The old top-level package. Public Archive only.
Bioinformatics tools for Elixir.
An Elixir implementation for restriction enzyme data based on the REBASE database.
Sequence manipulations, validations and general IUPAC data.
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 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
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
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:randomdefaults)--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)
The package can be installed by adding bio_ex to your list of dependencies
in mix.exs:
def deps do
[
{:bio_ex, "~> 0.3.0"}
]
endDocumentation can be generated with ExDoc and published on HexDocs. Once published, the docs can be found at https://hexdocs.pm/restrict_ex.
Big shout out to the BioPython team. I used many data sources according to their implementations, and referenced many details of the file types for parsing from their implementations as well. While I wouldn't consider this a port, it is definitely spiritually related to that project!