There should be a option like mirtop convert --format sql to convert a mirgff3 file into a table inside a sqlite database.
We can start with creating a script that takes a mirgff3 file and converts to sqlite file. Ideally we should keep all the information, I think the output of mirtop counts --add-extra would be a good table to directly add in a sqlite database file.
After that:
[ ] integrate the script in the mirtop code
[ ] add test units
[ ] start with filter or/and query function from the database
There should be a option like
mirtop convert --format sqlto convert a mirgff3 file into a table inside a sqlite database.We can start with creating a script that takes a mirgff3 file and converts to sqlite file. Ideally we should keep all the information, I think the output of
mirtop counts --add-extrawould be a good table to directly add in a sqlite database file.After that:
filteror/andqueryfunction from the database