bugfixes

src/pydna/assembly.py

@@ -245,8 +245,8 @@ def __init__(self, frags=None, limit=25, algorithm=common_sub_strings):
                     if start1 <= ft.location.start and start2 + G.nodes[node2]["length"] >= ft.location.end
                 ]
 
-                for feat in feats:
-                    feat.location += -start1
+                # for feat in feats:
+                #     feat.location += -start1
 
                 G.add_edge(
                     node1,
@@ -304,10 +304,11 @@ def assemble_linear(self, start=None, end=None, max_nodes=None):
                 node,
                 "end",
                 piece=slice(start, len(lastfragment["mixed"])),
-                features=[f for f in lastfragment["features"] if start <= f.location.end],
+                features=[f for f in lastfragment["features"] if start <= f.location.start],
                 seq=lastfragment["mixed"],
                 name=lastfragment["name"],
             )
+            # breakpoint()
 
         # add edges from nodes in last reverse complement sequence to "end_rc"
         lastfragmentrc = self.rcfragments[lastfragment["mixed"]]
@@ -316,7 +317,7 @@ def assemble_linear(self, start=None, end=None, max_nodes=None):
                 node,
                 "end_rc",
                 piece=slice(start, len(lastfragmentrc["mixed"])),
-                features=[f for f in lastfragmentrc["features"] if start <= f.location.end],
+                features=[f for f in lastfragmentrc["features"] if start <= f.location.start],
                 seq=lastfragmentrc["mixed"],
                 name=lastfragmentrc["name"],
             )

src/pydna/design.py

@@ -18,7 +18,7 @@
 import math as _math
 import os as _os
 import copy as _copy
-
+from pydna.amplicon import Amplicon as _Amplicon
 from pydna.amplify import Anneal as _Anneal
 from pydna.amplify import pcr as _pcr
 from pydna.dseqrecord import Dseqrecord as _Dseqrecord
@@ -121,11 +121,14 @@ def design(target_tm, template):
         """returns a string"""
         tmp = 0
         length = limit
+        tlen = len(template)
         p = str(template.seq[:length])
         while tmp < target_tm:
             length += 1
             p = str(template.seq[:length])
             tmp = tm_func(p)
+            if length >= tlen:
+                break
         ps = p[:-1]
         tmps = tm_func(str(ps))
         _module_logger.debug(((p, tmp), (ps, tmps)))
@@ -179,7 +182,7 @@ def design(target_tm, template):
 
     ampl = _Anneal((fp, rp), template, limit=limit)
 
-    prod = ampl.products[0]
+    prod = ampl.products[0] if ampl.products else _Amplicon("")
 
     if len(ampl.products) > 1:
         import warnings as _warnings

tests/test_module_assembly.py

@@ -737,6 +737,57 @@ def test_marker_replacement_on_plasmid(monkeypatch):
     assert pMEC1135.features[-1].extract(pMEC1135).seq == candidate.features[-1].extract(candidate).seq
 
 
+def test_linear_with_annotations2(monkeypatch):
+    # Thanks to James Bagley for finding this bug
+    # https://github.com/JamesBagley
+    from pydna._pretty import pretty_str
+    from pydna.assembly import Assembly
+    from pydna.dseqrecord import Dseqrecord
+
+    a = Dseqrecord("acgatgctatactgtgCCNCCtgtgctgtgctcta")
+    a.add_feature(0, 10, label='a_feat')
+    a_feat_seq = a.features[0].extract(a)
+    # 12345678901234
+    b = Dseqrecord("tgtgctgtgctctaTTTTTTTtattctggctgtatcCCCCCC")
+    b.add_feature(0, 10, label='b_feat')
+    b_feat_seq = b.features[0].extract(b)
+
+    # 123456789012345
+    c = Dseqrecord("GtattctggctgtatcGGGGGtacgatgctatactgtg")
+    c.add_feature(0, 10, label='c_feat')
+    c_feat_seq = c.features[0].extract(c)
+
+    feature_sequences = {'a_feat': a_feat_seq, 'b_feat': b_feat_seq, 'c_feat': c_feat_seq}
+
+    a.name = "aaa"  # 1234567890123456
+    b.name = "bbb"
+    c.name = "ccc"
+    asm = Assembly((a, b, c), limit=14)
+    x = asm.assemble_linear()[0]
+    # print(x.features)
+    # print(x)
+    answer = 'aaa|14\n    \\/\n    /\\\n    14|bbb|15\n           \\/\n           /\\\n           15|ccc'
+
+    assert x.figure() == answer.strip()
+    answer = 'acgatgctatactgtgCCNCCtgtgctgtgctcta\n                     TGTGCTGTGCTCTA\n                     tgtgctgtgctctaTTTTTTTtattctggctgtatc\n                                          TATTCTGGCTGTATC\n                                          tattctggctgtatcGGGGGtacgatgctatactgtg\n'
+    assert x.detailed_figure()
+    for feat in x.features:
+        try:
+            assert feat.extract(x).seq == feature_sequences[feat.qualifiers['label']].seq
+        except AssertionError:
+            print(feat.qualifiers['label'])
+            print(feat.extract(x).seq, 'extracted feat')
+            print(feature_sequences[feat.qualifiers['label']].seq, 'original feat')
+            assert feat.extract(x).seq == feature_sequences[feat.qualifiers['label']].seq
+
+
+# acgatgctatactgtgCCNCCtgtgctgtgctcta
+#                      TGTGCTGTGCTCTA
+#                      tgtgctgtgctctaTTTTTTTtattctggctgtatcCCCCCC
+#                                           TATTCTGGCTGTATC
+#                                          GtattctggctgtatcGGGGGtacgatgctatactgtg
+
+
 if __name__ == "__main__":
     # pytest.main([__file__, "-x", "-vv", "-s"])
     pytest.main([__file__, "-x", "-vv", "-s", "--profile"])

tests/test_module_design.py

@@ -300,5 +300,14 @@ def test_circular_assembly_fragments2():
     )
 
 
+def test_too_short_template():
+    from pydna.amplicon import Amplicon
+    from pydna.design import primer_design
+    from pydna.dseqrecord import Dseqrecord
+
+    fragment = Dseqrecord("GCCACCATGG")
+    assert primer_design(fragment) == Amplicon("")
+
+
 if __name__ == "__main__":
     pytest.cmdline.main([__file__, "-v", "-s"])