Mutate

[Gvnngithub]

Hi, I recently came across your tool and would like to try it. I used AMRFinderPlus on a unicycler assembly in conda environment with the --plus optiont and saved the output in a tsv file. When launchig pathotype with pathotypeR(indir =path/to/tsv, output = "patho_pred", "patho_prev") this error pops up:

Error in mutate():
ℹ In argument: Gene_name = Gene symbol.
Caused by error:
! 'Gene symbol' not found
Run rlang::last_trace() to see where the error occurred.
Called from: signal_abort(cnd, .file)

Looking at the AMRFinderPlus output file I have this columns:
Protein id, Contig id, Start, Stop, Strand, Element type, Element name, Scope, Type, Subtype, Class, Subclass, Method, Target length, Reference sequence length, % Coverage of reference, % Identity to reference, Alignment length, Closest reference accession, Closest reference name, HMM accession, HMM description.

Is there somthing I am missing? Should I edit the tsv output?
Thank you

[kevinsblake]

It appears that you're missing the Gene symbol and Sequence name columns. That may either be due to AMRFinder updating the column names in a recent update, or your run not outputting those columns. If it's the former, renaming the column whose contents look like Gene symbol to Gene symbol should be a quick fix. If it's not outputting that column, probably an issue with your AMRFinder run.

See an example output .tsv file HERE.

[Gvnngithub]

Thank you for the quick reply. I tried many combination of columns as well as some of your tsv files but I keep getting either the same error or an identical one but with "Element type" instead.