search

soedinglab / plass

sensitive and precise assembly of short sequencing reads
https://plass.mmseqs.com
GNU General Public License v3.0
149 stars 14 forks source link

Option to change genetic code (translation table)? #2

Closed sminot closed 6 years ago

sminot commented 6 years ago

Expected Behavior

Plass provides a flag for the translation table (genetic code) used to perform the conceptual six-frame translation of nucleotides to amino acids. For sequences expected to be bacterial this would correspond to the translation table 11.

Current Behavior

There is no option for the translation table in the command line flags.

Your Environment

I am running Plass from the static binary hosted at https://mmseqs.com/plass/plass-static_sse41.tar.gz

milot-mirdita commented 6 years ago

I just exposed the parameters in the last commit (d4071700cba48fd6551173329f3b71629cbf829e).

You need two parameters: --use-all-table-starts --translation-table N.

These tables are implemented:

1) CANONICAL, 2) VERT_MITOCHONDRIAL, 3) YEAST_MITOCHONDRIAL, 4) MOLD_MITOCHONDRIAL, 5) INVERT_MITOCHONDRIAL, 6) CILIATE, 9) FLATWORM_MITOCHONDRIAL, 10) EUPLOTID, 11) PROKARYOTE, 12) ALT_YEAST, 13) ASCIDIAN_MITOCHONDRIAL, 14) ALT_FLATWORM_MITOCHONDRIAL, 15) BLEPHARISMA, 16) CHLOROPHYCEAN_MITOCHONDRIAL, 21) TREMATODE_MITOCHONDRIAL, 22) SCENEDESMUS_MITOCHONDRIAL, 23) THRAUSTOCHYTRIUM_MITOCHONDRIAL, 24) PTEROBRANCHIA_MITOCHONDRIAL, 25) GRACILIBACTERIA, 26) PACHYSOLEN, 27) KARYORELICT, 28) CONDYLOSTOMA, 29) MESODINIUM, 30) PERTRICH, 31) BLASTOCRITHIDIA
sminot commented 6 years ago

Do you have any static binaries available from that commit? I'd love to test it out but I don't have the easiest time building from source.

milot-mirdita commented 6 years ago

Download the static binary again, it always points to the latest commit (that codeship or travis built).

What can we do to make the compiling process easier?

sminot commented 6 years ago

Any chance you could link to the Dockerfile you use to build soedinglab/plass?

sminot commented 6 years ago

An alternative to supporting the build from source would just be to tag the different versions so that you can pull a docker image the corresponds to a particular GitHub commit. That would help users ensure reproducible execution, while also letting them just use your Docker images for execution.

milot-mirdita commented 6 years ago

Its in the root folder of the repository: https://github.com/soedinglab/plass/blob/master/Dockerfile

I forgot to add the docker tag for releases. I am trying to get docker cloud to tag them now automatically.

sminot commented 6 years ago

Well, now I feel a bit silly :-) Thanks!

sminot commented 6 years ago

Ok, I can confirm now that the translation table param works in my hands. Thanks!