Bio Ex

Bioinformatics tools for Elixir.

Modules

Restriction

An Elixir implementation for restriction enzyme data based on the REBASE database.

Sequence

Sequence manipulations, validations and general IUPAC data.

Tasks

bio.restriction.*

update

Download and build the restriction enzymes using the REBASE Emboss files.

Parameters:

• --email/-p: email to use as password for the FTP of REBASE files
• --cache-dir/-d: directory to look for and store the emboss files

download

Download the REBASE emboss files. If the files exist in --cache-dir, then the download will be skipped.

Parameters:

• --email/-p: email to use as password for the FTP of REBASE files
• --cache-dir/-d: directory to look for and store the emboss files

build

Generate Bio.Restriction.Enzyme module content from the REBASE emboss files using the Bio.Rebase.Emboss.parse/1 function.

Parameters:

• --cache-dir/-d: directory to look the emboss files

bio.random

dna

Generate a number of random DNA sequences. See Erlang docs to understand the available options for algorithms.

Parameters:

• --seed/-s: seed value for the RNG (defaults to :random defaults)
• --algorithm/-a: algorithm value for the RNG (defaults to :exsss)
• --outfile/-f: path for output to be loaded (required)
• --seq-size/-z: size for the generated sequence in nucleotides (required)
• --seq-count/-c: number of sequences to generate (required)

Installation

Available in Hex.

The package can be installed by adding bio_ex to your list of dependencies in mix.exs:

def deps do
  [
    {:bio_ex, "~> 0.1.0"}
  ]
end

Documentation can be generated with ExDoc and published on HexDocs. Once published, the docs can be found at https://hexdocs.pm/restrict_ex.