any2fasta

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  "desc": "Convert various sequence formats to FASTA",
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  "full_name": "any2fasta",
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  "github_last_commit_at": "2025-12-30T04:47:05Z",
  "github_readme_excerpt": "[![CI](https://github.com/tseemann/any2fasta/actions/workflows/CI.yml/badge.svg)](https://github.com/tseemann/any2fasta/actions/workflows/CI.yml)\n[![GitHub release (latest by date)](https://img.shields.io/github/v/release/tseemann/any2fasta)](https://github.com/tseemann/any2fasta/releases)\n[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n![Don\u0027t judge me](https://img.shields.io/badge/Language-Perl_5-steelblue.svg)\n[![Bioconda Downloads](https://img.shields.io/conda/dn/bioconda/any2fasta.svg)](https://anaconda.org/bioconda/any2fasta)\n\n# any2fasta\n\nConvert various sequence formats to FASTA\n\n## Quick start\n```\n% conda install -c bioconda any2fasta\n% any2fasta genome.gbk \u003e genome.fasta\n% any2fasta seq.gbk.gz \u003e seq.fasta\n% any2fasta protein.pdb.bz2 \u003e protein.fasta\n```\n\n## Motivation\n\nYou may wonder why this tool even exists.  Well, I tried to do the right\nthing and use established tools like `readseq` and `seqret` from EMBOSS, but\nthey both mangled IDs containing `|` or `.` characters, and\nthere is no way to fix this behaviour.  This resulted in inconsitences\nbetween my `.gbk` and `.fna` versions of files in my pipelines.\n\nThen you may wonder why I didn\u0027t use Bioperl or Biopython. Well they are\nheavyweight libraries, and actually very slow at parsing Genbank files.\nThis script uses only core Perl modules, has no other dependencies, and\nruns very quickly.\n\nIt supports the following input formats:\n\n1. Genbank flat file, typically `.gb`, `.gbk`, `.gbff` (starts with `LOCUS`)\n2. EMBL flat file, typically `.embl`, (starts with `ID`)\n3. GFF with sequence, typically `.gff`, `.gff3` (starts with `##gff`)\n4. FASTA DNA, typically `.fasta`, `.fa`, `.fna`, `.ffn` (starts with `\u003e`)\n5. FASTQ DNA, typically `.fastq`, `.fq` (starts with `@`)\n6. CLUSTAL alignments, typically `.clw`, `.clu` (starts with `CLUSTAL` or `MUSCLE`)\n7. STOCKHOLM alignments, typically `.sth` (starts with `# STOCKHOLM`)\n8. GFA assembly graph, typica",
  "github_repo": "tseemann/any2fasta",
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  "homepage": "https://github.com/tseemann/any2fasta",
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  "license": "GPL-3.0-only",
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  "ruby_source_path": "Formula/a/any2fasta.rb",
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