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gbouras13 / dnaapler

Reorients assembled microbial sequences
MIT License
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[Question] Do reoriented contigs match the strandedness of the balst result? #41

Closed rpetit3 closed 1 year ago

rpetit3 commented 1 year ago

Hi @gbouras13!

Does the reoriented contig match the strandedness of the blast result? Or is it always positive?

This stems from https://github.com/rpetit3/dragonflye/issues/22 where I plan to add dnaapler as a final step.

Thank you so much! Robert

Also, I think I found the spot in the code where it happens, but wanted to make sure! Your code was so nice! And, the comments for very helpful, thank you for that!

gbouras13 commented 1 year ago

Hi @rpetit3

Thanks for the kind words mate!!

Yes, Dnaapler does always make the reoriented contig start (with dnaa) in the positive direction by design.

If that isn't suitable I can create a new subcommand for use with dragonflye, it shouldn't be too hard.

I'd imagine you want dnaapler all in dragonflye in case you have multiple contigs/plasmids etc.

There is a hierarchy: if multiple hits are found: 1) dnaA, 2) repA then 3) terL (which is likely on chromosomes if you have prophages).

The spot is here https://github.com/gbouras13/dnaapler/blob/8c55731b6790dee3c34b97c6cebd34e702606351/src/dnaapler/utils/processing.py#L221C1-L228C27

If you need any other advice or help integrating it into dragonflye please let me know.

PS Sorry to change topic but while I have you, if you know who or where to go with this, I'd love some help https://github.com/bioconda/bioconda-recipes/pull/42998 - only because I know you'd know better than me with bioconda!

I want to incorporate ALE into my hybracter scalable pipeline to estimate whether polishing improved the assembly. It could even be interesting to consider with dragonflye too perhaps. But we need a non-broken release on bioconda!

George

rpetit3 commented 1 year ago

@dfornika this sound like what you were looking for?

@gbouras13 I'll definitely take a look at this bioconda PR! (as in now haha)

dfornika commented 1 year ago

Yeah, this sounds great to me. I've been meaning to test out dnaapler a bit but haven't found the time to set anything up yet. But this sounds very similar to the functionality that unicycler has, which is what we're interested in replicating in our dragonflye assemblies.

rpetit3 commented 1 year ago

Thanks @dfornika!