BDVAL/Sequence

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This mode is used to read a sequence file and sequentially run several other modes. It is implemented by org.bdval.SequenceMode.

Sequence Files

Sequence files can be used by the Sequence Mode to run a number of modes in a specific order using a consistent set of parameters. Using sequence files, variables can be defined that get dynamically populated with runtime specific values which in turn get passed to the modes.

There are three basic sections to a sequence file:

  • variable definitions
  • required option definitions
  • the options that will get passed to the modes in the sequence.

Blank lines or lines that begin with the character '#' are ignored.

The following is an example of a sequence file that will execute svm-weights, write-model and predict modes. The following two variables are defined for this sequence: "label" and "predictions-filename". Three options are required beyond the base options for sequence mode, namely: "other-options", "split-id", and "num-features". Any tokens surrounded by the character "%" will be populated dynamically by the sequence mode.

   def label=baseline-global-svm-weights-%model-id%
   def predictions-filename=%dataset-name%-%label%-prediction-table.txt
   #
   addoption required:other-options:Other DAVMode options can be provided here
   addoption required:split-id:id of split being processed
   addoption required:num-features:Number of features in the generated model
   #
   -m svm-weights --overwrite-output true -o %dataset-name%-%split-id%-%label%-features.txt
   --output-gene-list --gene-list full --gene-features-dir %gene-features-dir%
   --num-features %num-features% %other-options% --split-type training
   
   -m write-model --overwrite-output true
   --gene-list %label%|%dataset-name%-%split-id%-%label%-features.txt
   %other-options% --split-type training --model-prefix libSVM_%dataset-name%-%split-id%-%label%
   
   -m predict --overwrite-output false --model libSVM_%dataset-name%-%split-id%-%label%.model
   -o %predictions-filename% %other-options% --split-type test --true-labels %conditions%

This file can be found in the binary distribution as "baseline.sequence"

Mode Parameters

The following options are available in this mode

Flag Arguments Required Description
--sequence-file sequence-file yes Specify the sequence file to use.
--pathway-components-dir pathway-components-dir no Directory where pathway components will be stored. (default: pathway-components)
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