Skip to content

Commit

Permalink
chore: clean outputs of jupyter notebook
Browse files Browse the repository at this point in the history
  • Loading branch information
@sehilyi
sehilyi committed Dec 13, 2023
1 parent c67c3e3 commit 20d6b0b
Showing 1 changed file with 5 additions and 115 deletions.
120 changes: 5 additions & 115 deletions python/notebooks/playground.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"id": "efd78655-78fa-46cc-856e-bef3163ceb46",
"metadata": {
"tags": []
Expand All @@ -15,14 +15,14 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"id": "632a94aa-aecf-491a-9656-45d38d72ceff",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"# !wget https://somatic-browser-test.s3.amazonaws.com/SVTYPE_SV_test_tumor_normal_with_panel.bedpe\n",
"!wget https://somatic-browser-test.s3.amazonaws.com/SVTYPE_SV_test_tumor_normal_with_panel.bedpe\n",
"\n",
"config = [{\n",
" \"id\": \"SRR7890905\",\n",
Expand Down Expand Up @@ -51,127 +51,17 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": null,
"id": "4487a2eb-83e6-47f8-a665-079a695b7f29",
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Collecting chromoscope\n",
" Obtaining dependency information for chromoscope from https://files.pythonhosted.org/packages/39/9c/86ef86cf387a5f9ebf0250a2620382fb37008d4e183da408580a580c62f5/chromoscope-0.0.2-py3-none-any.whl.metadata\n",
" Downloading chromoscope-0.0.2-py3-none-any.whl.metadata (2.9 kB)\n",
"Collecting jinja2 (from chromoscope)\n",
" Using cached Jinja2-3.1.2-py3-none-any.whl (133 kB)\n",
"Collecting servir>=0.0.5 (from chromoscope)\n",
" Obtaining dependency information for servir>=0.0.5 from https://files.pythonhosted.org/packages/31/4c/8090494565b40aba04642a197f1a859e23383d49988d49f94b32b4bbd261/servir-0.1.1-py3-none-any.whl.metadata\n",
" Downloading servir-0.1.1-py3-none-any.whl.metadata (2.8 kB)\n",
"Collecting portpicker (from servir>=0.0.5->chromoscope)\n",
" Obtaining dependency information for portpicker from https://files.pythonhosted.org/packages/32/2d/440e4d7041fff89f28f483733eb617127aa866135c2dc719e05893f089e1/portpicker-1.6.0-py3-none-any.whl.metadata\n",
" Downloading portpicker-1.6.0-py3-none-any.whl.metadata (1.5 kB)\n",
"Collecting starlette>=0.26.1 (from servir>=0.0.5->chromoscope)\n",
" Obtaining dependency information for starlette>=0.26.1 from https://files.pythonhosted.org/packages/cd/5b/77aabbfc64b335709d9f4ff9fb315ab63ccaeda7f5db1944cde75c22af12/starlette-0.33.0-py3-none-any.whl.metadata\n",
" Downloading starlette-0.33.0-py3-none-any.whl.metadata (5.8 kB)\n",
"Collecting uvicorn>=0.21.1 (from servir>=0.0.5->chromoscope)\n",
" Obtaining dependency information for uvicorn>=0.21.1 from https://files.pythonhosted.org/packages/7e/17/4b7a76fffa7babf397481040d8aef2725b2b81ae19f1a31b5ca0c17d49e6/uvicorn-0.24.0.post1-py3-none-any.whl.metadata\n",
" Downloading uvicorn-0.24.0.post1-py3-none-any.whl.metadata (6.4 kB)\n",
"Collecting MarkupSafe>=2.0 (from jinja2->chromoscope)\n",
" Obtaining dependency information for MarkupSafe>=2.0 from https://files.pythonhosted.org/packages/c0/c7/171f5ac6b065e1425e8fabf4a4dfbeca76fd8070072c6a41bd5c07d90d8b/MarkupSafe-2.1.3-cp311-cp311-macosx_10_9_x86_64.whl.metadata\n",
" Downloading MarkupSafe-2.1.3-cp311-cp311-macosx_10_9_x86_64.whl.metadata (3.0 kB)\n",
"Collecting anyio<5,>=3.4.0 (from starlette>=0.26.1->servir>=0.0.5->chromoscope)\n",
" Obtaining dependency information for anyio<5,>=3.4.0 from https://files.pythonhosted.org/packages/85/4f/d010eca6914703d8e6be222165d02c3e708ed909cdb2b7af3743667f302e/anyio-4.1.0-py3-none-any.whl.metadata\n",
" Downloading anyio-4.1.0-py3-none-any.whl.metadata (4.5 kB)\n",
"Collecting click>=7.0 (from uvicorn>=0.21.1->servir>=0.0.5->chromoscope)\n",
" Obtaining dependency information for click>=7.0 from https://files.pythonhosted.org/packages/00/2e/d53fa4befbf2cfa713304affc7ca780ce4fc1fd8710527771b58311a3229/click-8.1.7-py3-none-any.whl.metadata\n",
" Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB)\n",
"Collecting h11>=0.8 (from uvicorn>=0.21.1->servir>=0.0.5->chromoscope)\n",
" Using cached h11-0.14.0-py3-none-any.whl (58 kB)\n",
"Requirement already satisfied: psutil in /Users/sehilyi/.local/lib/python3.11/site-packages (from portpicker->servir>=0.0.5->chromoscope) (5.9.6)\n",
"Collecting idna>=2.8 (from anyio<5,>=3.4.0->starlette>=0.26.1->servir>=0.0.5->chromoscope)\n",
" Obtaining dependency information for idna>=2.8 from https://files.pythonhosted.org/packages/c2/e7/a82b05cf63a603df6e68d59ae6a68bf5064484a0718ea5033660af4b54a9/idna-3.6-py3-none-any.whl.metadata\n",
" Downloading idna-3.6-py3-none-any.whl.metadata (9.9 kB)\n",
"Collecting sniffio>=1.1 (from anyio<5,>=3.4.0->starlette>=0.26.1->servir>=0.0.5->chromoscope)\n",
" Using cached sniffio-1.3.0-py3-none-any.whl (10 kB)\n",
"Downloading chromoscope-0.0.2-py3-none-any.whl (3.6 kB)\n",
"Downloading servir-0.1.1-py3-none-any.whl (11 kB)\n",
"Downloading MarkupSafe-2.1.3-cp311-cp311-macosx_10_9_x86_64.whl (13 kB)\n",
"Downloading starlette-0.33.0-py3-none-any.whl (70 kB)\n",
"\u001b[2K \u001b[38;2;114;156;31m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m70.1/70.1 kB\u001b[0m \u001b[31m2.2 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[?25hDownloading uvicorn-0.24.0.post1-py3-none-any.whl (59 kB)\n",
"\u001b[2K \u001b[38;2;114;156;31m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m59.7/59.7 kB\u001b[0m \u001b[31m1.8 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[?25hDownloading portpicker-1.6.0-py3-none-any.whl (16 kB)\n",
"Downloading anyio-4.1.0-py3-none-any.whl (83 kB)\n",
"\u001b[2K \u001b[38;2;114;156;31m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m83.9/83.9 kB\u001b[0m \u001b[31m2.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[?25hUsing cached click-8.1.7-py3-none-any.whl (97 kB)\n",
"Downloading idna-3.6-py3-none-any.whl (61 kB)\n",
"\u001b[2K \u001b[38;2;114;156;31m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m61.6/61.6 kB\u001b[0m \u001b[31m1.8 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[?25hInstalling collected packages: sniffio, portpicker, MarkupSafe, idna, h11, click, uvicorn, jinja2, anyio, starlette, servir, chromoscope\n",
"Successfully installed MarkupSafe-2.1.3 anyio-4.1.0 chromoscope-0.0.2 click-8.1.7 h11-0.14.0 idna-3.6 jinja2-3.1.2 portpicker-1.6.0 servir-0.1.1 sniffio-1.3.0 starlette-0.33.0 uvicorn-0.24.0.post1\n",
"\n",
"\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m A new release of pip is available: \u001b[0m\u001b[31;49m23.2.1\u001b[0m\u001b[39;49m -> \u001b[0m\u001b[32;49m23.3.1\u001b[0m\n",
"\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n",
"here\n"
]
},
{
"data": {
"text/html": [
"\n",
"<iframe src=\"https://chromoscope.bio/app?external=http://localhost:56417/resources/9c1f0ba-content.json\" frameborder=\"0\" allowfullscreen style=\"width:100%;height:700px;\" />\n"
],
"text/plain": [
"<chromoscope._viewer.Viewer at 0x11820f990>"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"!pip install chromoscope\n",
"from chromoscope import Viewer\n",
"\n",
"Viewer.from_config(config)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "28a79bde-3cf5-43ea-92e5-b83f1a8a44ae",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
"<iframe src=\"https://chromoscope.bio?external=http://localhost:54230/resources/24aeb90-content.json\" frameborder=\"0\" allowfullscreen style=\"width:100%;height:700px;\" />\n"
],
"text/plain": [
"<chromoscope._viewer.Viewer at 0x7fdb70344dc0>"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"outputs": [],
"source": [
"from chromoscope import Viewer\n",
"\n",
"Viewer.from_config(config)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "642a0a11-fada-4537-9b60-b8e3a241d5a5",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand Down

0 comments on commit 20d6b0b

Please sign in to comment.