README.md

byconeer

The byconeer package contains essential utility scripts for the setup and maintenance of a Progenetix-style Beacon environment.

Progenetix Update Commands

1. Import / generate variants

2. Import / generate callsets

3. Process callsets & variants for statusmaps and CNV statistics

Core data element for the Progenetix environment are the "statusmaps", i.e. the binned CNV calls (currently im 1Mb bins). The statusmaps are stored inside the info parameter of each callset with a current structure of:

...
info:
  statusmaps:
  	dupcoverage: [ 0.023, 1, 1, 1, 1, 0.782, 0, 0, 0, ... ]
  	delcoverage: [ 0, 0, 0, 0, 0.002, 0.703, 0, 0, 0, ... ]
  	dupmax: [ 0.348, 0.348, 0.348, 0.348, 0.348, 0, 0, 0, ...]
  	delmin: [ 0, 0, 0, 0, -0.182, -0.182, 0, 0, 0, ...]
...

The maps are generated with the callsetsRefresher collecting all variants for each callset & then matching overlaps to the intervals.

byconeer/bin/callsetsRefresher.py -d progenetix 

This also allows just to add statusmaps and statistics for single series which have beed added / fixed:

byconeer/bin/callsetsRefresher.py -d progenetix -t 1 -f "icdom-85002"

4. Import / refresh biosamples

biosamplesInserter

biosamplesRefresher

The biosamplesRefresher.py script is used for global "data fixes", e.g. the addition of CNV statistics from callsets or population of attributes from other collections. This is a utility scriopt hich needs occasional adjustments depending on the use cases and changing data schemas.

byconeer/bin/biosamplesRefresher.py -d progenetix

5. Import / refresh individuals

6. Generate / refresh collations

Due to the possibly nested place of any given code collations can be only re-created right now and not just updated for individual matches. This may change...

byconeer/bin/collationsCreator.py -d progenetix

7. Generate frequencymaps

8. Add / refresh publications

9. Rebuild ontologymaps

10. Update the statistics database

byconeer/bin/beaconinfoCreator.py