clustal_options variable for filter_seqs

[alexpiper]

Hi PrimerTree developers,

I've come across a slight annoyance with the filter_seqs function, where if you have a custom clustal omega installation you will get an error:

Error in system(paste(exec, "--help"), intern = TRUE) : 'clustalo' not found

I have resolved this by moving the clustal omega installation files to the R working directory, but for cleanliness it would be nice to be able to provide a clustal_options = c(exec='filepath') variable, similar to as implemented in search_primer_pair.

Thanks for your work developing this handy little package!
Regards,
Alex

[jimhester]

Mainly the only change needed here would be to pass ... to the custalo() call in https://github.com/jimhester/primerTree/blob/018e066ee33fd71e0a39a0045c19c2dec9c0a8d0/R/filterResults.R#L39

[ucbtmae]

Hello @jimhester hope everything's going alright!
I'm in the final steps of using the pipeline, but I also have come across the issue with the filter_seqs function. I have clustal omega installed and it works perfectly with search_primer_pair (with the help of the clustal_option) but when trying to filter out some undesired sequences from the primerTree object it returns the following message:
"Error in system(paste(exec, "--help"), intern = TRUE) : 'clustalo' not found"
I even have tried by using setwd to work directly in the clustal omega path but no success.
Do you have a suggestion of how to tackle this issue?
@alexpiper How did you manage to solve the issue? I am working in a Macbook, intel version