https://github.com/marcom/biostockholm.jl

Julia parser for the Stockholm file format (.sto) used for multiple sequence alignments (Pfam, Rfam, etc)
https://github.com/marcom/biostockholm.jl

Last synced: 8 days ago
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Julia parser for the Stockholm file format (.sto) used for multiple sequence alignments (Pfam, Rfam, etc)

• Host: GitHub
• URL: https://github.com/marcom/biostockholm.jl
• Owner: marcom
• License: mit
• Created: 2022-10-06T18:54:18.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2024-01-17T20:01:44.000Z (about 1 year ago)
• Last Synced: 2024-12-13T04:35:42.601Z (about 1 month ago)
• Language: Julia
• Size: 34.2 KB
• Stars: 5
• Watchers: 2
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# BioStockholm.jl

[![Build Status](https://github.com/marcom/BioStockholm.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/marcom/BioStockholm.jl/actions/workflows/CI.yml?query=branch%3Amain)

[![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)

Julia parser for the [Stockholm file

format](https://en.wikipedia.org/wiki/Stockholm_format) (.sto) used

for multiple sequence alignments of protein, RNA, or DNA sequences

(Pfam, Rfam, etc databases).  This package uses

[Automa.jl](https://github.com/BioJulia/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

```julia

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](https://github.com/diegozea/MIToS.jl) is a package for

analysing protein sequences that also supports parsing the Stockholm

format (and many more things).