Rename BRC seq_region names #292
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JAlvarezJarreta
approved these changes
Feb 15, 2024
Dishalodha
approved these changes
Feb 15, 2024
Dishalodha
reviewed
Feb 15, 2024
| ) | ||
| seq_attrib = session.scalars(stmt).one() | ||
| seq_attrib.value = seq_region.brc_name | ||
| elif seq_region.operation == Operation.insert: |
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I am not able to replicate this case if i have such case as
if not db_brc_name: logging.info(f"Seq region {seqr.name} doesn't have a BRC name")
it gives the log message however seq_regions = [] so doesnt apply the insert operation for me
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Do you get the message that says the insert operation is not supported (I have only implemented the update part)?
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The value for return seq_regions in get_seq_regions_to_replace is an empty list for me, so I dont get any message
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Ok good spot, I've updated the logic
Co-authored-by: J. Alvarez-Jarreta <jalvarez@ebi.ac.uk>
Co-authored-by: J. Alvarez-Jarreta <jalvarez@ebi.ac.uk>
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A script to automate the renaming of seq_region
BRC4_seq_region_nameattributes.The script accepts a simple tab file with the current name and the new BRC name, and checks against the current database to see what it would do (not found, insert, update, or already exists). Then just add the usual
--updateargument to make the changes.NB: the current name can be the seq_region name or a synonym.