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tgvaughan / remaster

High-fidelity stochastic tree simulation for BEAST 2.
https://tgvaughan.github.io/remaster
GNU General Public License v3.0
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Using FASTA format instead of nexus to save simulated alignments #10

Closed CecileTK closed 4 months ago

CecileTK commented 5 months ago

Hello Tim,

Thank you so much for the great simulation tool, this has been very useful!

I was wondering whether there is a way to save simulated alignments (simulated using feast) using a FASTA format instead of a nexus one.

So far, I have been reopening the nexus files in R and converting them with a custom script but this is getting quite challenging for larger simulations where loading the nexus file takes a very long time.

Thank you! Cécile

tgvaughan commented 5 months ago

Hi Cécile, thanks for the kind words!

Unfortunately there's no way to directly generate FASTA files from the sequence simulation - at least not by using the simulator in feast. If there's enough call for this I could make this possible in the future, but in the meantime you might try replacing your R script with a rough shell script (maybe even awk) to convert just this output. This should be much faster! (If you'd like help with this, let me know.)

Tim

CecileTK commented 5 months ago

Thank you for clarifying and for the tip, using shell scripts appears to be speeding things quite a lot.