Skip to content

SalmonTE error when sample_sheet.csv has "condition" column #8

@fsantilli

Description

@fsantilli

I encountered the following problem with SalmonTE

Traceback (most recent call last):
  File "/scratch/santilli/hnRNPL_KD_pipeline/3t-seq/.snakemake/scripts/tmp_3v4751x.edit_condition_file.py", line 32, in <module>
    joined = sample_sheet.join(salmon_condition_sheet)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/conda-envs/50d812d8ce9078db884e008cdd1ec8ab/lib/python3.12/site-packages/pandas/core/frame.py", line 10744, in join
    return merge(
           ^^^^^^
  File "/conda-envs/50d812d8ce9078db884e008cdd1ec8ab/lib/python3.12/site-packages/pandas/core/reshape/merge.py", line 184, in merge
    return op.get_result(copy=copy)
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/conda-envs/50d812d8ce9078db884e008cdd1ec8ab/lib/python3.12/site-packages/pandas/core/reshape/merge.py", line 888, in get_result
    result = self._reindex_and_concat(
             ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/conda-envs/50d812d8ce9078db884e008cdd1ec8ab/lib/python3.12/site-packages/pandas/core/reshape/merge.py", line 840, in _reindex_and_concat
    llabels, rlabels = _items_overlap_with_suffix(
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/conda-envs/50d812d8ce9078db884e008cdd1ec8ab/lib/python3.12/site-packages/pandas/core/reshape/merge.py", line 2721, in _items_overlap_with_suffix
    raise ValueError(f"columns overlap but no suffix specified: {to_rename}")
ValueError: columns overlap but no suffix specified: Index(['condition'], dtype='object')

This is my sample_sheet:

name,filename_1,filename_2,condition
D4_SiCTR_Rep3,D4SiCTRRep3_1,D4SiCTRRep3_2,CTRL
D4_SihnRNPL_Rep3,D4SihnRNPLRep3_1,D4SihnRNPLRep3_2,KD
D4_SiCTR_Rep4,D4SiCTRRep4_1,D4SiCTRRep4_2,CTRL
D4_SihnRNPL_Rep4,D4SihnRNPLRep4_1,D4SihnRNPLRep4_2,KD
D4_SiCTR_Rep6,D4SiCTRRep6_1,D4SiCTRRep6_2,CTRL
D4_SihnRNPL_Rep6,D4SihnRNPLRep6_1,D4SihnRNPLRep6_2,KD

Metadata

Metadata

Assignees

Labels

No labels
No labels

Type

No type

Projects

No projects

Milestone

No milestone

Relationships

None yet

Development

No branches or pull requests

Issue actions