diff --git a/tools/fasta_tools/fasta_tool_filter_by_length.py b/tools/fasta_tools/fasta_tool_filter_by_length.py
index c8b96af1060..df62379e6a9 100644
--- a/tools/fasta_tools/fasta_tool_filter_by_length.py
+++ b/tools/fasta_tools/fasta_tool_filter_by_length.py
@@ -15,7 +15,7 @@ def parse_fasta_format(file_handle):
     tmp_seq = ''
     tmp_seq_count = 0
     for i, each_line in enumerate(file_handle):
-        each_line = each_line.rstrip('\n')
+        each_line = each_line.rstrip('\r\n')
         if (each_line[0] == '>'):
             if (len(tmp_seq) > 0):
                 tmp_seq_count += 1
diff --git a/tools/fasta_tools/tabular_to_fasta.py b/tools/fasta_tools/tabular_to_fasta.py
index b57c109d8d8..997825447d3 100644
--- a/tools/fasta_tools/tabular_to_fasta.py
+++ b/tools/fasta_tools/tabular_to_fasta.py
@@ -30,7 +30,7 @@ def __main__():
     out = open( outfile, 'w' )
 
     for i, line in enumerate( open( infile ) ):
-        line = line.rstrip( '\n' )
+        line = line.rstrip( '\r\n' )
         fields = line.split()
         fasta_title = []
         for j in title_col_list: