Header remover

kyles_script.py

import argparse
from Bio import SeqIO
parser=argparse.ArgumentParser()

parser.add_argument("inputFile", help="input fasta file")
parser.add_argument("outputFile",help="output file name")
parser.add_argument("sampleName",help="sample name to be removed")

args = parser.parse_args()

fileOut = open(args.outputFile, "w")

if args.sampleName:
        for seq_record in SeqIO.parse(args.inputFile, "fasta"):
                if not (args.sampleName in seq_record.id):
                        SeqIO.write(seq_record,args.input_file,"fasta")
fileOut.close()