BioPython can send sequences directly to NCBI and will download the results when they’re ready. Once you have the output, you can parse it to, say, just pull out the hits with the top 10 lowest E values. Or generate a list of the species most frequently found in the results . . . or other useful things. Continue reading ‘Run BLAST from BioPython’
Monthly Archive for December, 2007
Page 2 of 3
BioPython handles GenBank files nicely. Here are a couple of ways of getting them into Python and working with them. Continue reading ‘Parse GenBank files with BioPython’
You can start another thread in IPython to run a program in the background. Continue reading ‘Run programs in the background in IPython’
One great thing about Python is the interactive debugger, which lets you inspect the value of variables at the point an error occurred. Of course, IPython integrates nicely with the Python debugger and makes debugging code a cinch. Continue reading ‘Debug and optimize your code in IPython’
IPython makes it easy to edit source code, or create new scripts based on a couple of lines in your history, or paste examples from the web. Continue reading ‘Edit your code in IPython’
You can make use of your Python skills by interacting with system commands directly for things like file renaming, directory restructuring, or calling any arbitrary system command from within IPython. Here are some ways to do that. Continue reading ‘System commands from IPython’
For the pathologically lazy, there are some shortcuts in IPython to save you from typing often-used commands.
Continue reading ‘Shortcuts in IPython’
This post shows the different ways of keeping track of your work in IPython: the command history, saving the history (or parts of the history to file) for later use, and storing variables so you don’t have to create them next time you use IPython. Continue reading ‘History: keep track of your work in IPython’
After working in IPython for a while, sometimes you’d like to use a variable you created way back at the beginning, but you don’t remember exactly what it was called. Here are some useful commands for working with variables in IPython. Continue reading ‘Managing variables in IPython’
Running programs or scripts in IPython is easy, and here are the commands to use. Continue reading ‘Running a program in IPython’