Step 4: Edit file_factory.py

This file implements a class whose purpose is to create a list of all files that should be processed by parsomics-core.

Explanation

In file_factory.py you should include a subclass of the FileFactory class, from the parsomics-core library. The FileFactory class has ready-made code for recursively traversing a directory and creating a list of all valid files within it.

All you need to do in your implementation is specifying the file validation class that the factory should use. For that, use the class that we just implemented in validated_file.py.

Hands on

1. The template most likely generated the entire file correctly. All you need to do is remove the triple quotes and test the factory for correctness.

2. Stage file_factory.py and commit it

Result

file_factory.py

from typing import Sequence

from parsomics_core.factories import FileFactory

from .validated_file import InterproValidatedFile


class InterproFileFactory(FileFactory):
    def __init__(self, path: str, dereplicated_genomes: Sequence[str]):
        return super().__init__(
            validation_class=InterproValidatedFile,
            path=path,
            dereplicated_genomes=dereplicated_genomes,
        )