be given when using "
          "this\n"
-         "                              flag.\n"
+         "                              flag.  The input/output protobuf files "
+         "are\n"
+         "                              specified using the --protobuf_in and\n"
+         "                              --protobuf_out command line flags.\n"
+         "  --protobuf_in=FILE          Absolute path to the protobuf file "
+         "from which\n"
+         "                              input of encoding/decoding operation "
+         "will be\n"
+         "                              read.  If omitted, input will be read "
+         "from\n"
+         "                              standard input.\n"
+         "  --protobuf_out=FILE         Absolute path to the protobuf file "
+         "to which\n"
+         "                              output of encoding/decoding operation "
+         "will be\n"
+         "                              written.  If omitted, output will be "
+         "written to\n"
+         "                              standard output.\n"
          "  --descriptor_set_in=FILES   Specifies a delimited list of FILES\n"
          "                              each containing a FileDescriptorSet "
          "(a\n"
@@ -2123,7 +2184,9 @@
   return true;
 }
 
-bool CommandLineInterface::EncodeOrDecode(const DescriptorPool* pool) {
+bool CommandLineInterface::EncodeOrDecode(const DescriptorPool* pool,
+                                          int in_fd,
+                                          int out_fd) {
   // Look up the type.
   const Descriptor* type = pool->FindMessageTypeByName(codec_type_);
   if (type == NULL) {
@@ -2135,15 +2198,15 @@
   std::unique_ptr<Message> message(dynamic_factory.GetPrototype(type)->New());
 
   if (mode_ == MODE_ENCODE) {
-    SetFdToTextMode(STDIN_FILENO);
-    SetFdToBinaryMode(STDOUT_FILENO);
+    SetFdToTextMode(in_fd);
+    SetFdToBinaryMode(out_fd);
   } else {
-    SetFdToBinaryMode(STDIN_FILENO);
-    SetFdToTextMode(STDOUT_FILENO);
+    SetFdToBinaryMode(in_fd);
+    SetFdToTextMode(out_fd);
   }
 
-  io::FileInputStream in(STDIN_FILENO);
-  io::FileOutputStream out(STDOUT_FILENO);
+  io::FileInputStream in(in_fd);
+  io::FileOutputStream out(out_fd);
 
   if (mode_ == MODE_ENCODE) {
     // Input is text.
--- /src/google/protobuf/compiler/command_line_interface.h
+++ /src/google/protobuf/compiler/command_line_interface.h
@@ -288,7 +288,9 @@
       GeneratorContext* generator_context, std::string* error);
 
   // Implements --encode and --decode.
-  bool EncodeOrDecode(const DescriptorPool* pool);
+  bool EncodeOrDecode(const DescriptorPool* pool,
+                      int in_fd,
+                      int out_fd);
 
   // Implements the --descriptor_set_out option.
   bool WriteDescriptorSet(
@@ -420,6 +422,13 @@
   // parsed FileDescriptorSets to be used for loading protos.  Otherwise, empty.
   std::vector<std::string> descriptor_set_in_names_;
 
+  // When using --encode / --decode / --decode_raw absolute path to the output
+  // file. (Empty string indicates write to STDOUT).
+  std::string protobuf_out_path_;
+  // When using --encode / --decode / --decode_raw, absolute path to the input
+  // file. (Empty string indicates read from STDIN).
+  std::string protobuf_in_path_;
+
   // If --descriptor_set_out was given, this is the filename to which the
   // FileDescriptorSet should be written.  Otherwise, empty.
   std::string descriptor_set_out_name_;
--- /src/google/protobuf/compiler/command_line_interface_unittest.cc
+++ /src/google/protobuf/compiler/command_line_interface_unittest.cc
@@ -95,7 +95,7 @@
   virtual void SetUp();
   virtual void TearDown();
 
-  // Runs the CommandLineInterface with the given command line.  The
+  // Run the CommandLineInterface with the given command line.  The
   // command is automatically split on spaces, and the string "$tmpdir"
   // is replaced with TestTempDir().
   void Run(const std::string& command);
@@ -2491,6 +2491,17 @@
               std::string::npos);
   }
 
+  void ExpectBinaryFilesMatch(const string &expected_file,
+                              const string &actual_file) {
+    string expected_output, actual_output;
+    ASSERT_TRUE(File::ReadFileToString(expected_file, &expected_output));
+    ASSERT_TRUE(File::ReadFileToString(actual_file, &actual_output));
+
+    // Don't use EXPECT_EQ because we don't want to print raw binary data to
+    // stdout on failure.
+    EXPECT_TRUE(expected_output == actual_output);
+  }
+
  private:
   void WriteUnittestProtoDescriptorSet() {
     unittest_proto_descriptor_set_filename_ =
@@ -2585,6 +2596,19 @@
       "net/proto2/internal/no_such_file.proto: No such file or directory\n");
 }
 
+TEST_P(EncodeDecodeTest, RedirectInputOutput) {
+  string out_file = TestTempDir() + "/golden_message_out.pbf";
+  EXPECT_TRUE(
+      Run(TestUtil::MaybeTranslatePath("net/proto2/internal/unittest.proto") +
+          " --encode=protobuf_unittest.TestAllTypes" +
+          " --protobuf_in=" + TestUtil::GetTestDataPath(
+              "net/proto2/internal/"
+              "testdata/text_format_unittest_data_oneof_implemented.txt") +
+          " --protobuf_out=" + out_file));
+  ExpectBinaryFilesMatch(out_file, TestUtil::GetTestDataPath(
+      "net/proto2/internal/testdata/golden_message_oneof_implemented"));
+}
+
 INSTANTIATE_TEST_SUITE_P(FileDescriptorSetSource, EncodeDecodeTest,
                          testing::Values(PROTO_PATH, DESCRIPTOR_SET_IN));
 }  // anonymous namespace