rename_fasta_id

rename_fasta_id

rename_fasta_id.pl is a script to rename fasta IDs according to regular expressions.

• Synopsis
• Description
• Usage
• Options
  • Mandatory options
  • Optional options
• Output
• Run environment
• Author - contact
• Citation, installation, and license
• Changelog

Synopsis

perl rename_fasta_id.pl -i file.fasta -p "NODE_.+$" -r "K-12_" -n -a c > out.fasta

or

zcat file.fasta.gz | perl rename_fasta_id.pl -i - -p "coli" -r "" -o > out.fasta

Description

This script uses the built-in Perl substitution operator s/// to replace strings in FASTA IDs. To do this, a pattern and a replacement have to be provided (Perl regular expression syntax can be used). The leading '>' character for the FASTA ID will be removed before the substitution and added again afterwards. FASTA IDs will be searched for matches with the pattern, and if found the pattern will be replaced by the replacement.

IMPORTANT: Enclose the pattern and the replacement in quotation marks (' or ") if they contain characters that would be interpreted by the shell (e.g. pipes '|', brackets etc.).

For substitutions without any appendices in a UNIX OS you can of course just use the great sed (see man sed), e.g.:

sed 's/^>pattern/>replacement/' file.fasta

Usage

perl rename_fasta_id.pl -i file.fasta -p "T" -r "a" -c -g -o

Options

Mandatory options

• -i, -input

Input FASTA file or piped STDIN (-) from a gzipped file

• -p, -pattern

Pattern to be replaced in FASTA ID

• -r, -replacement

Replacement to replace the pattern with. To entirely remove the pattern use '' or "" as input for -r.

Optional options

• -h, -help

Help (perldoc POD)

• -c, -case-insensitive

Match pattern case-insensitive

• -g, -global

Replace pattern globally in the string

• -n, -numerate

Append a numeration/the count of the pattern hits to the replacement. This is e.g. useful to number contigs consecutively in a draft genome.

• -a, -append

Append a string after the numeration, e.g. 'c' for chromosome

• -o, -output

Verbose output of the substitutions that were carried out, printed to STDERR

• -v, -version

Print version number to STDERR

Output

• STDOUT

The FASTA file with substituted ID lines is printed to STDOUT. Redirect or pipe into another tool as needed.

Run environment

The Perl script runs under Windows and UNIX flavors.

Author - contact

Andreas Leimbach (aleimba[at]gmx[dot]de; Microbial Genome Plasticity, Institute of Hygiene, University of Muenster)

Citation, installation, and license

For citation, installation, and license information please see the repository main README.md.

Changelog

• v0.1 (09.11.2014)