Code refactor

mourisl · Sep 7, 2024 · ddb7137 · ddb7137
1 parent f0b7eb1
commit ddb7137
Showing 1 changed file with 38 additions and 12 deletions.
diff --git a/vizMSA_dev.ipynb b/vizMSA_dev.ipynb
@@ -44,7 +44,26 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 251,
+   "execution_count": null,
+   "id": "f8508020-34de-4cd6-8988-8bc1d57990c9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def GetStartEnd(msa, start, end):\n",
+    "    length = len(msa[0])\n",
+    "    if (start == None):\n",
+    "        start = 0\n",
+    "    elif (start < 0):\n",
+    "        start = length + start \n",
+    "    if (end == None):\n",
+    "        end = length - 1 \n",
+    "    elif (end < 0):\n",
+    "        end = length + end "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 253,
    "id": "37d12119-b410-453a-8ce4-ee254fb4b957",
    "metadata": {},
    "outputs": [],
@@ -61,14 +80,7 @@
     "    length = len(msa[0])\n",
     "    \n",
     "    # start, end: draw the [start,end] (both inclusive) region of the MSA\n",
-    "    if (start == None):\n",
-    "        start = 0\n",
-    "    elif (start < 0):\n",
-    "        start = length + start \n",
-    "    if (end == None):\n",
-    "        end = length - 1 \n",
-    "    elif (end < 0):\n",
-    "        end = length + end \n",
+    "    start, end = GetStartEnd(msa, start, end)\n",
     "    \n",
     "    if (axlim == None):\n",
     "        # Strange, why cols should be length, not end-start+1?\n",
@@ -123,20 +135,32 @@
     "    return ax"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "36e9ef94-9873-4ff2-9813-4ff62a4e575b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def GetConsensus(msa, start = None, end = None):\n",
+    "    "
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "id": "b8ca0d92-042e-4082-82b2-795084714cf5",
    "metadata": {},
    "outputs": [],
    "source": [
-    "def DrawMSAConsensus(msa, start = None, end = None):\n",
-    "    return"
+    "def DrawMSAConsensusHisto(msa, start = None, end = None, ax=None):\n",
+    "    ax = ax or plt.gca()\n",
+    "    "
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 247,
+   "execution_count": 255,
    "id": "9857702b-904f-4aa8-a330-d867bb91afd0",
    "metadata": {},
    "outputs": [
@@ -152,6 +176,8 @@
     }
    ],
    "source": [
+    "ax = plt.gca()\n",
+    "ax.set(xlim=[-20,20], ylim=[-20, 20])\n",
     "ax=DrawMSA(msa=[\"AC-G-T\", \"A-CGT-\"], seq_names = [\"r1\", \"r2\"],\n",
     "           start = 1, end = 3, color_order=\"ACGT-\")"
    ]