BioStockholm.jl
Julia parser for the Stockholm file format (.sto) used for multiple sequence alignments (Pfam, Rfam, etc). This package uses Automa.jl under the hood to generate a finite state machine parser.
Installation
Enter the package mode from the Julia REPL by pressing ], then
install with:
add BioStockholm
Usage
using BioStockholm
msa = MSA{Char}(;
seq = Dict("human" => "ACACGCGAAA.GCGCAA.CAAACGUGCACGG",
"chimp" => "GAAUGUGAAAAACACCA.CUCUUGAGGACCU",
"bigfoot" => "UUGAG.UUCG..CUCGUUUUCUCGAGUACAC"),
GC = Dict("SS_cons" => "...<<<.....>>>....<<....>>.....")
)
# read from file
# example2.sto contains an example Stockholm file
msa_path = joinpath(dirname(pathof(BioStockholm)), "..",
"test", "example2.sto")
msa_str = read(msa_path, String)
print(msa_str)
# read from a file or parse from a String
msa = read(msa_path, MSA)
msa = parse(MSA, msa_str)
# write to a file
write("foobar.sto", msa)
# pretty-print
print(msa)
print(stdout, msa)Limitations / TODO
- when writing, long sequences or text is never split over multiple lines
- integrate with BioJulia string types
Related packages
MIToS.jl is a package for analysing protein sequences that also supports parsing the Stockholm format (and many more things).