#bioinformatics #data #science #command-line #reproducibility #command-line-interface #command-line-utilities

bin+lib alpine-core

ALPINE (Anachronistic Lineage and Persistent INfection Explorer) Core Utilities

3 releases

0.1.2 Jan 23, 2024
0.1.1 Jan 20, 2024
0.1.0 Jan 19, 2024

#198 in Biology

MIT license

693 lines

ALPINE (Anachronistic Lineage and Persistent INfection Explorer) Core Utilities

Open Source Starter Files Rust CI Crates.io Crates.io

See the original ALPINE workflow repo here. This repo contains the in-development Rust source code meant to replace the core components of the ALPINE pipeline that were previously written in Julia. This tool has a rich command line interface intended to allow researchers to perform ALPINE-type analyses without invoking the entire Nextflow pipeline and associated Docker containers.

When you run alpine --help, the tool usage that comes up looks like this:


ALPINE: Anachronistic Lineage and Persistent INfection Explorer

Command line interface for the core Rust components of ALPINE.
These commands are called in the full pipeline, which is imple-
mented in Nextflow alongside `seqkit`, `csvtk`, `nushell`,
`vsearch`, and a bin of bespoke Python scripts. However, users
may also use the commands available in this crate to run
similar analyses themselves via the command line.

Usage: alpine [OPTIONS] [COMMAND]

  replace-gaps       Replace FASTA gap symbols '-' with masked bases 'N'.
  filter-by-n        Filter out FASTA records with more than the desired number of masked 'N' bases.
  separate-by-month  Use collection dates from FASTA record metadata to sort all FASTA records into a separate FASTA for each year-month combination.
  distance-matrix    Compute a symmetric pairwise distance matrix based on how dissimilar sequences in the provided FASTA are to one another.
  help               Print this message or the help of the given subcommand(s)

  -v, --verbose...         Increase logging verbosity
  -q, --quiet...           Decrease logging verbosity
  -t, --threads <THREADS>  [default: 3]
  -h, --help               Print help

To set up and try out the toolset, either install the Rust toolchain and build it yourself or run ./easy_install in this directory after cloning it to your machine.


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