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Techniques okay so this is my last Python lecture but it's going to come up more in David's lectures starting tomorrow I mean starting Thursday next lecture and then we're going to sort of trade off a couple times more and then we're going to hit you with some bio stats so today's lecture is mostly about bio Python and I'm going to reiterate in more detail some object-oriented concepts because bio Python is very much built on the object oriented model I'm going to teach you about seek objects and seek record objects I'm gonna teach you a new way to read and write files called seek i/o which is a little smarter several people noted that it's a pain in the butt to work with the fast day file just with the read function because the first line is a header and then all the other lines our sequence and why do you have to like figure out code to handle that why hasn't somebody already figured this out so yeah in some cases using pre-built tools makes more sense than building it yourself from scratch then I'm going to show you just a couple other cute pre-built tools that are in bio Python and suggest that there's a lot more there and I may also mention a few times that it's a work in progress and it could certainly be more elegant and you know you're all welcome to step up and become Python developers and make the thing work better than it does right now okay so we've talked about modular code and I'm going to say that Python modules are in three basic sets or types there's a core set of modules that are sort of always available sort of the functions that we've been using then there are a second set that are built in modules that you can load just by typing import so you have import math import OS that sort of thing and those are present in the basic Python distribution and then there are a very large number of optional modules that must be downloaded and installed before you can import them the anaconda that you've already downloaded actually had a large number of these optional modules pre-installed so up till now you haven't really had to add anything extra but the biopython I don't believe is not already pre-built into anaconda so you're gonna have to figure out how to install it it'll install pretty easily because all of the prerequisites the numpy and scifi are already there and so it should just install right off the biopython website the way the installer describes to you and if you have trouble ask the TAS because everyone's trouble is going to be unique to the way their computer is setup it does have dependencies so biopython is dependent on numerical Python numpy and probably some other things as well and it's not and unfortunately Python is not a monolithic toolkit that's all present in one website unlike our which is very nicely organized in well two or three repositories that have almost all of our code Python code is spread all over the place some in github some in SourceForge and the bio Python has its own website anyone can write new...
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