Translate fasta headers

Translate long fasta headers to short - and back!

Your alignment program X doesn't allow strings longer than n characters, but all your info is in the fasta headers of your file. What to do?

Use translate_fasta_headers.pl on your fasta file to create short labels and a translation table. Run your program X, and then back-translate your fasta headers by running translate_fasta_headers.pl again!

And if you created a tree with the short (or long) labels, try to back-translate using replace_taxon_labels_in_newick.pl!

If you only wish to transform your long fasta headers to short, without keeping the information about how they where translated, the quick solution might be to use awk:

$ awk '/>/{$0=">Seq_"++n}1' long.fas

But, if you want to be able to back-translate, read on!

Description

Replace fasta headers with headers taken from tab delimited file. If no tab file is given, the (potentially long) fasta headers are replaced by short labels "Seq_1", "Seq_2", etc, and the short and original headers are printed to a translation file.

If you wish, you may choose your own prefix (instead of Seq_). This could be handy if, for example, you wish to concatenate files.

The script for translating labels in Newick trees is somewhat limited in capacity due to the restrictions and/or peculiarities of the Newick tree format. Use with caution.

Usage

$ translate_fasta_headers.pl [options] <fasta input>
$ replace_taxon_labels_in_newick.pl [options] <newick file>

Examples

From long to short labels:

$ translate_fasta_headers.pl --out=short.fas long.fas

And back, using a translation table:

$ translate_fasta_headers.pl --tabfile=short.fas.translation.tab short.fas

Slightly shorter version (see note about the --out option below about the name of the auto-generated translation file!):

$ translate_fasta_headers.pl long.fas > short.fas
$ translate_fasta_headers.pl -t long.fas.translation.tab short.fas

Handle compressed (gzip) fasta files:

$ translate_fasta_headers.pl long.fas.gz | gzip > short.fas.gz
$ translate_fasta_headers.pl -t long.fas.gz.translation.tab short.fas.gz

Read fasta format from STDIN

$ cat short.fas | ./translate_fasta_headers.pl -t short.fas.translation.tab -

Use your own prefix:

$ translate_fasta_headers.pl --prefix='Own_' long.fas

Translate short seq labels in Newick tree to long:

$ replace_taxon_labels_in_newick.pl -t long.fas.translation.tab short.fas.phy

Print seq labels in Newick tree:

$ replace_taxon_labels_in_newick.pl -l short.fas.phy

Options

Script translate_fasta_headers.pl

• -t, --tabfile=<filename> -- Specify tab-separated translation file with unique "short" labels to the left, and "long" names to the right. Translation will be from left to right.
• -o, --out=<filename> -- Specify output file for the fasta sequences. Note: If --out=<filename> is specified, the translation file will be named <filename>.translation.tab. This simplifies back translation. If, on the other hand, --out is not used, the translation file will be named after the infile (and written in the same folder as the infile)!
• -i, --in=<filename> -- Specify name of fasta file (can be gzip-compressed). Can be skipped as script reads files from ARGV.
• -n, --notab -- Do not create a translation file.
• -p, --prefix=<string> -- User your own prefix (default is Seq_). A numerical will be added to the labels (e.g. Own_1, Own_2, ...)
• -v, --version -- Print version number and quit.
• -h, --help -- Show this help text and quit.

Script replace_taxon_labels_in_newick.pl

• -t, --tabfile=<translation.tab> -- File with table describing what will be translated with what.
• -l,-p, --labels -- Print taxon labels in tree. Option does not require a translation table.
• --no-quotemeta -- Turn off escaping of special symbols in the replacements.
• -o, --out=<out.file> -- Print to outfile out.file, else to STDOUT.
• -v, --version -- Print version number and quit.
• -h, --help -- Help text.

Author

Johan Nylander

Files

• translate_fasta_headers.pl -- Perl script
• replace_taxon_labels_in_newick.pl -- Perl script
• data/long.fas -- Example file with long fasta headers
• data/long.fas.gz -- Example file with long fasta headers, gzip compressed
• data/short.fas.translation.tab -- Example translation table
• data/short.fas -- Example output with short fasta headers
• data/short.fas.phy -- Example Newick tree with short labels
• README.md -- Documentation, markdown format

License and Copyright

Copyright (c) 2013-2026 Johan Nylander

LICENSE