finished notebook new cut implementation

pydna-group · Jan 25, 2024 · 9fa5684 · 9fa5684
1 parent c4acf48
commit 9fa5684
Showing 1 changed file with 30 additions and 13 deletions.
diff --git a/scripts/cutsite_pairs.ipynb b/scripts/cutsite_pairs.ipynb
@@ -80,12 +80,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Note how if the ovhg is negative, for an origin spanning cutsite, the position lies on the left side of the origin, and viceversa."
+    "Note in the above printed output how if the ovhg is negative, for an origin spanning cutsite, the position lies on the left side of the origin, and viceversa.\n",
+    "\n",
+    "Below, you can see that the `cut_watson` is defined with respect to the \"full sequence\""
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
@@ -124,16 +126,30 @@
    "metadata": {},
    "source": [
     "Cuts are only returned if the recognition site and overhang are on the double-strand part\n",
-    "of the sequence. Not 100% sure if that's the \"right\" way to do it."
+    "of the sequence."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[((1, -4), EcoRI)]\n",
+      "[]\n"
+     ]
+    }
+   ],
    "source": [
-    "\n"
+    "\n",
+    "seq = Dseq('GAATTC')\n",
+    "print(seq.get_cutsites([EcoRI]))\n",
+    "\n",
+    "seq = Dseq.from_full_sequence_and_overhangs('GAATTC', -1, 0)\n",
+    "print(seq.get_cutsites([EcoRI]))"
    ]
   },
   {
@@ -144,7 +160,7 @@
     "\n",
     "## Pairing cutsites\n",
     "\n",
-    "A fragment produced by restriction is represented by a tuple of length two that may contain cutsites or `None`:\n",
+    "A fragment produced by restriction is represented by a tuple of length 2 that may contain cutsites or `None`:\n",
     "\n",
     "- Two cutsites: represents the extraction of a fragment between those two cutsites, in that orientation. To represent the opening of a circular molecule with a single cutsite, we put the same cutsite twice. See below.\n",
     "- `None`, cutsite: represents the extraction of a fragment between the left edge of linear sequence and the cutsite.\n",
@@ -157,7 +173,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -190,8 +206,8 @@
    "source": [
     "dseq = Dseq('aaGAATTCaaGAATTCaa')\n",
     "cutsites = dseq.get_cutsites([EcoRI])\n",
-    "cutsite_pairs = dseq.get_cutsite_pairs(cutsites)\n",
     "\n",
+    "cutsite_pairs = dseq.get_cutsite_pairs(cutsites)\n",
     "pair_types = ['None, cutsite', 'cutsite, cutsite', 'cutsite, None']\n",
     "\n",
     "for pair, pair_type in zip(cutsite_pairs, pair_types):\n",
@@ -210,7 +226,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -228,11 +244,12 @@
     }
    ],
    "source": [
-    "# Note that the cutsite respects the ovhg of the sequence:\n",
+    "# Note that the cutsite respects the ovhg of the parent sequence:\n",
     "dseq = Dseq.from_full_sequence_and_overhangs('aaGAATTCaaGAATTCaa', 1, 1)\n",
-    "print(dseq.apply_cut(*cutsite_pairs[0]).__repr__())\n",
+    "f1, f2, f3 = dseq.cut([EcoRI])\n",
+    "print(f1.__repr__())\n",
     "print()\n",
-    "print(dseq.apply_cut(*cutsite_pairs[-1]).__repr__())\n"
+    "print(f3.__repr__())\n"
    ]
   }
  ],