How to install and run TAXXI

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Download and extract files from the archive https://drive5.com/downloads/taxxi.tar.gz.

You will find the following sub-directories:

  l1o_methods/  Wrapper scripts for leave-one-out methods
  info/ Miscellaneous information.
  methods/  Method scripts.
  metrics/  Output directory for metrics.
  pred/  Output directory for method predictions.
  py/  Python scripts.
  scripts/  Bash scripts.
  testfa/  FASTA files for test sets.
  trainfa/  FASTA files for training sets.

The py/ directory should be added to your shell PATH.

To run a method on a given test set, change to the methods/ directory and run ./methodname testsetname, e.g.:

./blca ten_16s_v35.97

Methods, e.g. BLCA, should be installed per the instructions for each method. Some TAXXI method scripts must be edited to reflect the installation on your computer. For example, the blcs method script invokes BLCA like this:

python2 /p/sw/blca/2.blca_main.py -i $traindir/q.fa -r $traindir/tax.txt -q $traindir/db

Here, you must replace /p/sw/blca by the directory where BLCA is installed on your machine.

To run a method on all test sets and update the metrics table, change to the scripts/ directory and run ./run_method methodname, e.g.:

./run_method blca

To run all methods, calculate all metrics and build the metrics table, change to the scripts/ directory and run:

./run_methods
./metrics
./metrics_table