使用 Homebrew, apt 安装 any2fasta

项目链接

• 主页

命令和别名

• any2fasta

项目历史

The official README explains the motivation directly: existing tools such as readseq and EMBOSS seqret mangled identifiers containing characters like pipes or dots, and heavier libraries such as BioPerl and Biopython were more dependency-heavy and slower for the author's pipeline needs. any2fasta was written as a fast, dependency-light alternative focused on preserving useful IDs.

The tool supports GenBank, EMBL, GFF with sequence, FASTA, FASTQ, CLUSTAL, STOCKHOLM, GFA, and PDB input, with gzip, bzip2, zip, and other Perl IO::Uncompress-supported compression formats.

采用历史

any2fasta's adoption is mostly in bioinformatics packaging rather than broad developer-tool culture. The input facts list Homebrew, Debian, and Ubuntu packages, and the README advertises Bioconda installation and shows a Bioconda downloads badge.

Its portability comes from the constraint that it requires Perl 5.10 or higher and only core modules, so it is easy for Linux distributions, Conda channels, and Homebrew to ship without pulling in a scientific Python or BioPerl stack.

使用方式

The common usage is shell redirection: run any2fasta on a GenBank, FASTQ, GFF, PDB, or compressed input file and redirect FASTA output. The README examples include converting genome.gbk, seq.gbk.gz, protein.pdb.bz2, stdin, multiple inputs, and compressed FASTQ streams.

Options are intentionally small and pipeline-friendly: print help/version, quiet mode, skip bad inputs, normalize nucleotide case, replace non-AGTC characters with N, include GBK/EMBL version IDs, or strip FASTA/FASTQ descriptions.

为什么软件包爱好者会关心

any2fasta is a good example of the bioinformatics single-script package that earns its place because it avoids both heavyweight frameworks and subtle format-loss bugs. It is not a platform, but it is exactly the kind of executable that becomes sticky in Snakemake, Nextflow, and ad hoc lab pipelines.

For package managers, its simplicity is the feature: a Perl script, GPL-3.0 licensing, no CPAN dependency tree, and tests that can be run with bats.

时间线

• 2010s: any2fasta is developed as a lightweight alternative to readseq, EMBOSS seqret, BioPerl, and Biopython for FASTA conversion.
• 2020s: The project is packaged across Bioconda and OS package managers, including Homebrew, Debian, and Ubuntu in the input facts.
• 2025: The public tag list reaches v0.8.1 in the official Git repository.

Related projects

• readseq and EMBOSS seqret are named by upstream as tools any2fasta was designed to avoid for ID-preservation reasons.
• BioPerl and Biopython are named by upstream as heavier libraries not needed for this script's conversion task.
• Bioconda is an important distribution channel for bioinformatics users.

来源

• Official README and source_facts.package-manager/license.