SEDA Conserved Genome Annotation (CGA) Pipeline plugin

This plugin allows the possibility of executing the Conserved Genome Annotation (CGA) Pipeline trough the SEDA Graphical User Interface.

By default, the intermediate files generated by this operation in temporary directories are removed. If you need to keep them (e.g. for debugging purposes os in case of unexpected errors), it is possible to keep them by running SEDA with -Dseda.cga.keeptemporaryfiles=true.

For developers

The CGA pipeline involes a series of steps implemented in the CgaPipeline class. In order to programmatically test this pipeline, the following code can be used with the test data available here. It tooks about 21 minutes to complete using a workstation with Ubuntu 18.04.6 LTS, 8 CPUs (Intel(R) Core(TM) i7-8565U CPU @ 1.80GHz), 16GB of RAM and SSD disk

  public static void main(String[] args) throws IOException, InterruptedException {
    System.setProperty(AbstractBinariesExecutor.SEDA_EXECUTION_SHOW_COMMANDS, "true");
    DatatypeFactory factory = DatatypeFactory.getDefaultDatatypeFactory();

    SequencesGroup input = factory.newSequencesGroup(new File("input.fasta").toPath());
    SequencesGroup reference = factory.newSequencesGroup(new File("ref.fasta").toPath());

    CgaCompiPipelineConfiguration config = new CgaCompiPipelineConfiguration(
      10000, 500, 200, SelectionCriterion.CRITERION_1, 10, false
    );

    new CgaPipeline(
      new DefaultDockerCgaBinariesExecutor(),
      new CgaPipelineParameters(new File("/tmp/seda-cga"), config, ""),
      input, reference
    ).run();
  }

Using the same test data, the CLI command can be tested as follows:

cga --reference-fasta /path/to/cga/ref.fasta --results predicted_cds --max-dist 10000 --intron-bp 500 --min-full-nucleotide-size 200 --selection-criterion criterion_1 -selection-correction 10 --input-file /path/to/cga/input.fasta --output-directory /path/to/cga/output --save-parameters-file /path/to/cga/seda-cga.params