Turn your functions into composable apps

This is super easy – just use the define_app decorator! This generates a wrapper class that has a reference to your function and can then become part of a composed function.

You need two things, your function and type hints on the first argument and the function return type.

A simple example

Let’s make an app that returns the elements of an alignment up to a specified index, with the index being a keyword argument. We now define a decorated function up_to and import the type hints and the decorator.

from cogent3.app.composable import define_app
from cogent3.app.typing import AlignedSeqsType

@define_app
def up_to(val: AlignedSeqsType, index=2) -> AlignedSeqsType:
    return val[:index]

We create an app instance for a specific value of index

first4 = up_to(index=4)
first4

up_to(index=4)

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

You use first4() like all composable apps, e.g.

from cogent3 import make_aligned_seqs

aln = make_aligned_seqs(
    data=dict(a="GCAAGCGTTTAT", b="GCTTTTGTCAAT"), array_align=False, moltype="dna"
)
result = first4(aln)
result

	0
a	GCAA
b	..TT

2 x 4 dna 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 SerialisableType indicates the data has the ability to be converted to json.

from typing import Union

from cogent3.app.composable import define_app
from cogent3.app.typing import SeqsCollectionType, SerialisableType

T = Union[SeqsCollectionType, SerialisableType]

@define_app
def rename_seqs(seqs: SeqsCollectionType) -> T:
    """upper case names"""
    return seqs.rename_seqs(lambda x: x.upper())

renamer = rename_seqs()
result = renamer(aln)
result

	0
A	GCAAGCGTTTAT
B	..TTTT..CA..

2 x 12 dna alignment

A user app with a different output type

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

from cogent3.app.composable import define_app
from cogent3.app.typing import AlignedSeqsType, PairwiseDistanceType

@define_app
def get_dists(aln: AlignedSeqsType, calc="hamming") -> PairwiseDistanceType:
    return aln.distance_matrix(calc=calc, show_progress=False)

percent_dist = get_dists(calc="percent")
result = percent_dist(aln)
result

names	a	b
a	0.0000	0.5000
b	0.5000	0.0000