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ed-lau / jcast

Junction centric alternative splicing translator
MIT License
19 stars 3 forks source link

Accessing the splice_type optional argument #25

Open mrcaleb01 opened 4 months ago

mrcaleb01 commented 4 months ago

Hi. I am trying to run JCAST 0.3.5 but I want to run the analysis for one specific rMATS output. I attempt to use the --splice_type optional argument but the output I get says "unrecognized arguments".

Could you please look into this for me?

Side note: I installed JCAST using "$ pip install jcast" in Ubuntu 22.04.3 terminal

ed-lau commented 4 months ago

Hi,

The --splice-type argument is available in the 0.3.5a pre-release. Let me know if you can access and install directly from GitHub here: https://github.com/ed-lau/jcast/releases/tag/v0.3.5a. If not I can also upload to PyPI for pip.

E

mrcaleb01 commented 4 months ago

Hi Edward,

Thanks for your response. I tried installing this new version in a new conda environment. I downloaded the tar.gz file and used $ pip install jcast-0.3.5a0.tar.gz - to install.

But unfortunately, jcast still doesn't recognize the "-s SE" argument.

I'd be glad if you could upload it to PyPI for pip or suggest possible ways for me to run this.

Thanks

mrcaleb01 commented 4 months ago

Hi Edward,

I have been able to install the new version. I initially ran into some issues with my conda environment. Thanks a lot for your assistance.

Best, C