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Add moa and compound annotation #444
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Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## main #444 +/- ##
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- Coverage 63.99% 62.98% -1.01%
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Files 37 42 +5
Lines 4438 4652 +214
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+ Hits 2840 2930 +90
- Misses 1598 1722 +124
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Thank youuu!
- Could you please always make the "available database" names links? Also to any of the older cell line metadata databases, please
- All of these
show
checks seem pretty repetitive. Is there a way to extract this as a helper function? You just need to also parameterize the type of data (protein, [...]), but that's easy. - I think that some of the code can be reduced and simplified. It's a bit verbose.
Co-authored-by: Lukas Heumos <[email protected]>
Co-authored-by: Lukas Heumos <[email protected]>
Co-authored-by: Lukas Heumos <[email protected]>
Co-authored-by: Lukas Heumos <[email protected]>
Co-authored-by: Lukas Heumos <[email protected]>
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Could you please check the types of many of your parameters again? I think they could be a bit more general. Maybe Iterable
instead of List
for some etc.
Also make the behavior clear if None
is an option. Sometimes you're not describing that.
Co-authored-by: Lukas Heumos <[email protected]>
Co-authored-by: Lukas Heumos <[email protected]>
Co-authored-by: Lukas Heumos <[email protected]>
for more information, see https://pre-commit.ci
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What are you deleting the whole cell line test and where did your new tests go?
We can merge this then!
Signed-off-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
for more information, see https://pre-commit.ci
Signed-off-by: zethson <[email protected]>
PR Checklist
docs
is updatedDescription of changes
Add compound and moa annotation
MoaMetaData
andCompoundMetaData
Improve
CelllineMetaData
: add new parametershow
for each annotating function to print out only thr given number of unmatched identifiers.Technical details
Compound annotation: fetch the compound annotation including the first synonym, cid and canonical smiles via pubchempy. query identifiers can be either CID or the name.
moa annotation: fetch moa annotation sourced from clue.io. query id should be the name of the perturbagens. Annotated moa is also filtered on an optional parameter
target
.Lookup objects for two new objects are also implemented.
Additional context