How to we specify indels? Advertised functions do not exist?

[YichaoOU]

Hi,

In the paper, you claimed that MOODS can process sequence variants such as SNPs, insertions and deletions. So, how do we use this feature?

Thanks,
Yichao

[jhkorhonen]

The moods_dna.py supports SNPs encoded using the IUPAC nucleotide symbols, as described on the Formats page in the wiki.

For insertions, deletions and other more complicated sequence variants, you'll currently need to implement custom python scripts to handle them—I never got around to implementing this in the moods_dna.py script, since figuring out a sane way to handle the possible formats was a pain. The documentation is in a quite unfortunate state currently, but I've added a simple example script that demonstrates the basic idea: ex-variants.py

I'll see if I can figure out some simple solution variant handling in moods_dna.py, since MOODS update is long overdue anyway, and I'm planning to find a bit of time for it soon.

[YichaoOU]

Thanks!

I think for deletion, you can just use -. And you can probably quickly include it in your moods_dna.py? That will be very helpful.

Thanks,
Yichao