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DasLab / SARSCoV2_Secstruct_Cons

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Reproducing get_rscape_powers.sh #2

Closed ruthkr closed 3 years ago

ruthkr commented 3 years ago

Hello,

This is really great work.

Background:

I am trying to follow your steps to get conserved RNA structure on plant viruses, especially using R-scape. Recently, I tried to reproduce the bash script get_rscape_powers.sh using your windowed alignment files . However, I did not get the same alignment power results as you have in alignment_powers.dat.

Results:

These results are identical (a quick run of diff will show that).

Question:

What version of R-scape did you use in this project? Is there any particular thing you did before running get_rscape_powers.sh?

I ran the script in R-scape version v1.5.16, in both macOS and GNU/Linux, and they don't match the results on your GitHub.

Thank you very much.

ramyarangan commented 3 years ago

Hi, thank you for reaching out! I am glad that you are using this script.

I am running with R-scape version v1.4.0, which may explain the discrepancy. I just tried pulling the directory from scratch and running the script again with R-scape version v1.4.0, and I'm getting the results currently uploaded on Github. I didn't run anything else prior to that script. I've just added a note pointing to this version in the README!

ruthkr commented 3 years ago

Hello, thank you very much for your reply. Your pipeline is great and easy to follow. Thank you for this.

I changed the version of my R-scape to v1.4.0, and it worked as expected (it has the same results as alignment_powers.dat).

I agree, it would be great if you add the version of tools you used in README. 😃