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Fix #149: Missing or mis-reported resistances #173

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@samuell samuell commented Jun 26, 2024

This fixes #149

The same change might need to be done for other matching as well.

Description

##Remove elements in cursive as needed.##

The features of this PR primarily concerns end-users/bioinformaticians/internals

Summary of the changes made:

If not self-evident, mention what prompted the change.

Primary function of PR

  • Hotfix
  • Patch
  • Minor functionality improvement
  • New type of analysis
  • Backward-breaking functionality improvement
  • This change requires internal documents to be updated
  • This change requires another repository to be updated

Testing

If the update is a hotfix, it is sufficient to rely on the development testing along with the Travis self-test automatically applied to the PR.

Test routine to verify the stability of the PR:

  • bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-stage.sh BRANCHNAME
  • us
  • source activate S_microSALT
  • (SITUATIONAL) export MICROSALT_CONFIG=/home/proj/dropbox/microSALT.json
  • Select a relevant subset of the following:
  • microSALT analyse project MIC3109
  • microSALT analyse project MIC4107
  • microSALT analyse project MIC4109
  • microSALT analyse project ACC5551

Verify that the results for projects MIC3109, MIC4107, MIC4109 & ACC5551 are consistent with the results attached to AMSystem doc 1490, Microbial_WGS.xlsx

Test results

These are the results of the tests, and necessary conclusions, that prove the stability of the PR.

Sign-offs

@samuell samuell changed the title Fix #149: Avoid promiscuous matching of gene name Fix #149: Missing or mis-reported resistances Jun 26, 2024
@samuell samuell force-pushed the 149-fix-missing-resistances branch 5 times, most recently from 79ed60b to 77d6961 Compare July 11, 2024 20:36
@@ -438,6 +438,7 @@ def scrape_blast(self, type="", file_list=[]):
self.name, str(e)
)
)
return hypo
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This hypo variable is something extra

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@samuell samuell Jul 15, 2024

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This return was added here in order to be able to check the outcome of the scraping in tests. Optimally one would have refactored the code more, so as not to save to the database inside the scraping function at all like is done now, but this was the smallest change I could find that would do the trick.

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we should include this in the git ignore

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Yes, well, I wasn't even sure if I wanted to keep the pixi stuff here at all, (after moving out of draft status). Will probably just get outdated as compared with the original config, so probably better to avoid.

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Looks good, I have made som comments, but I think all that is left is to check the differences of these two on validation data

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this one as well. So probably just add a pixi.*

@samuell samuell changed the base branch from master to rc400 July 31, 2024 08:08
@samuell samuell closed this Jul 31, 2024
@samuell samuell force-pushed the 149-fix-missing-resistances branch from c32b23f to d6290e0 Compare July 31, 2024 08:13
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Issue with reporting resistance OXA-48
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