rename orfs method to find_orfs

rnajena · Oct 14, 2024 · 63d3402 · 63d3402
1 parent f01b6c7
commit 63d3402
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/sugar/core/seq.py b/sugar/core/seq.py
@@ -604,9 +604,9 @@ def matchall(self, *args, **kw):
         kw['matchall'] = True
         return self.match(*args, **kw)
 
-    def orfs(self, *args, **kw):
+    def find_orfs(self, *args, **kw):
         """
-        Find ORFS in the sequence, see `.find_orfs()`
+        Find ORFS in the sequence, see `~.cane.find_orfs()`
         """
         from sugar.core.cane import find_orfs
         return find_orfs(self, *args, **kw)
@@ -890,12 +890,12 @@ def matchall(self, *args, **kw):
         kw['matchall'] = True
         return self.match(*args, **kw)
 
-    def orfs(self, *args, **kw):
+    def find_orfs(self, *args, **kw):
         """
-        Find ORFS in sequences, see `.find_orfs()`
+        Find ORFS in sequences, see `~.cane.find_orfs()`
         """
         return reduce(lambda orfs1, orfs2: orfs1 + orfs2,
-                      [seq.orfs(*args, **kw) for seq in self])
+                      [seq.find_orfs(*args, **kw) for seq in self])
 
     def tofmtstr(self, fmt, **kw):
         out = io.StringIO()

diff --git a/sugar/tests/test_core_seq.py b/sugar/tests/test_core_seq.py
@@ -195,14 +195,14 @@ def test_match():
 
 def test_orf():
     seqs=read()
-    orfs = seqs[0].orfs()
+    orfs = seqs[0].find_orfs()
     assert len(orfs) > 0
     longest_orf = orfs.sort()[-1]
     assert seqs[0][longest_orf] == seqs[0]['cds']
 
-    orfs2 = seqs[0].orfs(rf='both')
+    orfs2 = seqs[0].find_orfs(rf='both')
     assert len(orfs2) > len(orfs)
 
-    orfs = seqs.orfs()
+    orfs = seqs.find_orfs()
     for id_ in seqs.ids:
         assert seqs.d[id_][orfs.d[id_].sort()[-1]] == seqs.d[id_]['cds']