[![CI](https://github.com/tseemann/any2fasta/actions/workflows/CI.yml/badge.svg)](https://github.com/tseemann/any2fasta/actions/workflows/CI.yml)
[![GitHub release (latest by date)](https://img.shields.io/github/v/release/tseemann/any2fasta)](https://github.com/tseemann/any2fasta/releases)
[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
![Don't judge me](https://img.shields.io/badge/Language-Perl_5-steelblue.svg)
[![Bioconda Downloads](https://img.shields.io/conda/dn/bioconda/any2fasta.svg)](https://anaconda.org/bioconda/any2fasta)

# any2fasta

Convert various sequence formats to FASTA

## Quick start
```
% conda install -c bioconda any2fasta
% any2fasta genome.gbk > genome.fasta
% any2fasta seq.gbk.gz > seq.fasta
% any2fasta protein.pdb.bz2 > protein.fasta
```

## Motivation

You may wonder why this tool even exists.  Well, I tried to do the right
thing and use established tools like `readseq` and `seqret` from EMBOSS, but
they both mangled IDs containing `|` or `.` characters, and
there is no way to fix this behaviour.  This resulted in inconsitences
between my `.gbk` and `.fna` versions of files in my pipelines.

Then you may wonder why I didn't use Bioperl or Biopython. Well they are
heavyweight libraries, and actually very slow at parsing Genbank files.
This script uses only core Perl modules, has no other dependencies, and
runs very quickly.

It supports the following input formats:

1. Genbank flat file, typically `.gb`, `.gbk`, `.gbff` (starts with `LOCUS`)
2. EMBL flat file, typically `.embl`, (starts with `ID`)
3. GFF with sequence, typically `.gff`, `.gff3` (starts with `##gff`)
4. FASTA DNA, typically `.fasta`, `.fa`, `.fna`, `.ffn` (starts with `>`)
5. FASTQ DNA, typically `.fastq`, `.fq` (starts with `@`)
6. CLUSTAL alignments, typically `.clw`, `.clu` (starts with `CLUSTAL` or `MUSCLE`)
7. STOCKHOLM alignments, typically `.sth` (starts with `# STOCKHOLM`)
8. GFA assembly graph, typically `.gfa` (starts with `^[A-Z]\t`)
9. PDB protein data bank structure, typicall `.pdb` (starts with `^HEADER`)

Files may be compressed with:

1. gzip, typically `.gz`
2. bzip2, typically `.bz2`
3. zip, typically `.zip`

plus any other formats supported by
your installed version of Perl's
[`IO::Uncompress::AnyUncompress`](https://perldoc.perl.org/IO::Uncompress::AnyUncompress#DESCRIPTION)
module.

## Installation

`any2fasta` has no dependencies except [Perl 5.10](https://www.perl.org/)
or higher. It only uses core modules, so no CPAN needed.

### Conda
```
% conda install -c bioconda any2fasta
```
### Direct script download
```
% cd /usr/local/bin  # choose a folder in your $PATH
% wget https://raw.githubusercontent.com/tseemann/any2fasta/master/any2fasta
% chmod +x any2fasta
```
### Github
```
% git clone https://github.com/tseemann/any2fasta.git
% cp any2fasta/any2fasta $HOME/.local/bin # choose a folder in your $PATH
```

## Test Installation

### Sinple check
```
% ./any2fasta -v
any2fasta 1.0.2

% ./any2fasta -h
NAME
  any2fasta 1.0.2
SYNOPSIS
  Convert various sequence formats into FASTA
USAGE
  any2fasta [options] file.{gb,fa,fq,gff,gfa,clw,sth}[.gz,bz2,zip] > output.fasta
OPTIONS
  -h       Print this help
  -v       Print version and exit
  -q       No output while running, only errors
  -k       Skip, don't die, on bad input files
  -n       Replace non-[AGTC] with 'N'
  -l       Lowercase the sequence
  -u       Uppercase the sequence
  -g       Include VERSION from GBK/EMBL files
  -s       Strip sequence descriptions (FASTA,FASTQ)
END
```
### Extensive test
```
% bats $(dirname $(which any2fasta))/test/test.sh

 ✓ Script syntax check
 ✓ Version
 ...
 ✓ Multiple sequence with one bad one
 ✓ Allow skipping over bad files

29 tests, 0 failures, 2 skipped
```

## Examples
```
% any2fasta ref.gbk > ref.fna

% any2fasta in.fasta > out.fasta  # should behave like "cat"

% any2fasta prokka.gff > prokka.fna  # only if GFF has FASTA appended

% any2fasta - < file.gb > file.fasta  # '-' means stdin

% anyfasta genes.gff.gz > genes.ffn  # automatically decompresses

% any2fasta 1.gb 2.fa.gz 3.gff.bz2 - > out.fa  # multiple files and stdin

% any2fasta R1.fq.gz | bzip2 > R1.fa.bz2  # 'seqtk seq -A' is much faster

% any2fasta -q 23S.clw > 23S.aln  # gaps '-' will be preserved

% any2fasta pfam4321.sth > pfam4321.aln  # '.' gaps will become '-'
```

## Options

* `-n` replaces any characters that aren't A,C,G,T with N (gaps preserved)
* `-l` will lowercase all the letters
* `-u` will uppercase all the letters
* `-q` will prevent logging messages being printed
* `-k` will warn of bad inputs and continue on. not stop and error
* `-g` will appened the version to the sequence ID 
* `-s` removes `desc` from `>id desc` in FASTA,FASTQ,GFF

## Issues

Submit feedback to the [Issue Tracker](https://github.com/tseemann/any2fasta/issues)

## License

[GPL v3](https://raw.githubusercontent.com/tseemann/any2fasta/master/LICENSE)

## Author

[Torsten Seemann](http://tseemann.github.io/)
