Writing tabular data

With the write_tabular app, cogent3 “TabularTypes” (Table, DictArray, DistanceMatrix) are supported for writing to disk.

Let’s generate a cogent3 Table to use in the examples below. One way to do that is by applying the tabulate_stats app to a model result.

Writing a CSV file

To write in CSV format, we create the write_tabular app with format="csv".

Writing a TSV file

To write in TSV format, we create the write_tabular app with format="tsv".

Using write_tabular in a composed process

Instead of applying the apps sequentially as above, we can add apps into a composed process, and apply the process to a data store. In this example, we define a process that calculates an unaligned distance measure between sequences, writing these estimated distances to a tsv file.

Tip

When running this code on your machine, remember to replace path_to_dir with an actual directory path.