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quadram-institute-bioscience / faprotax-tools

Parser and annotation tools using the FAPROTAX database (Louca S. et al., 2016)
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Faprotax - Nitrosomonadaceae not counted as aerobic_ammonia_oxidation function #1

Open MarCarreras opened 3 weeks ago

MarCarreras commented 3 weeks ago

In the FAPROTAX DATABASE, the taxa ProteobacteriaNitrosomonadaceae* appears in the function aerobic_ammonia_oxidation. However, using the pipeline written below to obtain the faprotax table, I have realised that some of my taxa are Proteobacteria phylum and Nitrosomonadaceae family, and they have a 0 in the function aerobic_ammonia_oxidation.

aerobic_ammonia_oxidation

faprotax_mapping_dataset<-as.data.frame(f1_dataset$res_spe_func) faprotax_mapping_dataset$ASV<-rownames(faprotax_mapping_dataset) faprotax_mapping_dataset<-merge(faprotax_mapping_dataset,f1_dataset$tax_table,by="row.names") faprotax_mapping_dataset

Can this problem be solve? thank you so much!

telatin commented 1 week ago

Thanks for sharing. This repo has not been updated in a while but we will have a look when possible!

MarCarreras commented 5 days ago

I think it is an important issue. Is there another repo where it can fit better? Thank you.