update test

KalinNonchev · Nov 2, 2023 · 15fa51f · 15fa51f
1 parent f19164d
commit 15fa51f
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diff --git a/gnomad_db/pkgdata/.ipynb_checkpoints/gnomad_columns-checkpoint.yaml b/gnomad_db/pkgdata/.ipynb_checkpoints/gnomad_columns-checkpoint.yaml
diff --git a/scripts/GettingStartedwithGnomAD_DB.ipynb b/scripts/GettingStartedwithGnomAD_DB.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "09f4d260",
+   "id": "7303ebd0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -14,7 +14,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3fc686b3",
+   "id": "8d5a63f4",
    "metadata": {},
    "source": [
     "# Download SQLite preprocessed files\n",
@@ -27,7 +27,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "94f31d05",
+   "id": "f8529267",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -39,7 +39,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6c140086",
+   "id": "6bd9a9da",
    "metadata": {},
    "source": [
     "# Initialize Database"
@@ -48,7 +48,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4acdaab3",
+   "id": "c148a8df",
    "metadata": {
     "tags": [
      "parameters"
@@ -63,7 +63,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8c7b431e",
+   "id": "057a03cf",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -73,7 +73,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "34cea3dc",
+   "id": "6b664ad0",
    "metadata": {},
    "source": [
     "# Insert gnomAD variants into the database from single tsv file\n",
@@ -83,7 +83,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "dc60de98",
+   "id": "aa628e88",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -98,7 +98,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c3dcd83a",
+   "id": "2e0f8963",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -108,7 +108,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a837251b",
+   "id": "f7ee891c",
    "metadata": {},
    "source": [
     "# Query MAF"
@@ -117,7 +117,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "21de3d07",
+   "id": "b196b5e6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -128,7 +128,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "277d0201",
+   "id": "b3d2d014",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -138,7 +138,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7eb48461",
+   "id": "76b08258",
    "metadata": {},
    "source": [
     "## You can pass a dataframe with variants\n",
@@ -148,7 +148,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c62a4754",
+   "id": "00010e64",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -158,7 +158,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c179fedc",
+   "id": "da779a49",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -168,7 +168,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "44969569",
+   "id": "ac19d6eb",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -178,7 +178,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1a37c4e5",
+   "id": "bffce318",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -193,7 +193,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "537d8d7e",
+   "id": "a4108e52",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -202,7 +202,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7bbe5975",
+   "id": "c4818aec",
    "metadata": {},
    "source": [
     "## You can pass a single string as a variant"
@@ -211,7 +211,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14a15cf6",
+   "id": "2e788375",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -221,7 +221,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f667cb7d",
+   "id": "478d114f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -230,7 +230,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "81251ef8",
+   "id": "5b2d8caf",
    "metadata": {},
    "source": [
     "## You can look for the MAF scores in an interval"
@@ -239,7 +239,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "dababf3a",
+   "id": "efa19fcc",
    "metadata": {},
    "outputs": [],
    "source": [

diff --git a/scripts/README.md b/scripts/README.md
@@ -12,7 +12,7 @@ database_location: "test_out" # where to create the database, make sure you have
 gnomad_vcf_location: "data" # where are your *.vcf.bgz located
 tables_location: "test_out" # where to store the preprocessed intermediate files, you can leave it like this 
 script_locations: "test_out" # where to store the scripts, where you can check the progress of your jobs, you can leave it like this
-genome: "Grch37" # genome version of the gnomAD vcf file (2.1.1 = Grch37, 3.1.1 = Grch38)
+gnomad_version: "v4" # genome version of the gnomAD vcf file (e.g., v2, v3, v4)
 ```
 
 Once this is done, run