Export filtered table as an excel file about open-cravat HOT 2 CLOSED

Hi again, currently, exporting to an excel file with filters applied is not possible on the result viewer GUI, but it is being considered for a future release. Meanwhile, there is a couple of workaround. First, make the filter criteria on the result viewer GUI and then save it with the file save icon at the bottom right corner of the Filter tab. Give a name to the filter. Then, on the command-line, run the command

sqlite3 xxxxx.sqlite 'select viewersetup from viewersetup where name="<filter name>"'

(xxxxx.sqlite as your result database file and as the filter save name)
The result will be a string such as

{"filterSet":{"sample":{"require":[],"reject":[]},"genes":[],"variant":{"operator":"and","rules":[{"column":"base__so","test":"select","value":["MIS"]},{"column":"base__coding","test":"hasData","negate":false}]},"smartfilter":{"base":{"so":["MIS"],"coding":false}}}}

Make a text file such as filter.json with its content being the output of the above sqlite3 command. Save the file, and run

oc report xxxxx.sqlite -t excel -f filter.json

(replace xxxxx.sqlite and filter.json with your paths. Use -t option of your choice)
to get a filtered excel output, for example.

In the next version of oc, oc report xxxxx.sqlite -F <filter name> -t excel will be supported.

Another option is to make the filter.json file yourself. It is a bit more complicated, but if you prefer this way, we can explain, let us know.

from open-cravat.

What you want in filter.json is actually the value of "filterSet". So delete {"filterSet": from the start, and the last } from the end.

from open-cravat.