[enhancement] Including Clonal Complex in output

[dutchscientist]

In more and more bacteria, there are enough MLST data to use the Clonal Complexes rather than the specific sequence type. For instance, the Campylobacter and Listeria files provided include the Clonal Complex and in the case of Listeria, also the Lineage in the information.

I tried the Campylobacter scheme, and mlst does not output the clonal complex. The information file from PubMLST does include it:

ST aspA glnA gltA glyA pgm tkt uncA clonal_complex 1 2 1 54 3 4 1 5 ST-21 complex

Is it possible to include that in the output of the mlst program?

[tseemann]

I do not have any plans to support clonal_complex, mlst_clade, ribotype or the many other wierd columns that pubmlst have.

I will leave this open as an enhancement but we don't really need them and I am time poor at the moment, sorry.

[dutchscientist]

That's a pity, but no worries, I understand.

"We" definitely have a use for them ;-)

[ireneortega]

I agree, itt would be great if the clonal_complex is filled, too. Otherwise, I will continue doing it after mlst is executed.

[llk578496]

It would be great that if clonal_complex is included.