jayman1466
commented
1 year ago Hi there, Sorry you seem to be getting this shell error. I haven't run into it before. To try to get to the root cause, could you try to run the core script codon_opt(orf_aa = "", target_tir = "") with either int_RBS = False, terminators = False, or detailed_output = False
Wondering is one of these is the issue.
On Thu, Oct 20, 2022 at 2:17 AM leipan @.***> wrote:
Hi Jayman,
New to coding of any kind, and is trying to use iDOG for heterologous expression. I have a pool of sequence variants and the web interface does not support batch processing as far as I know. So when I try to use the command interface I ran into an issue and could not find a solution in the documentation.
Description as follows: I'm using a MacOS 12.5.1 with an intel processor. Environment was created using Anaconda with: python (version 3.9.17) python packages: biopython (version 1.7.9) pillow (version 9.2.0) Vienna RNA Package (version 2.5.1)
The iDOG scripts were downloaded and I cd to the iDOG-master folder. where I get "(SGE-CAD) @.*** iDOG-master %"
To run my sequence, this is what I input:
python codon_opt.py codon_opt(orf_aa = "my_aa_sequence", target_tir = "50000")
and I always get the error message "zsh: unknown sort specifier"
I tried troubleshooting by checking the documentation, but couldn't find information on installation or how to run the functions. Did I use the correct commands or I did do something wrong during installation? I'm not sure if you are still actively monitoring and maintaining this but I gotta try. Any detailed information is appreciated.
Thanks
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drofish6390
Hi Jayman,
New to coding of any kind, and is trying to use iDOG for heterologous expression. I have a pool of sequence variants and the web interface does not support batch processing as far as I know. So when I try to use the command interface I ran into an issue and could not find a solution in the documentation.
Description as follows: I'm using a MacOS 12.5.1 with an intel processor. Environment was created using Anaconda with: python (version 3.9.17) python packages: biopython (version 1.7.9) pillow (version 9.2.0) Vienna RNA Package (version 2.5.1)
The iDOG scripts were downloaded and I cd to the iDOG-master folder. where I get "(SGE-CAD) drofish@Ls-MacBook-Pro iDOG-master %"
To run my sequence, this is what I input:
python codon_opt.py codon_opt(orf_aa = "my_aa_sequence", target_tir = "50000")
and I always get the error message "zsh: unknown sort specifier"
I tried troubleshooting by checking the documentation, but couldn't find information on installation or how to run the functions. Did I use the correct commands or I did do something wrong during installation? I'm not sure if you are still actively monitoring and maintaining this but I gotta try. Any detailed information is appreciated.
Thanks