FastaParser

Extracts records from a fasta based on a list of fasta headers.

Dependencies:

• Python3
• Biopython
• Python pandas==1.3.4

Usage

python fastaParser.py <assembly.fasta> <records.txt>

If no arguments are provided, the script will return help message.

Outputs

• {records file prefix}_records.fasta
• {records file prefix}_records.lengths
• {records file prefix}_remaining.fasta
• {records file prefix}_remaining.lengths

Citation

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