diff --git a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
index 5a54570f060..53d683ead57 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
+++ b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
@@ -27,7 +27,7 @@ def __main__():
         else:
             if line:
                 sequence += line
-                if line.split()[0].isdigit():
+                if line.split() and line.split()[0].isdigit():
                     sequence += ' '
     if sequence:
         seq_hash[( sequence_count, title )] = sequence
diff --git a/tools/fasta_tools/fasta_compute_length.py b/tools/fasta_tools/fasta_compute_length.py
index 8714659bd85..3893072844b 100644
--- a/tools/fasta_tools/fasta_compute_length.py
+++ b/tools/fasta_tools/fasta_compute_length.py
@@ -34,7 +34,7 @@ def __main__():
             tmp_seq = ''
         else:
             tmp_seq = "%s%s" % ( tmp_seq, line )
-            if line.split()[0].isdigit():
+            if line.split() and line.split()[0].isdigit():
                 tmp_seq = "%s " % tmp_seq
     if len( tmp_seq ) > 0:
         seq_hash[ ( tmp_seq_count, tmp_title ) ] = tmp_seq
diff --git a/tools/fasta_tools/fasta_to_tabular.py b/tools/fasta_tools/fasta_to_tabular.py
index 6aa433cd499..42e79e63e2a 100644
--- a/tools/fasta_tools/fasta_to_tabular.py
+++ b/tools/fasta_tools/fasta_to_tabular.py
@@ -35,7 +35,7 @@ def __main__():
             sequence = ''
         else:
             sequence = "%s%s" % ( sequence, line )
-            if line.split()[0].isdigit():
+            if line.split() and line.split()[0].isdigit():
                 sequence += ' '
     if sequence:
         seq_hash[( sequence_count, title )] = sequence