{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Advanced ploidy estimation\n", "\n", "For instructions on installation and basic exploration steps, see [Getting started](getting_started.ipynb)." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Compiling C scripts...\n", "Done.\n" ] } ], "source": [ "import isomut2py as im2\n", "%matplotlib inline" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Ploidy estimation from scratch\n", "\n", "For a complete tutorial on how to perform ploidy estimation from a single bam file, we will be using the raw example dataset, that can be downloaded with:" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": true, "nbsphinx": "hidden" }, "outputs": [], "source": [ "exampleRawDataDir = 'isomut2py_download_dir/'" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Downloading file from URL \"http://genomics.hu/tools/isomut2py/isomut2py_raw_example_dataset.tar.gz\" to isomut2py_download_dir/isomut2py_raw_example_dataset.tar.gz\n", "File size: 528.5MiB\n", "Downloading might take a while...\n", "Download completed in 0 day(s), 2 hour(s), 49 min(s), 55 sec(s).\n", "----------------------------------------\n", "Extracting downloaded file to isomut2py_download_dir\n", "Extracting completed in 0 day(s), 0 hour(s), 0 min(s), 7 sec(s).\n" ] } ], "source": [ "im2.examples.download_raw_example_data(path=exampleRawDataDir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "And ploidy estimation settings can be loaded with:\n", "\n", "