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CAFA benchmark


A quick program to create CAFA benchmark, need more exhaustive testing


User can either use github interface Download or type the following command in command line:

git clone

User has to install python, and biopython (would recommend use anaconda package).


Within this directory when you clone it, the YEAST directory (downloaded from ) will provide input for creating the benchmark, users are encourage to test it on more database To create CAFA benchmark, choose the appropriate gfa files for t1, t2 time and a valid direction for ouput

./ -t1 YEAST/gene_association.goa_ref_yeast.23 -t2 YEAST/gene_association.goa_ref_yeast.52 -o output

The six files benchmark will be created in output directory with names indicate which knowledge (NK or LK), and ontology (bpo,cco,mfo).


We have also include the 2 file 1 and 2 in unit folder for testing purpose. Users can modify the files and the program to do unit testing. The unit_test already include some cases cover for the NK and LK knowledge. In order to run it, users can use this command line: