small C program (single file) doing Bioinformatic stuff to learn Python bindings
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10 months ago
pippo1980 • 0

I am really bad at PC and programming. Trying to figure-out how Biopython works and Python at the same time.

Discovered existence of Python bindings. I am looking for a small c program (one file) to try to learn how

to call it from Python using ctypes or cython. Any idea ? I am asking for this because the print 'Hello'

isnt usefull to me , no way to pass argument to me and my C is absolutely zero

(asked same question on bioinformatics.stackexchange.com got closed. Hope find more help here)

python ctypes cython • 311 views
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If you are as bad at programming as you say, starting out by trying to conflate C (a not very beginner-friendly language in the first place) with another language (python), whilst trying to get in to the weeds of more niche interface layers like cython is not the approach I would take.

Start with something easy like python. Get comfortable with it, then start to explore the wider world.

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10 months ago

Here's a post where I show how to use Cython to take a very fast reverse complement of a DNA sequence, a task that Biopython is, oddly, not able to do quickly:

https://bioinformatics.stackexchange.com/questions/3583/what-is-the-fastest-way-to-get-the-reverse-complement-of-a-dna-sequence-in-pytho/3587#3587

My second answer speeds up the original approach further:

https://bioinformatics.stackexchange.com/questions/3583/what-is-the-fastest-way-to-get-the-reverse-complement-of-a-dna-sequence-in-pytho/3595#3595

I think these two answers should be a decent intro to a basic usage of Cython for a "real-world" bioinformatics application, though you will need to learn a little C to figure out how it works.

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no good trying with something that returns value

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Maybe use the Github repository that the original poster created to bundle tests of all the different reverse complement approaches:

https://github.com/conchoecia/fastest_rc_python

That should take most of the work out of setting things up, and you can then play with it in more of a "sandbox", if that makes sense.

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But I think Joe's advice is pretty solid. You may need a bit of gentler introduction to programming before tackling this. C has a much steeper learning curve than Python, and that can cause some frustration. I'd suggest starting with the basics of Python, and then going from there once you're comfortable.

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yep thanks. Fell back to https://realpython.com/python-bindings-overview/#ctypes , the ctypes part. It gave me

an idea of what is like. Was wondering how pymol and chimera are able to handle all the mix flavours they have !!

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