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rki-mf1 / covsonar

A database-driven system for handling genomic sequences of SARS-CoV-2 and screening genomic profiles.
GNU General Public License v3.0
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If multiple --include are used and the first fails all fail #16

Closed silenus092 closed 2 years ago

silenus092 commented 3 years ago

In GitLab by @hoelzer on Jun 23, 2021, 22:31

python3 covsonar/sonar.py match --db rki.db --include S:L18F --include S:T19R --include S:T20N --include S:P26S \
--include S:del:69:2 --include S:del:144:1 --include S:del:157:2 --include S:R190S --include S:D215G \
--include S:R190S --include S:del:241:3 --include S:K417N --include S:K417T --include S:L452R --include S:T478K \
--include S:E484K --include S:N501Y --include S:A570D --include S:D614G --include S:H655Y --include S:P681H \
--include S:P681R --include S:A701V --include S:T716I --include S:D950N --include S:S982A --include S:T1027I \
--include S:D1118H --include S:V1176F --lineage B.1.617.2 --date 2021-05-01:2021-06-21

S:L18F does not have any match in this scenario which is correct. Still hits should be reported for some of the other --includes. If I remove the first --include S:L18F the command works bc/ S:T19R can be found.

silenus092 commented 3 years ago

In GitLab by @hoelzer on Jun 23, 2021, 22:33

Switching just the order and having S:T19R in the first position also works:

python3 covsonar/sonar.py match --db rki.db --include S:T19R --include S:L18F --include S:T20N --include S:P26S --include S:del:69:2 --include S:del:144:1 --include S:del:157:2 --include S:R190S --include S:D215G --include S:R190S --include S:del:241:3 --include S:K417N --include S:K417T --include S:L452R --include S:T478K --include S:E484K --include S:N501Y --include S:A570D --include S:D614G --include S:H655Y --include S:P681H --include S:P681R --include S:A701V --include S:T716I --include S:D950N --include S:S982A --include S:T1027I --include S:D1118H --include S:V1176F --lineage B.1.617.2 --date 2021-05-01:2021-06-21
silenus092 commented 3 years ago

In GitLab by @hoelzer on Jun 23, 2021, 22:36

But, I also noticed that the order impacts the results which should be not the case? Or do I misunderstood the multiple --include statement?

silenus092 commented 3 years ago

In GitLab by @s.fuchs on Aug 24, 2021, 08:20

Thank you for this important report! Right now I am working on a redesign of the database to allow even more complex queries. I will take care of that this bug will be eliminated then.

silenus092 commented 2 years ago

In GitLab by @kunaphas.kon on Nov 17, 2021, 13:02

mentioned in commit 03054148bd8ddd83b38bc7b6f85f97baffb8c1e5

silenus092 commented 2 years ago

In GitLab by @spsofia on Nov 17, 2021, 15:30

Just to have mentioned here what was discussed earlier today: when using the "OR" option to search for mutations, the order of entries changes the number of hits returned. E.g., -i S:N501Y -i S:E484K returned 151652 seqs, whereas -i S:E484K -i S:N501Y returned 9027 seqs

silenus092 commented 2 years ago

In GitLab by @kunaphas.kon on Jan 16, 2022, 12:35

Resolves in #!14 🛠

Feel free to reopen if the problem still exists.

Thank you