Could the printPerf R script be updated to support Binsanity bin output?

[Former user]

Hi,

Thanks for the wonderful software and great bin evaluation scripts. I am running MetaBAT and comparing with some different assemblers, including BinSanity. I tried using the printPerf R script to summarize the CheckM output from those bins so I can compare with Binsanity but it doesn't appear to be able to parse the data. Would it be possible to add support for this binning software?

Thanks very much,

Jesse McNichol Fuhrman Lab, USC

[Feng Li]

Hi, I conducted the experiment on comparing Binsanity with Metabat2.

a simple way to solve this is to rename the binsanity bins to make them have no additional "-" character in the bin name.

a command like this will work(replace - with +).

sed -i 's/gz-bin/gz+bin/g; s/kmean-bin/kmean+bin/g; s/-bin/+bin/g; s/-refined/+refined/g' *

if you'd like to read into this file ‘http://portal.nersc.gov/dna/RD/Metagenome_RD/MetaBAT/Files/benchmark.R’, you'll know deeper from the key function "calcPerfBySCG" and the comment line inside this func (#TODO need to warn the additional '-' character in the bin name).

Thanks for using MetaBAT.

Feng