Available MLST scheme list is out of date

[eam12]

The list of MLST schemes available (https://github.com/tseemann/mlst/blob/master/db/scheme_species_map.tab) is out of date and so does not work with the --mlst-scheme flag for some scheme names. For example, senterica is now senterica_achtman_2.

[apetkau]

Hello @eam12 . Thanks for reporting. Which version of the mlst software do you have installed? As in mlst --version?

The --mlst-scheme option in StarAMR is passed directly to the mlst software, as seen below:

https://github.com/phac-nml/staramr/blob/d050a21694f42a33045c5b03c7a626bf0810bcdf/staramr/blast/JobHandler.py#L145-L148

So the valid schemes to use depends on which version of mlst you have installed.

[eam12]

I have mlst version 2.23.0 installed. If I specify the updated scheme name (e.g. senterica_achtman_2) it runs perfectly, but the --help menu tells users to look at mlst's scheme_species_map.tab file to get a list of available scheme names. This file is out of date (e.g. still lists senterica, not senterica_achtman_2. It would be great if the --help menu directed users to an updated list of mlst scheme names. Maybe https://github.com/tseemann/mlst/blob/master/db/pubmlst? Small thing, I know, but would be very helpful!

--mlst-scheme MLST_SCHEME
                        Specify scheme name, visit https://github.com/tseemann/mlst/blob/master/db/scheme_species_map.tab for supported scheme genus available. [None]

[apetkau]

Ah, okay. Thanks. Yes, maybe changing the help documentation to point to a different location to get a list of schemes would be helpful (I did not realize that file was out of date).

Note by default schemes should be auto-detected if you don't specify anything.

[apetkau]

Fixed in #186