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Support sqlite database #56

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3 tasks
lpantano opened this issue Aug 22, 2019 · 0 comments
Open
3 tasks

Support sqlite database #56

lpantano opened this issue Aug 22, 2019 · 0 comments

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@lpantano
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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
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