Update notebook

Author: jwinter3

docs/notebooks/base_sequence_quality.ipynb

@@ -10,20 +10,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 14,
    "id": "58b40aa6",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/jwinter/TBD/proj2/polars-bio/venv/lib/python3.12/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
-      "  from .autonotebook import tqdm as notebook_tqdm\n",
-      "INFO:polars_bio:Creating BioSessionContext\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import pandas as pd\n",
     "\n",
@@ -40,7 +30,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 15,
    "id": "b0d81403",
    "metadata": {},
    "outputs": [],
@@ -58,26 +48,26 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 16,
    "id": "0420c240",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "    pos        avg    q1  median    q3  lower  upper\n",
-      "88    0  32.548723  31.0    34.0  34.0   26.5   38.5\n",
-      "46    1  32.719772  31.0    34.0  34.0   26.5   38.5\n",
-      "99    2  32.789697  31.0    34.0  34.0   26.5   38.5\n",
-      "75    3  36.162011  37.0    37.0  37.0   37.0   37.0\n",
-      "84    4  36.122733  37.0    37.0  37.0   37.0   37.0\n",
-      "..  ...        ...   ...     ...   ...    ...    ...\n",
-      "19   96  32.998462  34.0    35.0  35.0   32.5   36.5\n",
-      "64   97  32.922582  33.0    35.0  35.0   30.0   38.0\n",
-      "70   98  32.883908  33.0    35.0  35.0   30.0   38.0\n",
-      "80   99  32.836223  33.0    35.0  35.0   30.0   38.0\n",
-      "51  100  31.190304  30.0    34.0  35.0   22.5   42.5\n",
+      "    pos     avg    q1  median    q3  lower  upper\n",
+      "46    0  30.135  31.0    33.0  34.0   26.5   38.5\n",
+      "14    1  31.210  31.0    34.0  34.0   26.5   38.5\n",
+      "54    2  32.015  31.0    34.0  34.0   26.5   38.5\n",
+      "99    3  35.690  35.0    37.0  37.0   32.0   40.0\n",
+      "7     4  35.680  35.0    37.0  37.0   32.0   40.0\n",
+      "..  ...     ...   ...     ...   ...    ...    ...\n",
+      "95   96  31.315  32.0    34.0  35.0   27.5   39.5\n",
+      "62   97  30.670  31.0    34.0  35.0   25.0   41.0\n",
+      "67   98  31.550  32.0    34.0  35.0   27.5   39.5\n",
+      "53   99  31.250  32.0    34.0  35.0   27.5   39.5\n",
+      "55  100  31.105  31.0    34.0  35.0   25.0   41.0\n",
       "\n",
       "[101 rows x 7 columns]\n"
      ]
@@ -98,7 +88,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 17,
    "id": "7322aae3",
    "metadata": {},
    "outputs": [
@@ -145,7 +135,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 18,
    "id": "66c3af24",
    "metadata": {},
    "outputs": [
@@ -182,7 +172,7 @@
        "└─────┴────────┴──────┴────────┴──────┴───────┴───────┘"
       ]
      },
-     "execution_count": 20,
+     "execution_count": 18,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -201,7 +191,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 19,
    "id": "a2cb9c97",
    "metadata": {},
    "outputs": [
@@ -238,7 +228,7 @@
        "└─────┴────────┴──────┴────────┴──────┴───────┴───────┘"
       ]
      },
-     "execution_count": 21,
+     "execution_count": 19,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -257,7 +247,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 20,
    "id": "1899ca01",
    "metadata": {},
    "outputs": [
@@ -279,7 +269,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "200rows [00:00, 211459.74rows/s]\n"
+      "200rows [00:00, 212477.41rows/s]\n"
      ]
     },
     {
@@ -315,7 +305,7 @@
        "└─────┴────────┴──────┴────────┴──────┴───────┴───────┘"
       ]
      },
-     "execution_count": 22,
+     "execution_count": 20,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -336,7 +326,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 21,
    "id": "7830b8aa",
    "metadata": {},
    "outputs": [
@@ -345,7 +335,7 @@
      "output_type": "stream",
      "text": [
       "INFO:polars_bio:Table: example registered for path: ./example.fastq\n",
-      "200rows [00:00, 182877.87rows/s]"
+      "200rows [00:00, 177236.59rows/s]"
      ]
     },
     {
@@ -395,7 +385,7 @@
        "└─────┴────────┴──────┴────────┴──────┴───────┴───────┘"
       ]
      },
-     "execution_count": 23,
+     "execution_count": 21,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -417,7 +407,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 22,
    "id": "56817174",
    "metadata": {},
    "outputs": [
@@ -426,7 +416,7 @@
      "output_type": "stream",
      "text": [
       "INFO:polars_bio:Table: example registered for path: ./example.fastq\n",
-      "200rows [00:00, 193508.84rows/s]"
+      "200rows [00:00, 74651.67rows/s]"
      ]
     },
     {
@@ -476,7 +466,7 @@
        "└─────┴────────┴──────┴────────┴──────┴───────┴───────┘"
       ]
      },
-     "execution_count": 24,
+     "execution_count": 22,
      "metadata": {},
      "output_type": "execute_result"
     }