Fix subgary indexing in cnary.by_gene() #580
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cnary.by_gene() iterates over chromosomes, which are represented as dataframe slices which preserve the original indexes. Because of this, accessing them by .iloc is not going to be possible, and .loc needs to be used instead.
tskir
commented
Mar 18, 2021
| @@ -83,7 +83,6 @@ def by_gene(self, ignore=params.IGNORE_GENE_NAMES): | |||
| Pairs of: (gene name, CNA of rows with same name) | |||
| """ | |||
| ignore += params.ANTITARGET_ALIASES | |||
| start_idx = end_idx = None | |||
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Removed this line because it's never used—both start_idx and end_idx are initialised again below
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P. S. It also solves the problem with the chromosome diagrams in #579 because the underlying reason is exactly the same. |
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Do you see any other related code where The fixes in |
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Closes #573. Closes #576. Closes #579. Thank you @diushiguzhi @eriktoo @hrkemp @drmrgd @HYan-lei for reporting and initial investigations!
cnary.by_gene() iterates over chromosomes, which are represented as dataframe slices which preserve the original indexes. Because of this, accessing them by
.ilocis not going to be possible, and.locneeds to be used instead. (An alternative solution would be to keep.ilocbut reset the sub-dataframe index somewhere along the way, but I don't see a good reason to do this.)The autotests don't seem to be working but I've ran the full suite locally and everything's fine.