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[EXP] support LCA functionality for SqliteIndex + LineageDB_Sqlite databases. #1933

Merged
merged 39 commits into from
Apr 12, 2022
Merged

[EXP] support LCA functionality for SqliteIndex + LineageDB_Sqlite databases. #1933

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b87b432
preliminary victory over rankinfo
ctb Apr 6, 2022
72bafc9
provide generic LCA Database functionality via sqlite
ctb Apr 6, 2022
d44b21e
refactor and comment
ctb Apr 6, 2022
2342bc0
refactor and document
ctb Apr 6, 2022
8551384
add sqlite_utils
ctb Apr 7, 2022
1196554
cleanup
ctb Apr 7, 2022
37ae598
parse out SqliteIndex.create
ctb Apr 7, 2022
91f4649
rm comment
ctb Apr 7, 2022
efcb36e
add database_format to lca index
ctb Apr 7, 2022
e8819b1
get sql database output working for LCA index
ctb Apr 7, 2022
1e745f3
get all lca tests working on SQL version of LCA_Database
ctb Apr 7, 2022
ce4b467
Merge branch 'add/sqlite_index' into add/sqlite_index_lca
ctb Apr 9, 2022
7fd3a94
adjust protocol
ctb Apr 9, 2022
36cfc4b
update to match protocol
ctb Apr 9, 2022
1ec70a8
Merge branch 'add/sqlite_index' into add/sqlite_index_lca
ctb Apr 9, 2022
214dcaf
Merge branch 'add/sqlite_index' into add/sqlite_index_lca
ctb Apr 9, 2022
e3ff9f0
update row check to ignore _ prefixes
ctb Apr 9, 2022
b7191de
implement remaining lca_db protocol for sqlite
ctb Apr 9, 2022
3139e4c
fix up rankinfo for sqlite LCA_Database
ctb Apr 9, 2022
dace619
Merge branch 'add/sqlite_index' into add/sqlite_index_lca
ctb Apr 10, 2022
08ac110
cleanup LCA_Database creation
ctb Apr 10, 2022
fe5ce83
Merge branch 'add/sqlite_index' into add/sqlite_index_lca
ctb Apr 10, 2022
a3fea8a
add sqlite loading to CollectionManifest
ctb Apr 10, 2022
10b0ff3
update manifest writing to support SQL, too
ctb Apr 10, 2022
00c98f5
switch to using generic manifest.write_to_filename
ctb Apr 10, 2022
cd84ca6
catch pre-existing sqlite DBs
ctb Apr 10, 2022
a36b197
Merge branch 'add/sqlite_index' into add/sqlite_index_lca
ctb Apr 10, 2022
4f8d069
work through various merge implications
ctb Apr 10, 2022
d4259f9
Merge branch 'add/sqlite_index' into add/sqlite_index_lca
ctb Apr 10, 2022
88f8c78
Merge branch 'add/sqlite_index' into add/sqlite_index_lca
ctb Apr 11, 2022
79903b4
Merge branch 'add/sqlite_index' into add/sqlite_index_lca
ctb Apr 11, 2022
d1e67a2
fix sig check reliance on internal manifest mechanism
ctb Apr 11, 2022
32c2f0a
fix picklist stuff when using Sqlite manifests
ctb Apr 11, 2022
1bafd43
add lots of debug stmts
ctb Apr 12, 2022
a279e84
remove SQLite pickset as impractical
ctb Apr 12, 2022
6c176d3
remove some expensive debugs
ctb Apr 12, 2022
66b2c8c
remove sql picklist code as too slow
ctb Apr 12, 2022
ba8928f
comments and cleanup
ctb Apr 12, 2022
50976f7
much cleanup
ctb Apr 12, 2022
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6 changes: 6 additions & 0 deletions src/sourmash/cli/lca/index.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,12 @@ def subparser(subparsers):
'--fail-on-missing-taxonomy', action='store_true',
help='fail quickly if taxonomy is not available for an identifier',
)
subparser.add_argument(
'-F', '--database-format',
help="format of output database; default is 'json')",
default='json',
choices=['json', 'sql'],
)

add_ksize_arg(subparser, 31)
add_moltype_args(subparser)
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