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Update sublineage query for covsonar 2, add warning note�[1~
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matthuska committed Sep 6, 2023
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Expand Up @@ -84,11 +84,13 @@ Semi-globally aligned Sequence: ATGCCATGATTAGGTGA--------
|Optimize sqlite database |`./sonar.py optimize --db test.db` |`sonar optimize --db test.db` |
|Calculate database statistics |`./sonar.py info --db ${db}` |`sonar info --db test.db` |
|Remove a set of sequences by ID |`./sonar.py remove --db test.db --file sequences-to-delete.ids` |`sonar delete --db test.db --sample-file sequences-to-delete.ids` |
|Identify sequences with a given lineage or any of its sublineages |`./sonar.py match --lineage B.1.1.7 --with-sublineage --db test.db --tsv` |`sonar match --db test.db --LINEAGE B.1.1.7 --with-sublineage LINEAGE` |
|Identify sequences with a given lineage or any of its sublineages |`./sonar.py match --lineage B.1.1.7 --with-sublineage --db test.db --tsv` |`sonar match --db test.db --LINEAGE "B.1.1.7*"` (see NOTE1 below!) |
|Output all sequences, including purely ambiguous variations in profiles (e.g. N stretches)|`./sonar.py match --ambig --tsv --db test.db` |`sonar match --db test.db --showNX` |
|Output all sequences that contain frameshift mutations |`./sonar.py match --only_frameshifts --db test.db` |`sonar match --db test.db --frameshifts-only` |
|Output all sequences that do not belong to a given lineage, in a date range |`./sonar.py match --lineage ^B.1.1.529 --lineage ^BA.% --date 2021-12-01:2021-12-31 --db test.db --tsv` |`sonar match --db test.db --LINEAGE "^B.1.1.529" "^BA%" --DATE 2021-12-01:2021-12-31` |

NOTE1: Sublineage queries will not work if you have never run the `update-lineages` command on your database. Without that command, covSonar doesn't know the relationships between children and parent Pangolin lineages.

## Troubleshooting

**Q: `covSonar2` crashes with: `sqlite3.OperationalError: attempt to write a readonly database`**
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