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Add hack script to update existing core meta table sample example genes #101
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This is not a final solution to this problem, but it provides a quick way to create a patch for cores with bad or inappropriate example genes. Python would be better IMO but until we have a discussion this could wait. Since I made the script to make a patch for staging Im sharing the code here. Thanks |
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Just a few minor comments. Feel free to merge though. Thanks
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Thanks!
Thanks Vasily |
Add new quick patch script to update meta table sample gene meta info.
The script attempts to quickly but considerately update meta example info on a input set of cores or input of cores + hand picked example gene (stable_id).
The script first selects a sub sample of stable ids per core (n=25). Then checks if these genes have associated homologies in the appropraite compara db on the same host.
As soon as a gene with homology is found, it then moves to create a patch on that basis.
Users can provide a list of cores and run in auto mode, or a list of cores+stable_ids they hand picked and run in manual mode.
Script creates some log into, including TSV of core+gene+description of new eg gene within output patch SQL file.