Package: pamogk
PAMOGKInstallationGetting the Code BaseYou can either checkout the code base through git:gitclonehttps://github.com/tastanlab/pamogk.gitor you can download the master branch from:https://github.com/tastanlab/pamogk/archive/master.zipPython EnvironmentProject mainly uses python, but some of the plot generation codes use matlab or output html files (plotly.js). Also some
libraries might be dependent on operating system. In our tests we used Debian 12.04LTS and macOS Catalina.First installpipenvusing the instructions given:https://github.com/pypa/pipenv#installationWe are usingpipenvbecause of version locking and predictive builds.Setting up MOSEKWe are usingMOSEK Optimizer APIfor optimizing view weights, and in
order to use MOSEK you will need a license file. MOSEK provides free certificates for academic purposes and free trial
certificates for Commercial usages. You can see check the link below for information on how to acquire an academic license:https://www.mosek.com/products/academic-licenses/License File PlacementYou can either place the license file under user's home directory in a folder namedmoseke.g:$HOME/mosek/mosec.lic# *nix/macOS users%USERPROFILE%\mosek\mosek.lic# windows usersOther option is to set theMOSEKLM_LICENSE_FILEenvironment variable to your license file location.We also look for the license file paths in some custom paths (by overwritingMOSEKLM_LICENSE_FILEif not present).
You can checkpamogk.config.MOSEK_SUPPORTED_PATHSto see a list of supported paths.For more information:https://docs.mosek.com/9.2/install/installation.html#setting-up-the-licenseDependenciesInstall dependencies with:pipenvinstallRequired Environment VariablesYou can add a.envfile that will be loaded bypipenvAlso please don't forget to exportMOSEKLM_LICENSE_FILEvariable as well if you are using a path other
than$HOME/mosek/mosek.lic:# required for experiment runningPYTHONPATH=${PYTHONPATH}:.MOSEKLM_LICENSE_FILE=$MY_MOSEK_LICENSE_FILE_PATHFolder Structurepamogk:package root folderkernels:Kernel methods to calculate distance between patients. Will try to extend these!data_processor:Data processors/converters used to convert different forms of data to usable forms.
Will try to extend these!gene_mapper:Uniprot/Entrez gene mapping matcher for different datasets using different gene IDs. Will try to
separate to its own package or along with other tools.pathway_reader:https://.ndexbio.org CX format, andhttp://kegg.jpKGML format reader and converters. Will try
to separate to its own package or along with other tools.data:Data files that are both raw or generated by the project. Keeping intermediate files saves a lot of
computation time where applicable. (not included in package)experiments:Experiments done on real data. (not included in package)ExperimentsRunning ExperimentsYou should run experiments either by starting a pipenv environment shell by:pipenvshellor through pipenv with:pipenvrunexperiments/pamogk_all_exp_1.pyThis ensures that experiments are run with correct environment.Experiment ParametersExperiments are code entry points that have arguments that change per experiment. You can see their arguments by
running them with--helpparameter. e.g:./experiments/pamogk_all_exp_1.py--helpand you should see help as such:usage: pamogk_all_exp_1.py [-h] [--rs-patient-data file-path]
                           [--rp-patient-data file-path]
                           [--som-patient-data file-path]

Run PAMOGK-mut algorithms on pathways

optional arguments:
  -h, --help            show this help message and exit
  --rs-patient-data file-path, -rs file-path
                        rnaseq pathway ID list
  --rp-patient-data file-path, -rp file-path
                        rppa pathway ID list
  --som-patient-data file-path, -s file-path
                        som mut pathway ID list