remove ternary, add test for one based flag

brentp · May 31, 2011 · 5bc5127 · 5bc5127
1 parent 131db65
commit 5bc5127
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Showing 2 changed files with 5 additions and 1 deletion.
diff --git a/pyfasta/fasta.py b/pyfasta/fasta.py
@@ -185,7 +185,7 @@ def sequence(self, f, asstring=True, auto_rc=True
             sequence = self._seq_from_keys(f, fasta, exon_keys)
 
         if sequence is None:
-            start = (f['start'] - 1) if one_based else f['start'] 
+            start = f['start'] - int(one_based) 
             sequence = fasta[start: f['stop']]
 
         if auto_rc and f.get('strand') in (-1, '-1', '-'):

diff --git a/tests/test_all.py b/tests/test_all.py
@@ -40,6 +40,7 @@ def test_classes():
             yield check_full_slice, f
             yield check_array_copy, f
             yield check_array, f
+            yield check_one_based, f
 
             fasta_name = f.fasta_name
 
@@ -234,6 +235,9 @@ def check_array_copy(f):
 
     assert a[1:5].tostring() == 'NNNN', a[1:5].tostring()
 
+def check_one_based(f):
+    assert f.sequence({'chr': 'chr1', 'start': 2, 'stop': 9})  == 'CTGACTGA'
+    assert f.sequence({'chr': 'chr1', 'start': 2, 'stop': 9}, one_based=False) == 'TGACTGA'
 
 if __name__ == "__main__":
     import nose