Edit or replace certain character in fasta header from a large fasta sequence file

Question

[Pratanu]

Hi all, I have 2.5 million covid-19 sequence file and i want to edit or replace certain character in fasta header for those sequences.

can anyone please give some type of algorithm to do so?

Thank You

Answer 1

[Wayne]

You put this in Python or R. Most likely though using sed would be among the fastest. The find and replace syntax is spelled out here.

sed -i -e 's/abc/XYZ/g' file.txt

Though recently I saw a recommendation for sd for the find and replace aspect. (sed can do more than just that.) I haven't checked out sd myself yet. It has examples there.