Import Cancer Hotspots Data

[onursumer]

Basic workflow:

• Get the v2 file from https://raw.githubusercontent.com/cBioPortal/cancerhotspots/master/webapp/src/main/resources/data/v2_multi_type_residue.txt
• Get the 3d file from https://raw.githubusercontent.com/cBioPortal/cancerhotspots/master/webapp/src/main/resources/data/3d_hotspots.txt
• Merge these 2 files into one
• Add a new column Type:
  • for all 3d mutations -> 3d
  • v2 -> use Indel_Size to determine (either single residue or in-frame indel)
• Run the script (on non-3d mutations) to generate these additional columns: Missense_Count, Trunc_Count, Inframe_Count, Splice_Count
• Import the final file into database:
  • Columns that are absolutely required for now: Hugo_Symbol, Residue, Type, Tumor_Count, Missense_Count, Trunc_Count, Inframe_Count, and Splice_Count
  • Use this command to avoid duplicates: import hotspot.mutation ${DIR}/../export/hotspots_v2_and_3d.txt '--type tsv --headerline --mode upsert --upsertFields Hugo_Symbol,Residue,Type,Tumor_Count'

[inodb]

merged to master