From 222d643f65d24dc468a26a5e88a31c855388069f Mon Sep 17 00:00:00 2001
From: BjornFJohansson <bjornjobb@gmail.com>
Date: Tue, 19 Dec 2023 07:50:39 +0000
Subject: [PATCH] fusion PCR kind of works

---
 src/pydna/fusionpcr.py         | 40 ++++++++++++++++++++++++++--------
 tests/test_module_fusionpcr.py | 27 ++++++++++-------------
 2 files changed, 43 insertions(+), 24 deletions(-)

diff --git a/src/pydna/fusionpcr.py b/src/pydna/fusionpcr.py
index e8533805..cee6cfe1 100644
--- a/src/pydna/fusionpcr.py
+++ b/src/pydna/fusionpcr.py
@@ -26,15 +26,20 @@ def anneal(x, y, limit=limit):
                     new = Dseqrecord(Dseq(a.seq.watson, b.seq.crick, ovhg=-s1))
                     new.features = copy(a.features)
                     new.features.extend([f._shift(s1) for f in b.features])
-                    new.parents = b, a  # Setting a new property dynamically
+                    new.left = b  # Setting a new property dynamically
+                    new.right = a  # Setting a new property dynamically
                 elif s1 == 0:
                     new = Dseqrecord(Dseq(b.seq.watson, a.seq.crick, ovhg=-s2))
                     new.features = copy(b.features)
                     new.features.extend([f._shift(s2) for f in a.features])
-                    new.parents = b, a  # Setting a new property dynamically
+                    new.left = a  # Setting a new property dynamically
+                    new.right = b  # Setting a new property dynamically
         return new
 
     argument = fragments
+    for arg in argument:
+        arg.left = None
+        arg.right = None
     newfragments = []
     while True:
         for a, b in combinations(fragments, 2):
@@ -50,15 +55,32 @@ def anneal(x, y, limit=limit):
             newfragments = []
         else:
             break
+
     return [x for x in fragments if x not in argument]
 
 
-if __name__ == "__main__":
-    import os as _os
+def list_parts(fusion_pcr_fragment):
+    stack = [fusion_pcr_fragment]
+    processed = []
+
+    while stack:
+        obj = stack.pop()
+        try:
+            a, b = obj.right, obj.left
+        except AttributeError:
+            pass
+        else:
+            stack.extend((a, b))
+        processed.append(obj)
+
+    parts = [x for x in processed[::-1] if x]
+
+    msg = "---\n\n"
 
-    cached = _os.getenv("pydna_cached_funcs", "")
-    _os.environ["pydna_cached_funcs"] = ""
-    import doctest
+    for part in parts:
+        if hasattr(part, "anneal"):
+            msg += repr(part.anneal) + "\n\n"
+            msg += f"{part.name}\n{part.seq.watson}\n{part.seq.crick[::-1]}\n\n---\n\n"
+        msg += repr(part.seq) + "\n\n"
 
-    doctest.testmod(verbose=True, optionflags=(doctest.ELLIPSIS | doctest.NORMALIZE_WHITESPACE))
-    _os.environ["pydna_cached_funcs"] = cached
+    return msg
diff --git a/tests/test_module_fusionpcr.py b/tests/test_module_fusionpcr.py
index 0ae8a64f..08df0207 100644
--- a/tests/test_module_fusionpcr.py
+++ b/tests/test_module_fusionpcr.py
@@ -78,21 +78,18 @@ def test_fusionpcr3():
         assert eq(result, r)
 
 
-# from Bio.SeqFeature import SeqFeature, SimpleLocation
-# x = Dseqrecord(Dseq("tctggtcaagctgaagggtattc"),
-#                features=[SeqFeature(SimpleLocation(5, 10, strand=1),
-#                                     type="misc_feature")])
-# y = Dseqrecord(Dseq("tattcgtacacagatg"),
-#                features=[SeqFeature(SimpleLocation(5, 10, strand=1),
-#                                     type="misc_feature")])
-# z = Dseqrecord(Dseq("acagatgacgtgt"),
-#                features=[SeqFeature(SimpleLocation(5, 10, strand=1),
-#                                     type="misc_feature")])
-
-
-# seqtuples = [ (x, y, z)]
-# for arg in seqtuples:
-#     result = fuse_by_pcr(arg, limit=5).pop()
+from Bio.SeqFeature import SeqFeature, SimpleLocation
+
+x = Dseqrecord(
+    Dseq("tctggtcaagctgaagggtattc"), features=[SeqFeature(SimpleLocation(5, 10, strand=1), type="misc_feature")]
+)
+y = Dseqrecord(Dseq("tattcgtacacagatg"), features=[SeqFeature(SimpleLocation(5, 10, strand=1), type="misc_feature")])
+z = Dseqrecord(Dseq("acagatgacgtgt"), features=[SeqFeature(SimpleLocation(5, 10, strand=1), type="misc_feature")])
+
+
+seqtuples = [(x, y, z)]
+for arg in seqtuples:
+    result = fuse_by_pcr(arg, limit=5).pop()
 
 
 if __name__ == "__main__":