Simplified how the Dseqrecord __add__ handles features. (#598)

* Simplified how the Dseqrecord __add__ handles features.
Now it simply observes the difference between the
length of the separate parts and the ligated fragment
without calling seq object methods. Also only one
loop to push features.

* Removed duplication and improved how adding something that is not a Dseqrecord/Dseq  is handled.

* fixed tailed primer

* reset kernel name

Author: BjornFJohansson

docs/notebooks/Example_Restriction.ipynb

@@ -585,8 +585,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "ACCATGTCGACATGCAAACAGTAATGATGGA , Tm:  57.24061148156318\n",
-      "GGCGCGCCATTAAAAGCCTTCTTCTCCC , Tm:  56.64459495003314\n"
+      "ACCATGTCGACATGCAAACAGTAATGATGGA , Tm:  58.57602926085667\n",
+      "GGCGCGCCATTAAAAGCCTTCTTCTCCC , Tm:  58.36015907667411\n"
      ]
     }
    ],
@@ -603,8 +603,8 @@
     "amplicon = primer_design(pombe_chromosome_I[min(gene):max(gene)], target_tm=55)\n",
     "\n",
     "fwd_align, rvs_align = amplicon.primers()\n",
-    "fwd_primer_ase1 = Dseqrecord(\"ACCATGTCGAC\") + fwd_align # Adding a SalI cut site\n",
-    "rvs_primer_ase1 = Dseqrecord(\"GGCGCGCCAT\") + rvs_align # Adding a AscI cut site\n",
+    "fwd_primer_ase1 = \"ACCATGTCGAC\" + fwd_align # Adding a SalI cut site\n",
+    "rvs_primer_ase1 = \"GGCGCGCCAT\" + rvs_align # Adding a AscI cut site\n",
     "\n",
     "# Printing out the primers\n",
     "\n",
@@ -622,13 +622,13 @@
      "output_type": "stream",
      "text": [
       "LOCUS       2263bp_PCR_prod         2263 bp    DNA     linear   UNK 01-JAN-1980\n",
-      "DEFINITION  pcr_product_description_description.\n",
+      "DEFINITION  pcr_product_f2242 CU329670.1_r2242 CU329670.1.\n",
       "ACCESSION   2263bp\n",
       "VERSION     2263bp\n",
       "DBLINK      BioProject: PRJNA13836\n",
       "            BioSample: SAMEA3138176\n",
       "KEYWORDS    .\n",
-      "SOURCE      .\n",
+      "SOURCE      \n",
       "  ORGANISM  .\n",
       "            .\n",
       "FEATURES             Location/Qualifiers\n",
@@ -653,13 +653,13 @@
       "                     NVPLSPPKQRVVNEHALNIMSEKLQRTNLKEQTPEMDIENSSQNLPFSPMKISPIRASP\n",
       "                     VKTIPSSPSPTTNIFSAPLNNITNCTPMEDEWGEEGF\"\n",
       "     primer_bind     12..31\n",
-      "                     /label=\"name\"\n",
+      "                     /label=\"f2242\"\n",
       "                     /PCR_conditions=\"primer\n",
       "                     sequence:ACCATGTCGACATGCAAACAGTAATGATGGA\"\n",
       "                     /ApEinfo_fwdcolor=\"#baffa3\"\n",
       "                     /ApEinfo_revcolor=\"#ffbaba\"\n",
       "     primer_bind     complement(2236..2254)\n",
-      "                     /label=\"name\"\n",
+      "                     /label=\"r2242\"\n",
       "                     /PCR_conditions=\"primer\n",
       "                     sequence:GGCGCGCCATTAAAAGCCTTCTTCTCCC\"\n",
       "                     /ApEinfo_fwdcolor=\"#baffa3\"\n",
@@ -759,7 +759,7 @@
       "ACCESSION   id\n",
       "VERSION     id\n",
       "KEYWORDS    .\n",
-      "SOURCE      .\n",
+      "SOURCE      \n",
       "  ORGANISM  .\n",
       "            .\n",
       "FEATURES             Location/Qualifiers\n",
@@ -861,13 +861,13 @@
       "                     NVPLSPPKQRVVNEHALNIMSEKLQRTNLKEQTPEMDIENSSQNLPFSPMKISPIRASP\n",
       "                     VKTIPSSPSPTTNIFSAPLNNITNCTPMEDEWGEEGF\"\n",
       "     primer_bind     3918..3937\n",
-      "                     /label=\"name\"\n",
+      "                     /label=\"f2242\"\n",
       "                     /PCR_conditions=\"primer\n",
       "                     sequence:ACCATGTCGACATGCAAACAGTAATGATGGA\"\n",
       "                     /ApEinfo_fwdcolor=\"#baffa3\"\n",
       "                     /ApEinfo_revcolor=\"#ffbaba\"\n",
       "     primer_bind     complement(6142..6160)\n",
-      "                     /label=\"name\"\n",
+      "                     /label=\"r2242\"\n",
       "                     /PCR_conditions=\"primer\n",
       "                     sequence:GGCGCGCCATTAAAAGCCTTCTTCTCCC\"\n",
       "                     /ApEinfo_fwdcolor=\"#baffa3\"\n",
@@ -1008,9 +1008,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.2"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

src/pydna/dseqrecord.py

@@ -812,22 +812,24 @@ def _repr_pretty_(self, p, cycle):
 
     def __add__(self, other):
         if hasattr(other, "seq") and hasattr(other.seq, "watson"):
+            # other is likely another Dseqrecord with a Dseq object
+            # deepcopy is necessary since we will change other's features
             other = copy.deepcopy(other)
-            other_five_prime = other.seq.five_prime_end()
-            if other_five_prime[0] == "5'":
-                # add other.seq.ovhg
-                for f in other.features:
-                    f.location = f.location + other.seq.ovhg
-            elif other_five_prime[0] == "3'":
-                # subtract other.seq.ovhg (sign change)
-                for f in other.features:
-                    f.location = f.location + (-other.seq.ovhg)
-
-            answer = Dseqrecord(SeqRecord.__add__(self, other))
-            answer.n = min(self.n, other.n)
+            newseq = self.seq + other.seq
+            # offset is the length of the self Dseq object added to the
+            # other Dseq object minus the sum of each length
+            # offset is <= 0
+            offset = len(newseq) - (len(self) + len(other))
+            for f in other.features:
+                # adding an integer to a feature location shifts it.
+                f.location = f.location + offset
         else:
-            answer = Dseqrecord(SeqRecord.__add__(self, Dseqrecord(other)))
-            answer.n = self.n
+            # If other is not a Dseqrecord with a Dseq object, the Dseq class
+            # handles the result of adding for consistency.
+            newseq = self.seq + other
+        answer = Dseqrecord(SeqRecord.__add__(self, other))
+        answer.n = min(self.n, getattr(other, "n", self.n))
+        answer.seq = newseq
         return answer
 
     def __mul__(self, number):