From 20d6b0b6bbf7e69e69f1198aac794784e85409c2 Mon Sep 17 00:00:00 2001 From: sehilyi Date: Tue, 12 Dec 2023 19:06:40 -0500 Subject: [PATCH] chore: clean outputs of jupyter notebook --- python/notebooks/playground.ipynb | 120 ++---------------------------- 1 file changed, 5 insertions(+), 115 deletions(-) diff --git a/python/notebooks/playground.ipynb b/python/notebooks/playground.ipynb index 60f24d9e..ce8926cd 100644 --- a/python/notebooks/playground.ipynb +++ b/python/notebooks/playground.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "efd78655-78fa-46cc-856e-bef3163ceb46", "metadata": { "tags": [] @@ -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", @@ -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", - "