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 module.

Installation

any2fasta has no dependencies except Perl 5.10 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

License

GPL v3

Author

Torsten Seemann