DeepPhe Output - DeepPhe/DeepPhe-Release GitHub Wiki
Overwriting
NOTE: Subsequent runs of the system will overwrite the output of a previous run unless you change the Output Directory.
Formats
By default, the system outputs data in four manners
- a neo4j graph database
- bar-delimited files
- HTML files
- Run Log
The subdirectory names can be changed by modifying the piper file used to run the system.
Neo4j graph database
Found by default under the output_graph subdirectory The neo4j database is used by DeepPhe-Viz
Browsing the neo4j database is described in Quick Start
Bar-delimited files
Found by default under the CI_EVAL subdirectory
One file for each type
- Cancer
- Tumor
Files have .bsv extension
First line contains column names
You can use your favorite tool for comparing text files to compare differences between runs of the system
HTML files
Found by default under the HTML subdirectory
These files contain only basic information parsed from valid sections in each document.
Run Log
Contains a log of system progress information as well as summaries of patient cancers and tumors.