deploy: b428c2a

RasmussenLab · May 29, 2024 · e45eed1 · e45eed1
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diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/scripts/0_Tutorial.doctree b/.doctrees/scripts/0_Tutorial.doctree
diff --git a/.doctrees/scripts/1_Data_obtention.doctree b/.doctrees/scripts/1_Data_obtention.doctree
diff --git a/.doctrees/scripts/2_Run_CLASTER.doctree b/.doctrees/scripts/2_Run_CLASTER.doctree
diff --git a/.doctrees/scripts/2b_Run_HyenaDNA_and_Enformer.doctree b/.doctrees/scripts/2b_Run_HyenaDNA_and_Enformer.doctree
diff --git a/.doctrees/scripts/3_Data_analysis.doctree b/.doctrees/scripts/3_Data_analysis.doctree
diff --git a/_sources/scripts/0_Tutorial.ipynb b/_sources/scripts/0_Tutorial.ipynb
@@ -83,7 +83,11 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-input"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Import the required packages\n",
@@ -118,7 +122,11 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-input"
+    ]
+   },
    "outputs": [],
    "source": [
     "def visualize_input_array(a,\n",
@@ -246,7 +254,12 @@
   {
    "cell_type": "code",
    "execution_count": 59,
-   "metadata": {},
+   "metadata": {
+    "lines_to_next_cell": 2,
+    "tags": [
+     "hide-input"
+    ]
+   },
    "outputs": [
     {
      "data": {
@@ -309,7 +322,7 @@
     "                     scaling_factor,\n",
     "                     track_dict)\n",
     "    fig.show()\n",
-    "    plot_microc_original_and_rotated(pathlist, num_bins, window_of_observation, name=f\"{sample_name}_{orientation}.npy\")\n"
+    "    plot_microc_original_and_rotated(pathlist, num_bins, window_of_observation, name=f\"{sample_name}_{orientation}.npy\")"
    ]
   },
   {
@@ -327,7 +340,11 @@
   {
    "cell_type": "code",
    "execution_count": 60,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-input"
+    ]
+   },
    "outputs": [
     {
      "data": {
@@ -762,7 +779,11 @@
   {
    "cell_type": "code",
    "execution_count": 64,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-input"
+    ]
+   },
    "outputs": [
     {
      "name": "stdout",
@@ -844,7 +865,11 @@
   {
    "cell_type": "code",
    "execution_count": 5,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-input"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Create folder to store configuration files\n",
@@ -1430,7 +1455,11 @@
   {
    "cell_type": "code",
    "execution_count": 22,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-input"
+    ]
+   },
    "outputs": [],
    "source": [
     "#### Functions:\n",
@@ -1541,7 +1570,7 @@
     "    fig.legend(bbox_to_anchor=(.48,.8), fancybox=True, shadow=False, fontsize=7)\n",
     "\n",
     "    return fig\n",
-    "    "
+    "    \n"
    ]
   },
   {
@@ -1555,7 +1584,12 @@
   {
    "cell_type": "code",
    "execution_count": 23,
-   "metadata": {},
+   "metadata": {
+    "lines_to_next_cell": 2,
+    "tags": [
+     "hide-input"
+    ]
+   },
    "outputs": [
     {
      "data": {
@@ -1597,7 +1631,7 @@
     "    line_a = actual.loc[f\"{sample_name}_forward\"].values\n",
     "\n",
     "    fig = plot_target_predictions(line_p, line_a)\n",
-    "    fig.show()\n"
+    "    fig.show()"
    ]
   },
   {
@@ -1620,6 +1654,9 @@
   }
  ],
  "metadata": {
+  "jupytext": {
+   "formats": "ipynb,py:percent"
+  },
   "kernelspec": {
    "display_name": "Python 3.11.9 ('claster_env_tutorial')",
    "language": "python",
@@ -1637,7 +1674,6 @@
    "pygments_lexer": "ipython3",
    "version": "3.undefined.undefined"
   },
-  "orig_nbformat": 4,
   "vscode": {
    "interpreter": {
     "hash": "12187645b0fe86aeeeb7c7a27e94503590520c2ee4730b6cfd81a67885c82988"