28 June 00 Brad

* Fix to Andrew's FASTA.py so that it imports modules inside the Bio namespace.
* Fixed setup.py. The ext_modules item in setup.py was missing commas between the tuples so it wouldn't build.

Bio/SeqIO/FASTA.py

@@ -1,14 +1,14 @@
 import string
-import Alphabet
+import Bio.Alphabet
 
-from Seq import Seq
-from SeqRecord import SeqRecord
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
 
 # This can be made a lot faster by using infile.readlines!
 # (Alas, that's a bit complicated to write.)
 
 class FastaReader:
-    def __init__(self, infile, alphabet = Alphabet.generic_alphabet):
+    def __init__(self, infile, alphabet = Bio.Alphabet.generic_alphabet):
         self.infile = infile
         self.alphabet = alphabet
 

setup.py

@@ -33,10 +33,10 @@
                 ],
       ext_modules = [('Bio.Tools.Classification.cSVM',
                       { 'sources' : ['Bio/Tools/Classification/cSVMmodule.c'] }
-                      )
+                      ),
                      ('Bio.Tools.clistfns',
                       { 'sources' : ['Bio/Tools/clistfnsmodule.c'] }
-                      )
+                      ),
                      ('Bio.Tools.cmathfns',
                       { 'sources' : ['Bio/Tools/cmathfnsmodule.c'] }
                       )