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Bugfix/biotek parsing#38

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danolson1 wants to merge 2 commits intoFAIRChemistry:mainfrom
danolson1:bugfix/biotek-parsing
Open

Bugfix/biotek parsing#38
danolson1 wants to merge 2 commits intoFAIRChemistry:mainfrom
danolson1:bugfix/biotek-parsing

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@danolson1
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Problem:

The read_biotek function failed to parse my Gen5 data file "gen5_data_export_test_12-1-2025.xlsx" due to hardcoded measurement interval locations.

Solution:

I modified read_biotek to search for 'Start Kinetic' entries in column A and extract the measurement interval dynamically from the adjacent column, providing more robust parsing.

Testing:

  • I added a new test case (test_read_gen5_data_with_dynamic_kinetic_interval.xlsx). This is an Excel file that represents the default Excel export of a Gen5 file (Biotek software). This file demonstrates the parsing bug in the unfixed code. You're welcome to rename the file if needed. My guess is that eventually you'll want to have several examples from each type of platereader.
  • Link to failing test commit: 572d9ee
  • Link to fixed code commit: 43dc056

biotek.py is not parsing a file correctly. I am uploading the problematic file and adding a test to show the problem.
I modified the biotek.py file to search for the text "start kinetic" in the first column of the Excel file. This is how the Gen5 software defines kinetic reads. Then parse the data in the next cell to the right to get the interval information.
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