Enable leafcutter-ds to handle a group_file with no confounder columns#255
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lianos wants to merge 1 commit intodavidaknowles:leafcutter2from
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Enable leafcutter-ds to handle a group_file with no confounder columns#255lianos wants to merge 1 commit intodavidaknowles:leafcutter2from
lianos wants to merge 1 commit intodavidaknowles:leafcutter2from
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When no confounder columns were present in `group_file`, there would be multiple errors. This is an attempt to fix that. 1. A default `confounders = None` is set 2. A chunk of code that manipulates the `confounders` DataFrame was pushed up into the `if len(meta.columns) > 2` block 3. If no confounders are present, the `counts` DataFrame is subset to just include the samples defined in `meta` Please note I'm not a Python or pandas guru, so I'm sure there may be better (more idiomatic) ways to do this, but this seems to do what I think is intended to setup the ultimate call to `differential_splicing()`
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leafcutter-dswould error out when no confounder columns were present ingroup_file, this is an attempt to fix that.confounders = Nonevariable is setconfoundersDataFrame was pushed up into theif len(meta.columns) > 2blockcountsDataFrame is subset to just include the samples defined inmetaPlease note I'm not a Python or pandas guru, so I'm sure there may be better (more idiomatic) ways to do this, but this seems to do what I think is intended to setup the ultimate call to
differential_splicing()