Closest improved #185
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Closest improved #185
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…osest hits and are not separate chromosomes. Problem: If the segment does not have closest (e.g., in ignore_upstream=True setting), it will simply drop out of output table. Solution: Added checking the indexes of df1 that are absent form the final returned hits Why it was not observed before: No detiled testing for options ignore_upstream/ignore_downstream/ignore_overlap and their combinations. If df1 has a segment from a chromosome X and df2 has a segment from it, but they are in an arrangements that won't produce a hit, this segment will be dropped out of df1 output.
gfudenberg
reviewed
Feb 7, 2024
| @@ -511,8 +510,8 @@ def overlap( | |||
| index_col = return_index if isinstance(return_index, str) else "index" | |||
| index_col_1 = index_col + suffixes[0] | |||
| index_col_2 = index_col + suffixes[1] | |||
| df_index_1 = pd.DataFrame({index_col_1: df1.index[events1]}) | |||
| df_index_2 = pd.DataFrame({index_col_2: df2.index[events2]}) | |||
| df_index_1 = pd.DataFrame({index_col_1: df1.index[events1]}, dtype=pd.Int64Dtype()) | |||
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I believe @nvictus introduced the _to_nullable_dtype() in the last update... maybe there is a way we can remove boilerplate & also use same strategy for closest ?
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We can, but I don't see how it will help in this case, frankly. It's storage of the index that is always integer and not absent.
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Yup, I agree that we do not seem to need a nullable type here.
…tream/downstream when there is no region to match.
golobor
approved these changes
Feb 8, 2024
| @@ -511,8 +510,8 @@ def overlap( | |||
| index_col = return_index if isinstance(return_index, str) else "index" | |||
| index_col_1 = index_col + suffixes[0] | |||
| index_col_2 = index_col + suffixes[1] | |||
| df_index_1 = pd.DataFrame({index_col_1: df1.index[events1]}) | |||
| df_index_2 = pd.DataFrame({index_col_2: df2.index[events2]}) | |||
| df_index_1 = pd.DataFrame({index_col_1: df1.index[events1]}, dtype=pd.Int64Dtype()) | |||
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Yup, I agree that we do not seem to need a nullable type here.
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Problem: If the segment does not have closest (e.g., in ignore_upstream=True setting), it will simply drop out of output table.
Solution: Added checking the indexes of df1 that are absent form the final returned hits
Why it was not observed before: No detiled testing for options ignore_upstream/ignore_downstream/ignore_overlap and their combinations.
If df1 has a segment from a chromosome X and df2 has a segment from it, but they are in an arrangements that won't produce a hit, this segment will be dropped out of df1 output.
Dragged modifications: overlap returned float indexes with failing the tests (numpy v1.22.4, pandas v1.5.2). Solution added for robustness of code across different software versions.