Keemei: Validate tabular bioinformatics file formats in Google Sheets

How do I use Keemei?

In this section you’ll learn how to use Keemei to validate some example data. These data are derived from:

1. QIIME 1’s Illumina Overview Tutorial mapping file
2. “88 Soils” QIIME 1 mapping file (Lauber et al., 2009)
3. geneGIS example SRGD file

These data are for demonstration purposes only. Errors have been intentionally introduced to illustrate validation with Keemei. Do not use these data for analysis.

Getting started

1. Log in to your Google Account and install Keemei if you haven’t already.
2. Open this Google Sheet. This is a publicly-viewable spreadsheet with the example data described above.
3. Click File > Make a copy... and name your copy of the spreadsheet.

You now have a copy of the example data to validate with Keemei.

Validating your data

First we’ll see how to validate a QIIME 1 mapping file with Keemei.

1. Make QIIME 1 Illumina Overview Tutorial the active sheet if it isn’t already.

2. Validate this sheet by clicking Add-ons > Keemei > Validate QIIME 1 mapping file:

   

3. Cells with warnings are colored yellow and cells with errors are colored red. A sidebar summarizes the validation report and lists invalid cells:

   

4. Click cell A3 in the sidebar to see why it is invalid. We see there are duplicate sample IDs in cells A3 and A5:

   

5. In the spreadsheet (not the sidebar!), hover your mouse over cell A3. This is another way to find out why a cell is invalid.

   

6. Make fixes to any number of invalid cells and re-validate by clicking Add-ons > Keemei > Validate QIIME 1 mapping file. Repeat this process until all cells are valid.

Resetting the status

1. To clear the validation status on the active sheet, resetting cell background colors to white and clearing notes, click Add-ons > Keemei > Clear validation status:

   

Locating invalid cells

Keemei’s sidebar provides a way to focus on an invalid cell in order to fix it. This feature is especially useful if you’re working with large sheets that would require scrolling to find and fix invalid cells.

1. Make QIIME 1 88 Soils the active sheet.
2. Validate this sheet by clicking Add-ons > Keemei > Validate QIIME 1 mapping file.

3. The two invalid cells (O46 and O66) are not visible in the sheet. Click the magnifying glass next to cell O46…

   

4. …to scroll to that cell in the sheet and focus on it:

   

5. Hit “Enter” after gaining focus to begin typing in the cell.

Validating SRGD files

In the previous sections we validated QIIME 1 mapping files. Keemei also supports validating SRGD files by clicking Add-ons > Keemei > Validate SRGD file. Validation results are displayed in a similar manner.

Make SRGD_example the active sheet and try validating it as an SRGD file. How many invalid cells are there?