Scout demo database doesn't load Ancestry (pred.) or Parenthood

Hi all, thankyou for the great software!

I’m having loading some values into scout that should be included through these variables/files in the config file:

peddy_ped: scout/demo/643594.peddy.ped
peddy_ped_check: scout/demo/643594.ped_check.csv
peddy_sex_check: scout/demo/643594.sex_check.csv

When the demo database is loaded, scout doesn’t appear to be grabbing the values from these files to populate the Ancestry (pred.) and Parenthood columns of the ‘Individuals’ panel in the 643594 case (see images below):

• No error messages are thrown when creating or serving the database.

• I’m using scout version 4.19 and python 3.7.6 installed within a conda environment.

Please let me know if you require any further details from me, thanks in advance for your help!

[northwestwitch]

Hi again @leahkemp , I’ve found out what the problem is.

The command scout setup demo at the moment doesn’t load the peddy info (thanks for opening the issue!), but this will be fixed in the next Scout release (later thin month).

The workaround for the demo case (or your clinical cases) is: Rename 2 fields in the config file:

• peddy_ped_check --> peddy_check
• peddy_sex_check --> peddy_sex

And then load the demo case with the command scout --demo load case scout/demo/643594.config.yaml

The command for one of your own cases would be scout (--demo) load case path/to/your/config/file

This way it should work. I’m going to fix the naming of these fields also in the documentation. Sorry for the inconvenience, and thanks again for your feedback!

[leahkemp]

Fantastic the workaround has worked perfectly for our clinical data! Many thanks for your help @northwestwitch!