Download.jl

# Download Pfam
# =============

"""
It downloads a gzipped Stockholm alignment from InterPro for the Pfam family with the
given `pfamcode`.

By default, it downloads the `full` Pfam alignment. You can use the `alignment` keyword
argument to download the `seed` or the `uniprot` alignment instead. For example,
`downloadpfam("PF00069")` will download the **full alignment** for the
*PF00069 Pfam family*, while `downloadpfam("PF00069", alignment="seed")` will download the
**seed alignment** of the family.

The extension of the downloaded file is `.stockholm.gz` by default; you can change it
using the `filename` keyword argument, but the `.gz` at the end is mandatory.
"""
function downloadpfam(
    pfamcode::String;
    filename::String = "$pfamcode.stockholm.gz",
    alignment::String = "full",
    kargs...,
)
    if alignment != "full" && alignment != "seed" && alignment != "uniprot"
        throw(ErrorException("alignment must be \"full\", \"seed\" or \"uniprot\""))
    end
    endswith(filename, ".gz") || error("filename must end in .gz")
    if occursin(r"^PF\d{5}$"i, pfamcode)
        download_file(
            "https://www.ebi.ac.uk/interpro/wwwapi/entry/pfam/$pfamcode/?annotation=alignment:$alignment&download",
            filename;
            kargs...,
        )
    else
        throw(ErrorException("$pfamcode is not a correct Pfam code"))
    end
end