Manual overhaul

[fephyfofum]

Manual overhaul

[josephwb]

Ok I fixed that one (missing condition). The rest seem fine, but will test thoroughly later today.

[josephwb]

Most of this is done (and thanks to @jfwalker for redoing this in latex format!).

I have not touched on the last thing yet:

The pxcontrates example gave me nan values when using the provided files

[josephwb]

I think we can considered this completed.

[Cactusolo]

Sorry, I can not find a good place to ask this question, and it's not a issue. So I put here:

For the function "pxconsq" in phyx, the manual says that it will return user "the consensus sequence"; but I can't figure out the "the consensus sequence" is strictly consensus or MJR consensus? If this could explained in the manual or can provide different flavors (or use defined consensus threshold) should be great.

Thanks!

Miao

[josephwb]

I suppose it would be considered strict for DNA: IUPAC ambiguity codes are used to represent all bases present at a site (try pxconsq -s TEST/test.fa and more TEST/test.fa in the src directory for an example). Not sure what happens with AAs.

[josephwb]

Hrm there may be a bug here. The first site in the example (A,G,A,T,T) should be 'D', but 'R' (A.G) is reported. The next few sites are correct. But this should be examined in detail.

[Cactusolo]

@josephwb Also, for the output:

Is it possible to have a flag (or option) that user can choose preferred symbol for gap?
Like "-" or "N", or no gap generated in the consensus sequence (like the strict major rule consensus sequences generated by Geneious)? I can work on Geneious, but finger clicking for generating consensus sequences from 353 genes can be tedious.

I think these are useful when assembling target enrichment data, where people want consensus sequence for each gene as reference. If this feature provided, then the pxconsq results will directly meet the needs (the current output containing too many 'N's).

[josephwb]

Sure. We would need to know the permutations that would be desired. For example, if one sequence has A and all the rest gaps, should the consensus be A or - (or something else)? It is also not rare to have both N (ambiguity) and - (gap) within a single sequence. If all sequences are a gap at a site, are you suggesting dropping the site from the consensus completely?

Happy to do whatever you'd like. Maybe start a fresh issue to elaborate on things. Maybe provide a small example input and expected output(s).

[Cactusolo]

Thanks! Will do.