Simple Fasta Editing

Quickly alter the headers of fasta entries using a CSV.

Installation

git clone git@github.com:brwnj/fastedit.git
cd fastedit
python setup.py install

Usage

Our test fasta:

>entry_1
ACGTACTGACGTACTG
>entry_2
ACGTACTGACGTAC
>entry_3
TGACGTACGTA

Retrieve the headers from the fasta:

fastedit get --verbose -o headers.csv my.fasta
3 headers exported.

Edit your CSV file to rename or exclude from resultant fasta:

entry_1,new_name_for_entry_1
entry_2,

Create new fasta using your CSV:

fastedit put --verbose my.fasta headers.csv
>new_name_for_entry_1
ACGTACTGACGTACTG
>entry_2
ACGTACTGACGTAC
Input fasta contained 3 records
You renamed 1 and kept a total of 2