Extracts records from a fasta based on a list of fasta headers.
Dependencies:
- Python3
- Biopython
- Python pandas==1.3.4
python fastaParser.py <assembly.fasta> <records.txt>
If no arguments are provided, the script will return help message.
- {records file prefix}_records.fasta
- {records file prefix}_records.lengths
- {records file prefix}_remaining.fasta
- {records file prefix}_remaining.lengths
If this script is useful to you, please cite the following in your publication:
@software{FastaParser,
author = {Sim, Sheina B.},
title = {FastaParser},
url = {https://github.com/sheinasim/FastaParser}
}
Sheina B. Sim
USDA-ARS
US Pacific Basin Agricultural Research Service
Hilo, Hawaii, 96720 USA
[email protected]
This script is in the public domain in the United States per 17 U.S.C. § 105