How to obtain Sequence/Alignment file paths
Hi, I am trying to locate and use sequence and alignment files to complete a MrBayes API call. I was wondering how can i find the path of the file?
Please sign in to leave a comment.
I want to get the file path of the alignment and sequences displayed in Geneious.
It's not really possible to get the file location because documents aren't necessarily stored as a file, they may be on a shared SQL server. Even if you could, they are stored in a format that is internal to Geneious and generally cannot be read by other tools.
If you need a file for input to another program then you have to export to a format compatible with that tool first:
File nexusInputFile = FileUtilities.createTempFile("input", ".nex", false);
// TODO: use nexusInputFile to run MrBayes
This is very helpful. Thank you Richard.