Constants

This module contains all the constants used in the PathwayForte repo.

pathway_forte.constants.BIO2BEL_DATA_DIR = '/home/docs/.bio2bel/pathwayforte'

Cancer Data Sets

pathway_forte.constants.make_classifier_results_directory()

Ensure that the result folder exists.

pathway_forte.constants.MSIG_GSEA = '/home/docs/checkouts/readthedocs.org/user_builds/pathwayforte/checkouts/latest/data/results/gsea/msig'

Output files with results for GSEA

pathway_forte.constants.make_gsea_export_directories()

Ensure that gsea export directories exist.

pathway_forte.constants.MSIG_SSGSEA = '/home/docs/checkouts/readthedocs.org/user_builds/pathwayforte/checkouts/latest/data/results/ssgsea/msig'

Pickles with results for ssGSEA

pathway_forte.constants.make_ssgsea_export_directories()

Ensure that gsea export directories exist.

pathway_forte.constants.check_gmt_files()

Check if GMT files exist and returns GMT files as constant variables.

pathway_forte.constants.GENESET_COLUMN_NAMES = {'kegg': 'KEGG Geneset', 'reactome': 'Reactome Geneset', 'wikipathways': 'WikiPathways Geneset'}

Columns to read to perform ORA analysis.