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Ho-Lab-Colostate / zhunt

An algorithm for predicting the propensity of DNA to flip from the B-form to the Z-form
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RSC Tasks #2

Open ryansczarny opened 4 years ago

ryansczarny commented 4 years ago

run the C code in python

figure out how to use the code (zhunt)

make file is an example to work with and test

make a python wrapper

argparce (command line interface)

ryansczarny commented 4 years ago

Cool cool. So for today:

to compile c code clang file.c -o file will create an exicutable file

now... I need to figure out how to get it to pull in the file

I reached out to David King and he is going to help me tomorrow and walk through what I should know with this

I built zhunt.py that should open the C program but I am not in love with that

I also want to go back and look at the GUI stuff I did before and see what I can remember from the wrapper and GUI code. I might need to get a book or take a course on that to refresh/learn well for the first time

ryansczarny commented 4 years ago

What I am working on right now, I am getting this error:

ld: warning: ignoring file pBR322.txt, file was built for unsupported file format ( 0x74 0x74 0x63 0x74 0x63 0x61 0x74 0x67 0x74 0x74 0x74 0x67 0x61 0x63 0x61 0x67 ) which is not the architecture being linked (x86_64): pBR322.txt

From what I can see in the C code, it should be able to handle that file so I am trying to figure out what is happening here

Also, running my python script is giving me the error of:

https://medium.com/@RyanDeschamps/what-to-do-with-a-segmentation-fault-11-1c9aad1d2ebe

I have a feeling that this might be related to the fact that /bin/ has a password protection and I am wondering if I can get rid of that

ethho commented 4 years ago

Compiling to ./bin/zhunt should fix this, or running from Docker with make tests-bin.

ryansczarny commented 4 years ago

Compiling to ./bin/zhunt should fix this, or running from Docker with make tests-bin.

I tried getting Docker but it isn't compatible with this version of Mac :/ and I thought I had compiled to ./bin but I will check again

Getting this error now: (base) drosophila:Zhunt Team_HoLab$ sudo clang -o ./bin/zhunt /Users/Team_HoLab/Desktop/RSC/Documents/Coding/Zhunt/zhun3.c Password: ld: can't open output file for writing: ./bin/zhunt, errno=2 for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation)

ryansczarny commented 4 years ago

Update from RSC:

ISSUES NOW TO WORK ON: