provide pema main data product in a 7-level taxonomy format

[hariszaf]

It would be super useful to return the pema main output (otu/asv table) in a 7-level taxonomy format, meaning all taxonomy assignments are as:

d__Bacteria; p__Abyssubacteria; c__SURF-5; o__SURF-5; f__SURF-5; g__SURF-5; s__SURF-5 sp003598085

[hariszaf]

Regarding COI, this is now covered under #56 --> the outputs are already in the required 7-levels.

Regarding 16S, we still wait for the Silva update. However, we have been waiting for a while and are getting a bit fed-up with waiting, hence it would be useful to do this ourselves. For advice on how to do this (and if it is feasible), consult with @hariszaf and @cpavloud

[hariszaf]

Regarding the ITS gene and the Unite database: one thing you could do is to get the General FASTA release (download) file and from there get the sequences id.

For example:
>Glomeraceae|AM076560|SH146432.05FU|refs|k__Fungi;p__Glomeromycota;c__Glomeromycetes;o__Glomerales;f__Glomeraceae;g__;s__uncultured_Glomus

The AM076560 is the sequence id.

Using that, you can get from the NCBI the organism it comes from
https://www.ncbi.nlm.nih.gov/nuccore/AM076560
and therefore, its NCBI taxonomy id.

[kmexter]

may be some interplay with #29 here