{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# BLAST on the Command Line and Integrating with Python\n", "\n", "This will get example sequence data from an external source, prepare it, and then run BLAST with it. Then, subsequent steps will parse the resulting data into something useful in Python. And, even cover how to convert to Excel. \n", "\n", "To make things easier and to allow integrating with the nice features provided by the Jupyter environment, we will access the command line from inside a Jupyter notebook using the `!` symbol at the start of the command to direct it to the shell. (Alternatively, cells to direct to the shell can be started with `%%bash` on the first line. Or, if you feel more confortable working on the actual command line, you can open a terminal from within this active Jupyter environment by clicking the Jupyter logo in the upper left corner of this notebook and then selecting `New` > `Terminal` form the dropdown on the right of the Jupyter environment dashboard and run the initial parts without the `!` or `%%bash` tags.)\n", "\n", "
If you haven't used one of these notebooks before, they're basically web pages in which you can write, edit, and run live code. They're meant to encourage experimentation, so don't feel nervous. Just try running a few cells and see what happens!
\n", "\n", "\n", " Some tips:\n", "