How to add description information?

Microbial community profiling ShortBRED
1

Hi,
I have downloaded Antibiotic Resistance Database (ARDB) Markers,and run shortbred_quantify.py.This is the output reults:

Family	Count	Hits	TotMarkerLength
1112175A	0.0	0	68
AAA21889	0.0	0	95
AAA22905	0.0	0	44
AAA25680	0.0	0	121
AAA25683	0.0	0	128
AAA25688	0.0	0	109
AAA25717	0.0	0	252
AAA26549	0.0	0	90
AAA26613	0.0	0	55

I want to add description of Family.Could you tell my how to do it?

Thanks!

2

Do you have a file that maps the family IDs to human-readable names (e.g. as two columns)? If so, there is a script in HUMAnN called rename_table that will attach the names to the row headers you have here. You can also do this with a function like VLOOKUP in Excel.

3

I’m bumping this - I used the database from the 2015 publication with the pre-computed markers. Is there a mapping file that has been saved by those who curated that database that can be shared?

I’m having trouble finding an equivalent online, or maybe I am missing something between the quantify and identify steps?

4

Would this be the proper file? shortbred/ShortBRED_ABR_Metadata.tab at master · biobakery/shortbred · GitHub

5

That looks like the right file for associating ARDB sequences/IDs with names and other metadata from the time of the method and paper’s development.

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