#bioinformatics #dna #genetics #protein #rna

app nucleob

bioinformatics: nucleobases and amino acids statistics

3 stable releases

new 1.1.1 Jan 30, 2023
1.1.0 Nov 25, 2022
1.0.0 Oct 14, 2022
1.0.0-alpha.1 Oct 10, 2022
0.0.0 Oct 2, 2022

#18 in Science

Download history 30/week @ 2022-10-12 4/week @ 2022-10-19 2/week @ 2022-10-26 1/week @ 2022-11-02 4/week @ 2022-11-16 29/week @ 2022-11-23 5/week @ 2022-11-30 1/week @ 2022-12-14 4/week @ 2022-12-21 3/week @ 2022-12-28 6/week @ 2023-01-04 11/week @ 2023-01-11 6/week @ 2023-01-18 33/week @ 2023-01-25

57 downloads per month

MIT license

165KB
1K SLoC

INTRODUCING NUCLEOB

nucleob is a tool that performs statistical analysis on .fasta files containing nucleotide or amino acid sequences. It is engineered to produce highly reliable, clearly formatted results while maintaining a minimalistic design and cross-platform compatibility.

[keywords: amino acids, bioinformatics, biology, DNA, fasta, genes, genetics, molecular, nucleic acids, nucleobases, nucleotides, proteins, RNA, scientific computing, statistics, stats]

EXAMPLES

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CITATION AND REUSE

nucleob can be modified and forked under the terms of the MIT License. When citing nucleob in research articles, it is important to refer to a specific program version, such as:

Bajdek, P., 2023. nucleob (version 1.1.1). [computer software] https://github.com/piotrbajdek/nucleob

INSTALLATION ON LINUX

nucleob is designed to be compatible with Windows and macOS, and can be easily installed using cargo. However, the primary development and testing environment for nucleob is Fedora Linux.

The current version of nucleob (v1.1.1) has been verified to work properly on Fedora Linux 37 and Ubuntu 22.10.

METHOD 1 – USING CARGO

[Recommended for programmers]

1. To install nucleob from crates.io, use the following cargo command:

cargo install nucleob

The executable will be saved in the hidden .cargo/bin/ directory within your home directory.

2a. For easy access, you may want to copy the nucleob file to the /usr/bin/ directory. This can be done by following the instructions in Method 2 (3a, 3b).

2b. As an alternative, you can add the ~/.cargo/bin/ directory to your system's PATH variable, which can be configured using rustup.

METHOD 2 – UNIVERSAL LINUX BINARIES

1. To install nucleob, first download the distro-independent binary from GitHub.

2. Then, make the file executable by running the command:

sudo chmod +x ./nucleob

3a. On most Linux distributions, install nucleob by copying the binary to /usr/bin/:

sudo cp nucleob /usr/bin/

3b. For Fedora Silverblue / Kinoite, use this command:

sudo cp nucleob /var/usrlocal/bin/

METHOD 3 – DISTRO-SPECIFIC PACKAGES

[Recommended for most users]

Distro-specific packages for .rpm and .deb-based Linux distributions are also available for download. To install nucleob on different Linux distributions, follow these instructions:

Fedora Linux / RHEL / openSUSE:

sudo rpm -i nucleob-1.1.1-1.x86_64.rpm

Fedora Silverblue / Kinoite:

rpm-ostree install nucleob-1.1.1-1.x86_64.rpm

Ubuntu:

sudo dpkg -i nucleob_1.1.1_amd64.deb

METHOD 4 – MANUAL COMPILATION

First, download and unpack the nucleob source code from GitHub. Next, to build and install the program, use the command:

cargo build --release && sudo cp target/release/nucleob /usr/bin/

No runtime deps