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Update deprecated pandas to_csv parameter - #67

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yu-liu24:update-pandas-lineterminator
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Update deprecated pandas to_csv parameter#67
yu-liu24 wants to merge 1 commit into
LangilleLab:masterfrom
yu-liu24:update-pandas-lineterminator

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@yu-liu24 yu-liu24 commented Jun 4, 2026

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This updates the deprecated pandas line_terminator keyword to lineterminator in convert_picrust2_to_stratified_output_format.py.

The old keyword was deprecated in pandas 1.5.0 for consistency with read_csv and the standard library csv module. No behavior change is intended; the line terminator remains '\n'.

Tested with:

  • python3 -m py_compile microbiome_helper2/MMSeqs2_functional_annotation/convert_picrust2_to_stratified_output_format.py
  • Ran the script on a minimal TSV input using pandas 3.0.3 and confirmed tab-separated output, expected function column output, and \n line endings.

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