Taxonomy output

[askerdb]

Dear authors of Amphora,

Thank you for making this software available.

The taxonomic output format seems to not handle that some taxonomic levels are incertae sedis. This shifts all the taxonomic labels making it impossible to parse downstream. In this example the class is missing, and so the genus is shifted into the family field, the species into the genus field etc.

cat -T phylotypes.list|head
Query^IMarker^ISuperkingdom^IPhylum^IClass^IOrder^IFamily^IGenus^ISpecies
k87_338378_3^Iadk^IArchaea(1.00)^IThaumarchaeota(1.00)^INitrosopumilales(0.84)^INitrosopumilaceae(0.84)^INitrosopumilus(0.84)^INitrosopumilus maritimus(0.84)
k87_19798_2^Iadk^IArchaea(1.00)^IThaumarchaeota(1.00)^INitrosopumilales(0.82)^INitrosopumilaceae(0.82)^INitrosopumilus(0.82)^INitrosopumilus maritimus(0.82)
k87_19402_1^Iadk^IArchaea(0.97)^IThaumarchaeota(0.97)^INitrosopumilales(0.93)^INitrosopumilaceae(0.93)^INitrosopumilus(0.93)^INitrosopumilus maritimus(0.93)

Is it possible to work around this in any way?

Regards,

Asker Brejnrod