updatecsv

Command-line tool for transferring data from one CSV file to another. This is done based on a unique identifiers column (e.g., ID numbers).

It is intended for updating data from experiments, where each row represents an experimental unit and each column a variable. Thus, the program it is like a merge, but with a few constraints:

• It does not add new rows.
• The identifiers in the input file must be a subset of those in the original file.
• Data in the original file cannot be overwritten.

The program creates a backup file, updates the original file, and prints the changes in the terminal.

Why?

I work with many plants, each identified by a unique ID. During and after experiments, I measure various attributes for these plants, but the new data is rarely ordered by ID. Manually entering values into a spreadsheet—jumping from plant ID 4 to 132, then 54, and so on—is both time-consuming and prone to errors.

Usage

updatecsv [OPTIONS] original_data.csv input_data.csv

Options:
  -s   [separator]    Specify the item separator in the csv files (default is comma)
  -d                  Dry-run with no changes made
  --by [column name]  Defines the column to use for the merge (default is id)

Examples

Adding new data with default values (comma as separator, id as merge column):

updatecsv experiment_2023.csv aboveground_biomass.csv

Adding new data with custom options (semicolon as the separator, dry-run mode, and a custom merge column named 'key'):

updatecsv -s ';' -d --by key experiment_2022.csv alkaloids.csv

Installation

git clone https://github.com/fdecunta/updatecsv.git
cd updatecsv
sudo make install

To remove the program:

cd updatecsv
sudo make uninstall

Requirements

• Python 3.6+
• CSV library