diff --git a/lib/galaxy/datatypes/sniff.py b/lib/galaxy/datatypes/sniff.py
index 6d352abb08d..35f7dba4a5f 100644
--- a/lib/galaxy/datatypes/sniff.py
+++ b/lib/galaxy/datatypes/sniff.py
@@ -14,7 +14,11 @@ import sys
 import tempfile
 import zipfile
 
-from six import StringIO, text_type
+from six import (
+    PY3,
+    StringIO,
+    text_type,
+)
 from six.moves import filter
 from six.moves.urllib.request import urlopen
 
@@ -110,27 +114,30 @@ def convert_newlines(fname, in_place=True, tmp_dir=None, tmp_prefix="gxupload",
     """
     fd, temp_name = tempfile.mkstemp(prefix=tmp_prefix, dir=tmp_dir)
     i = 0
+    if PY3:
+        NEWLINE_BYTE = 10
+        CR_BYTE = 13
+    else:
+        NEWLINE_BYTE = "\n"
+        CR_BYTE = "\r"
     with io.open(fd, mode="wb") as fp:
         with io.open(fname, mode="rb") as fi:
-            line = b''
-            converted_line = b""
             last_char = None
             block = fi.read(block_size)
+            last_block = b""
             while block:
-                if last_char == "\r" and block.startswith(b"\n"):
-                    # last block ended with "\r", new block startswith "\n"
-                    # since we replace "\r" with "\n" in the previous iteration we skip the first byte
+                if last_char == CR_BYTE and block.startswith(b"\n"):
+                    # Last block ended with CR, new block startswith newline.
+                    # Since we replace CR with newline in the previous iteration we skip the first byte
                     block = block[1:]
-                # splitlines(True) splits at line terminators but keeps them so we can replace them
-                lines = block.splitlines(True)
-                for line in lines:
-                    converted_line = line.replace(b"\r\n", b"\n").replace(b"\r", b"\n")
-                    if b"\n" in converted_line:
-                        i += 1
-                    fp.write(converted_line)
-                last_char = util.unicodify(line, error='replace')[-1]
-                block = fi.read(block_size)
-            if not converted_line.endswith(b"\n"):
+                if block:
+                    last_char = block[-1]
+                    block = block.replace(b"\r\n", b"\n").replace(b"\r", b"\n")
+                    fp.write(block)
+                    i += block.count(b"\n")
+                    last_block = block
+                    block = fi.read(block_size)
+            if last_block and last_block[-1] != NEWLINE_BYTE:
                 i += 1
                 fp.write(b"\n")
     if in_place: