Neither BitBucket or GitHub currently allow include in *.rst

github/markup#172
https://bitbucket.org/site/master/issue/5411/restructuredtext-include-directive

reading_sequence_files/README.rst

@@ -103,7 +103,12 @@ Instead, using your favourite editor (e.g. ``nano`` or ``gedit``) create a plain
 text file (in the same directory as the *E. coli* files) named ``count_fasta.py``
 which contains the following::
 
-.. include:: count_fasta.py
+    from Bio import SeqIO
+    filename = "NC_000913.faa"
+    count = 0
+    for record in SeqIO.parse(filename, "fasta"):
+        count = count + 1
+    print("There were " + str(count) + " records in file " + filename)
 
 This time it should be easy to copy & paste in one go. We can now run this::