Custom composable apps

You can make a simple customised app using the user_function app. This is a wrapper class that takes a reference to your function and the input, output and data types. The resulting app can then become part of a composed function.

Defining a user_function requires you consider four things.

func

A function you have written. This is required.

input_types

A type, or collection of type that your function can handle. This setting dictates what other apps have an output that is a compatable input for your function.

output_types

A type, or collection of type that your function produces. This setting dictates what other apps can have yours as input.

data_types

The data class names, as strings, that your function can handle. Not required, but useful.

A simple example

We make a very simple function first4, that returns the first 4 elements of an alignment.

Now we define a user_function instance that takes and returns an ALIGNED_TYPE.

The repr() of your user_function instance indicates the wrapped function and the module it’s in.

You use it like all composable apps which we demonstrate using a small sample alignment.

Renaming sequences

This time we wrap a method call on a SequenceCollection (and the alignment sub-classes) for renaming sequences. We also illustrate here that to support both aligned and unaligned data types as input/output, we have to include these in the construction of the custom function.

Note

The SERIALISABLE_TYPE indicates the data has the ability to be converted to json.

A user function for with a different output type

In this example, we make an function that returns DistanceMatrix of an alignment.