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snayfach / MicrobeCensus

MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
http://genomebiology.com/2015/16/1/51
GNU General Public License v3.0
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training.py: Unused test set? #14

Closed psaxcode closed 7 years ago

psaxcode commented 7 years ago

Hi Stephen, I just came across the line for evaluation which reads: error += test_error(train_genomes, train_rates, prop_constant, genome2size) Does it mean to use train_genomes, train_rates as the parameters? Thanks

snayfach commented 7 years ago

Sorry, but I'm not exactly sure what you are asking. Could you try rephrasing the question?

psaxcode commented 7 years ago

Sorry for the confusion. I am talking about line 85 in the file https://github.com/snayfach/MicrobeCensus/blob/master/training/training.py, which is a statement in the function "xvalidation". I am just curious that the test set does not seem to be used here.

snayfach commented 7 years ago

Ah, I see what you mean now. I fixed the issue and the line now reads: error += test_error(test_genomes, test_rates, prop_constant, genome2size)

The reported performance of MicrobeCensus in the paper is not affected by this bug.

Thanks, Stephen