Possibility to include NAs in taxonomy csv format for easier parsing? about genomad

[apcamargo]

Fixed in version 1.8.0. Thanks @LanderDC!

[apcamargo]

Hi @LanderDC,

You make a good point. I'm not sure about adding an "unclassified" taxon to the lineage (your second option) because it might confuse users. They could think that geNomad couldn't assign the sequence to an order but could assign it to a family, when in reality, the family isn't part of any order at all

I like your first option, though.

Another possibility would be adding prefixes to the taxa names, like GTDB does? For instance:

Viruses;r__Duplodnaviria;k__Heunggongvirae;p__Uroviricota;c__Caudoviricetes;f__Straboviridae;

This could make parsing easier. The problem is that "Viruses" is not a taxon at all and doesn't have a named rank.

[LanderDC]

Thanks for your swift reply!

You are right that my second option might cause some confusion. I like your suggestion to add prefixes, because you immediately see which taxonomic rank you're dealing with and don't have to remember which suffix belongs to which rank. However, if possible I would still like empty places for ranks that are not yet classified by ICTV, because then you can just split the taxonomy column based on the semicolon:

Viruses;r__Duplodnaviria;k__Heunggongvirae;p__Uroviricota;c__Caudoviricetes;;f__Straboviridae;;

About the "Viruses" problem, I don't feel that it is really an issue but I understand that you would like to have everything consistent.

[apcamargo]

I like your suggestion. The "Viruses" thing does bother me, though. If I add the additional semicolons, the ranks would be could be inferred by the number of the column, so the prefixes are not strictly required.

[LanderDC]

True, whatever is easier to implement should be fine 🙂

[apcamargo]

I'll will work on that for the next release :)

[LanderDC]

Nice, thanks!

[LanderDC]

Are you ok with a pull request on this issue? I forked your repo and slightly modified taxonomy.py to get these empty fields for unclassified ranks (LanderDC@14eb85d). Incidentally, the "Viruses" rank is also removed by these modifications.

[apcamargo]

Thanks, @LanderDC

If it's easy enough, I'd appreciate that. I'd need to evaluate what could break with this change (the removal of the "Viruses" taxon), but I don't forsee any issues.

[LanderDC]

Great!