vragh / seqvisr Goto Github PK

Thanks for making this tool. I have installed and tried to use msavisr but have not been able to get an output.
Using:

• R 3.5.1
• seqvisr 0.2.5

I have this MSA from Clustal Omega which I have saved as a FASTA file.
MSA.fasta.txt

But when I use it in the msavisr command with Hsap as the reference sequence, it always results in the following error:

(curpos + 1):(nextpos - 1) : NA/NaN argument

Can you advise me what I'm doing wrong? Is it an issue with the file?

Hi,

I found your code in biostars and it is great. However, I have an issue. When I am running my dataset I often got an error message like this:

Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 2940, 0

I say often because after some trying, I could visualize a dataset, then R crashed, I had to restart it and when I reopen it again, the same dataset could not be visualized anymore. The dataset you used in Biostars worked always fine. I am almost sure my fasta file is fine (at least, I can generate trees with it) . You can find it attached to the post.
Thanks for patience
Cris
All_species_Rha_test.txt