search

hoelzer-lab / hypro

Extend hypothetical prokka protein annotations using additional homology searches against larger databases
GNU General Public License v3.0
9 stars 0 forks source link

Mmseqs2 #22

Closed marlt closed 4 years ago

marlt commented 4 years ago

Added alignment params, a final_outs subdir in mmseqs2_out to store the tsv, fix issue #21

hoelzer commented 4 years ago

Looks good!

I tested based on the README:

(hypro) ➜  hypro git:(mmseqs2) scripts/hypro.py -i run/prokka/testrun.gff -o run/hypro -d uniprotkb -t scripts/mmseqs2.sh -m full 
usage: hypro.py [-h] [-m ['restricted', 'full']] -i PATH -o PATH [-d STR] -f
                PATH [-c STR] [-e FLOAT] [-a INT] [-p FLOAT] [-t INT]
hypro.py: error: the following arguments are required: -f/--mmseqs2

so I think -t should be -f now? because -t is used for threads? With -f it was working.

can you check and fix @CoffeeMA2go and push to the mmseqs2 branch? then you can merge, thx!

marlt commented 4 years ago

Readme is updated: params changed accordingly. More adjustments according to mods in the tool code. Shall e fine now!