https://github.com/nylander/translate_fasta_headers

Translate long fasta headers to short - and back!
https://github.com/nylander/translate_fasta_headers

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Translate long fasta headers to short - and back!

• Host: GitHub
• URL: https://github.com/nylander/translate_fasta_headers
• Owner: nylander
• License: mit
• Created: 2013-03-14T22:18:50.000Z (over 13 years ago)
• Default Branch: main
• Last Pushed: 2024-04-17T13:49:02.000Z (about 2 years ago)
• Last Synced: 2024-04-17T20:08:33.682Z (about 2 years ago)
• Language: Perl
• Size: 332 KB
• Stars: 4
• Watchers: 3
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# 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] 

    $ replace_taxon_labels_in_newick.pl [options] 

## 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):

    $ translate_fasta_headers.pl long.fas > short.fas

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

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=` --  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=` --  Specify output file for the fasta sequences.

  **Note**: If `--out=` is specified, the translation file will be

  named `.translation.tab`. This simplifies back translation.  If, on

  the other hand, `--out` is not used, the translation file will be named after

  the infile!

- `-i, --in=` --  Specify name of fasta file. Can be skipped as

  script reads files from STDIN.

- `-n, --notab` --  Do not create a translation file.

- `-p, --prefix=` --  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=` --  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=` --  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`](translate_fasta_headers.pl) -- Perl script

- [`replace_taxon_labels_in_newick.pl`](replace_taxon_labels_in_newick.pl) --  Perl script

- [`data/long.fas`](data/long.fas) --  Example file with long fasta headers

- [`data/short.fas.translation.tab`](data/short.fas.translation.tab) --  Example translation table

- [`data/short.fas`](data/short.fas) --  Example output with short fasta headers

- [`data/short.fas.phy`](data/short.fas.phy) --  Example Newick tree with short labels

- [`README.md`](README.md) --  Documentation, markdown format

- [`README.pdf`](README.pdf) --  Documentation, PDF format

## License and Copyright

Copyright (c) 2013-2024 Johan Nylander

[LICENSE](LICENSE)