Combining PlaScope with gplas

[jpaganini]

I've been testing the combination of PlaScope outputs with gplas (ref: https://doi.org/10.1093/bioinformatics/btaa233) to get individual plasmid reconstructions (instead of just binary classfication of contigs). We got great results for E. coli!

I think it would be nice to get an optional flag in PlaScope that provides the output in the right format for gplas. I would be able to make a pull request for this in the coming weeks. Let me know if you are interested, and we could have a meeting about this!

Cheers,

[jpaganini]

Hi guys, let me know if you are still interested in this feature. I think combining PlaScope with gplas could be very benefitial for reconstructing plasmids from different species!

Cheers,

[duboism]

Hello,

Thanks for you contributions. I think this option would be useful. @GuilhemRoyer, any opinion ?

I will review your PR soon.

Mathieu

[GuilhemRoyer]

Hi jpaganini!

Thank you for the suggestion. I think it is a very good idea and and I'm curious to see your results ! Perhaps the easiest way is to add a new output file without adding any specific option if the generated file is not so big (it's a .gfa isn't it?).

Guilhem

[jpaganini]

Hi guys,
Thanks for your ansewers and suggestions.

I will explain better the intention of the "gplas compatibility" flag. In the PR that I made, I've modified the code of PlaScope so the user can select an optional "-g" flag. When using this flag, PlaScope will generate a tab separated file, named ${isolate}_plasmid_prediction.tab. This file will contain the classification results but formatted in an specific way to be compatible with gplas.

I think that having the flag as optional will avoid the creation of unnecesary files, if the user is not interested in reconstructing individual plasmids. However, the file is not big at all, so we could set it up as a default option.

I'll be waiting for your answers.

Cheers,

PD: We are prearing a new manu with results from combining Plascope_gplas, I'll share the preprint soon!

[GuilhemRoyer]

Well, I agree with your suggestion to set it up as a default option.

I look forward to seeing your manuscript! Will you focus only on E. coli or also on other species (there is also a plascope-formatted DB for K. pneumoniae) ?

[jpaganini]

Hi!

I've set up the gplas argument as default, and made some modifications on how to extract the information from unicycler headers (since I found a bug while re-testing). Let me know if there is anything else we would need to do to merge the PR. Also, would it be possible to update the conda package for plascope? If the latter version is in conda, I could maybe addition plascope as a default tool in gplas (which would make it much easier to use).

Regarding the manu, we will be focusing on E. coli. Although, it would've been nice to test gplas and plascope for k.pn plasmids reconstructions. I konw that Plascope is among the best-performers for classifying k.pn contigs as well.