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Local Clone and ML tools #11

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@AlexanderGress AlexanderGress commented Aug 2, 2022

Hi,

I implemented some features:

  • Search MaveDB with some filters to get a list of urns (or without filters to get all of them)
  • Download scoretables from MaveDB
  • Create a local clone of MaveDB
  • Different features that aim to create datasets used in Machine Learning applications, like data aggregation and effect value scaling (currently limited to SAVs)

If you have questions or anything: alexander.gress@helmholtz-hips.de

best wishes,
Alexander Gress

@AlexanderGress
Added Classes, Datastructures and Methods for ML usage
cbcfef9 
ML tools include
 - aggregation of scoresets from same expirements
 - scaling effect values
 - fetching whole protein sequences and updating the hgvs_pro ids
   accordingly
 - outputting datasets in a specialized fasta format
 - currently works just for savs
Implementating a search feature to collect urns with coresponding meta
data from the database.
Added the feature to actually download score tables
Also added features for cloning the whole database locally
@AlexanderGress
Documented the newly added ML features
719955e 
Added three example scripts to show how to use the ML features
@AlexanderGress
Implemented support for ProteinGym
6721d78 
- also updated procession of MaveDB data to newest standards
- capable to process the now downloadable full MaveDB
@AlexanderGress
Added unscaled dataset output
fff8c13
@AlexanderGress
Fixed a bug setting the proteingym folder path
7e16c38
@AlexanderGress
Update for publication
0648ec6
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@AlexanderGress