Filter FASTA files by sequence id using a regular expression

Use a regular expression for filtering sequences by id from a FASTA file, e.g. just certain chromosomes from a genome. There are other tools as part of bigger packages to install (and no regex support), mostly awk-based awkward (sorry for the pun) bash solutions, and scripts using packages that one needs to install and with still no support for regular expressions. This however is a simple, straightforward little python script for a simple task. It doesn’t do anything else and doesn’t need anything but a stock python installation. Based on the FASTA reader snippet

Download here. 

Usage:

python FASTAfilter.py [-h] regex infile outfile

From a FASTA-file with multiple >entries, filter by sequence ids using a
regex.

positional arguments:
regex Regex to filter entry ids, e.g. ‘chr[1-4]’. Note that the id does not contain the initial > character.
infile A FASTA input file, usually with multiple entries.
outfile The new file with only the matching entries.

optional arguments:
-h, –help show this help message and exit

Leave a Reply

Your email address will not be published. Required fields are marked *


Please simplify: \(\cos (180\pi)=\)