As a module

Convert-Pheno core is a Perl module available at CPAN.

Usage¶

The module can be used within a Perl script, but it can also be utilized in scripts written in other languages, such as Python.

use Convert::Pheno;

my $my_pxf_json_data = {
    "phenopacket" => {
        "id"      => "P0007500",
        "subject" => {
            "id"          => "P0007500",
            "dateOfBirth" => "unknown-01-01T00:00:00Z",
            "sex"         => "FEMALE"
        }
    }
};

# Create object
my $convert = Convert::Pheno->new(
    {
        data   => $my_pxf_json_data,
        method => 'pxf2bff'
    }
);

# Apply a method
my $data = $convert->pxf2bff;

Inside PerlInside Python

Find here an example script.

It should work out of the box with the containerized version.
You also have instructions in how to run it in a conda environment.

Perl inside Python, is that even possible ?

Perl easily integrates with other languages and allows for embedding them into Perl code (e.g., using Inline). However, embedding Perl code into other languages is not as simple. Fortunately, the PyPerler library provides a solution for this issue.