Pfam.jl downloads and caches files from Pfam.

using Pkg
Pkg.add("Pfam")

Before downloading files, configure a local cache directory and the Pfam release to use:

import Pfam

Pfam.set_pfam_directory(mkpath(joinpath(homedir(), ".pfam")))
Pfam.set_pfam_version("35.0")

The chosen values are stored with Preferences.jl, so they persist across Julia sessions.

Each helper downloads a file the first time it is requested and then returns the local cached path.

import Pfam

pdbmap_path = Pfam.pdbmap()
hmm_path = Pfam.Pfam_A_hmm()
seed_alignment_path = Pfam.alignment_file("PF00013", :seed)

• Pfam.pdbmap()
• Pfam.Pfam_A_hmm_dat()
• Pfam.Pfam_A_hmm()
• Pfam.Pfam_A_seed()
• Pfam.Pfam_A_full()
• Pfam.Pfam_A_fasta()
• Pfam.pfamseq()
• Pfam.uniprot()
• Pfam.alignment_file(id, which=:full)

Pfam.alignment_file downloads Stockholm alignments for a Pfam family identifier such as PF00013. The which argument accepts :full, :seed, and :uniprot.