variant effect scripts

kundajelab · Aug 27, 2024 · d5448e4 · d5448e4
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diff --git a/src/evaluation/figure_notebooks/figure_4/4d_marginal_footprinting_motifs.ipynb b/src/evaluation/figure_notebooks/figure_4/4d_marginal_footprinting_motifs.ipynb
diff --git a/src/evaluation/figure_notebooks/figure_5/5a_motif_grid_uncorrected.ipynb b/src/evaluation/figure_notebooks/figure_5/5a_motif_grid_uncorrected.ipynb
diff --git a/src/evaluation/figure_notebooks/figure_5/5b_marginal_footprinting_motifs_atac.ipynb b/src/evaluation/figure_notebooks/figure_5/5b_marginal_footprinting_motifs_atac.ipynb
diff --git a/src/evaluation/figure_notebooks/figure_5/5b_marginal_footprinting_motifs_dnase.ipynb b/src/evaluation/figure_notebooks/figure_5/5b_marginal_footprinting_motifs_dnase.ipynb
diff --git a/src/evaluation/figure_notebooks/figure_5/5d_heterodimers_coordinated_effect-ap1-tead.ipynb b/src/evaluation/figure_notebooks/figure_5/5d_heterodimers_coordinated_effect-ap1-tead.ipynb
diff --git a/src/evaluation/figure_notebooks/figure_5/5e_heterodimers_syntax_exhaustive_imr90.ipynb b/src/evaluation/figure_notebooks/figure_5/5e_heterodimers_syntax_exhaustive_imr90.ipynb
diff --git a/src/evaluation/figure_notebooks/figure_5/FOS_simulations.ipynb b/src/evaluation/figure_notebooks/figure_5/FOS_simulations.ipynb
@@ -3,6 +3,7 @@
   {
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    "execution_count": 1,
+   "id": "92299645",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -318,6 +319,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
+   "id": "aa5015e6",
    "metadata": {},
    "outputs": [
     {
@@ -336,6 +338,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
+   "id": "9d31abfc",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -399,6 +402,7 @@
   {
    "cell_type": "code",
    "execution_count": 9,
+   "id": "4053513a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -422,6 +426,7 @@
   {
    "cell_type": "code",
    "execution_count": 10,
+   "id": "5980fb41",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -431,6 +436,7 @@
   {
    "cell_type": "code",
    "execution_count": 22,
+   "id": "0585d7a3",
    "metadata": {
     "tags": []
    },
@@ -475,6 +481,7 @@
   {
    "cell_type": "code",
    "execution_count": 25,
+   "id": "823dd882",
    "metadata": {},
    "outputs": [
     {
@@ -553,6 +560,7 @@
   {
    "cell_type": "code",
    "execution_count": 26,
+   "id": "be437a4d",
    "metadata": {},
    "outputs": [
     {
@@ -631,35 +639,39 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "b47c5edc",
    "metadata": {},
    "outputs": [],
    "source": []
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "74df790f",
    "metadata": {},
    "outputs": [],
    "source": []
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "7c0e7639",
    "metadata": {},
    "outputs": [],
    "source": []
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "36b73f37",
    "metadata": {},
    "outputs": [],
    "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -673,7 +685,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.8.16"
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diff --git a/src/evaluation/figure_notebooks/figure_5/Untitled.ipynb b/src/evaluation/figure_notebooks/figure_5/Untitled.ipynb
diff --git a/src/evaluation/figure_notebooks/figure_5/amr_ad_values.ipynb b/src/evaluation/figure_notebooks/figure_5/amr_ad_values.ipynb
@@ -0,0 +1,170 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import json"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data = json.load(open(\"/oak/stanford/groups/akundaje/amr1/pho4_final/lite_data/preds/ets1_gm12878.json\"))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "13675"
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "len(set(data.keys()))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "13675"
+      ]
+     },
+     "execution_count": 11,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "len(data.keys())"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "100"
+      ]
+     },
+     "execution_count": 18,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "len(data['AAAAAAAAAAAAAACCGGAAATGGGTCCTACCATCT'][0])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "100"
+      ]
+     },
+     "execution_count": 19,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "len(data['AAAAAAAAAAAAAACCGGAAATGGGTCCTACCATCT'][1])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'0.008304882'"
+      ]
+     },
+     "execution_count": 20,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "data['AAAAAAAAAAAAAACCGGAAATGGGTCCTACCATCT'][2]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[0.8181924223899841, 0.8155251741409302]"
+      ]
+     },
+     "execution_count": 21,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "data['AAAAAAAAAAAAAACCGGAAATGGGTCCTACCATCT'][1][0]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}