How to test a new method on TAXXI
To test a new method, you need to create your own method wrapper script
similar to those in the benchmark/methods directory.
The script can
be written in any convenient language, including a compiled language such as
Java, C or C++, if you prefer. The requirement is that there is an
executable file in methods/
with the name of your method. There is one command-line argument, which is
the name of the test set, so it is invoked like this:
./my_method ten_16s_v4.97
The input data
is the FASTA files for the test and training sets:
../testfa/ten_16s_v4.97
../trainfa/ten_16s_v4.97
Typically, the method script converts
from TAXXI format to the native file format(s) for the method.
Output
must be written to a file named ../pred/methodname/setname,
e.g.:
../pred/my_method/ten_16s_v4.97
The format of the output file must be as
follows: tab-separated text with two fields (1) the query label, (2) the
prediction. The query label must exactly as the defline of the FASTA file
for the test set, including the tax= annotation giving the correct taxonomy.
The prediction must be formatted in the same way without the tax= or the
closing semi-colon.