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Modelling validation
MODELLING VALIDATION TEST
What this touorial does it that it takes all your template structures from an existing modeling project and then removes them one by one and tries to re-model them using the remaining template structures. Each sub-moddeling project will get it's own project folder residing in the validation folder of the main project.
Preparation:
This tutorial assumes that you have already performed a modelling of a sequence(in this case that you have run the test described in "~biskit/test/test_modeling.txt" and that you want to validate the quality of this model.
You will also need to start pvm.
Run the test:
There are two options to running the test. You can execute the shell script test_modeling_validation.zsh in the ~biskit/test folder:
>>> ./test_modeling_validation.zsh
Or you can run the commands one by one (see commands and comments below).
Manual test:
The easiset vay to run a modelling validation is to do it from within the main project folder, so we'll go there:
>>> cd Mod/project
>>> setup_validation.py
This sets up the folder structure for the validation project.
>>> align_parallel.py
Will create (in parallell using pvm) the alignments for all the sub-projects in the validation folder created by the setup script.
Since we have already run the main moddeling run, we don't want to run it again so just hit enter when the script asks you:
T-Coffee output folder alredy exists in /mnt/data/shared_bin/biskit/test/Mod/project Overwrite folder? (y/N)
>>> model_parallel.py
Will build (in parallell using pvm) the models in the validation folder.
And again ansewer 'No' on the question that you'll get:
Modeller output folder alredy exists in /mnt/data/shared_bin/biskit/test/Mod/project Overwrite folder? (y/N)
>>> benchmark.py
Will calculate various data for each sub-validation project.
>>> analyze.py
Will run the analysis script for the main project. The result will appear in the ~/project/analyse folder