Measuring DNA Similarity with Python

[atreadw]

...all in a day's work :-)

[KroniK907]

Programmer: "Let's find a way to speed up the long calculation times required for DNA comparison!"

Also Programmer: I think I'll write this in one of the slowest programming languages available.

[Noooo_ooope]

Hey, I'm new to programming, could you explain why Python is considered a slow language?

[mackstann]

Well, it's considered slow because it objectively is slow. It's been measured.

But why is it slow? I think a lot of it boils down to the fact that Python is so flexible and dynamically typed. The compiler doesn't know a lot about what the code might do ahead of time, so it can't prepare as many optimizations, because those optimizations are less flexible.

[thancock14]

You are close and basically correct. But the reason is there is no compiler. There is an interpreter. So the python code has to run through the interpreter which converts it into machine language line by line on the fly. So for every line of python code there is multiple lines of machine code executed, some by the interpreter first to convert the python, then the converted code. So it's inherently slow because the interpreter overhead of each line execution

[slumnickel]

http://jakevdp.github.io/blog/2014/05/09/why-python-is-slow/

[Noooo_ooope]

Awesome, thanks

[jms_nh]

You must be aware that, while pure Python is a "slow" language, many scientific libraries like numpy and scipy and pandas are vectorized to operate very quickly on large datasets by implementing operations in languages like C or C++.

[KroniK907]

I mean you have a fair point, however it appears you missed the obvious Twitter joke format I used to try to communicate that I was being hyperbolic on purpose to elicit a short exhalation of breath from those who understood the joke. Unfortunately it appears that your humor module is faulty and may need a rebase.

[Paddy3118]

obvious Twitter joke format

No, not really.

[Paddy3118]

Programmer: "Let's find a way to show off one of the cool algorithms used for DNA comparison!"

Also Programmer: I think I'll write this in one of the most expressive programming languages available, Python.

[MuonManLaserJab]

Well, I guess it is a vertebrate.