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kjolley / BIGSdb

Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
https://pubmlst.org/software/bigsdb/
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Allele sequence checkbox occasionally is not automatically checked when an exact match allele is found on web scan #970

Closed kjolley closed 1 month ago

kjolley commented 5 months ago

This seems to happen very occasionally and not reproducibly. The allele designation checkbox is checked.

When it was noticed, the new allele had been assigned after the run had started - this may not be relevant.

kjolley commented 4 months ago

This may be fixed with commit dd8b995b6b360ca0fda42f497ab090a629ed3c63.

kjolley commented 1 month ago

Message from James Bray: With regards to the scan/tagging check box issue, I took some screenshots to help explain. I think several things are happening:

  1. For alleles that don't exist at the start of the scan (allele id=2065), only the 'Designate allele' check box is filled in. The 'Tag sequence' checkbox is left blank. (Note: I manually checked the 'Tag sequence' box for id=46201).

  2. The 'Designate allele' check box is not working properly for alleles that don't exist before the scan was started. The box gets checked but it does not designate the allele.

  3. When the 'Tag sequence' box is manually filled in (id=46201) - this box works and the sequence is tagged.

For example:

Screenshot 1

Screenshot_1 Scan results for single locus NEIS1952 against Neisseria isolates (PubMLST Neisseria sp.) - allele 2065 was added during the scan. All isolates matching this allele only have the 'Designate allele' box checked (except the last one id=46201 where I manually checked the second checkbox).

Scan results for two isolates near the bottom of the scan page id=46175 - only the 'Designate allele' box is checked id=46201 - initially on the 'Designate allele' box was checked but I manually checked the second box - so both boxes were checked when I pressed the 'Tag Alleles/Sequences' blue button

Screenshot 2

Screenshot_2 report of Allele designations set and Allele sequences set Note no allele designations (allele 2065) for either id=46175 or id=46201. But there is an allele sequence set for id=46201

Screenshot 3

Screenshot_3 In isolate history for id=46175 No history record has been added

Screenshot 4

Screenshot_4 Isolate history for id=46201 One history record has been added 46201 [G97_0802]  2024-07-24 14:26:49     NEIS1952: sequence tagged. Seqbin id: 4445470; 57676-58896 (sequence bin scan)

kjolley commented 1 month ago

Issue 2: The 'Designate allele' check box is not working properly for alleles that don't exist before the scan was started. The box gets checked but it does not designate the allele - cannot be replicated following the above change.