gistfile1.txt

import argparse
from __future__ import with_statement
from Bio import SeqIO

def main():
  parser = argparse.ArgumentParser()
  parser.add_argument("inputFile", help="Input FASTA file")
  parser.add_argument("outputFile",help="Filtered FASTA output")
  parser.add_argument("-d", "--header", default=None, dest="sampleName", help="Sample name to remove")
  args = parser.parse_args()

  if not args.sampleName:
    raise Exception('Please specify a sample name to remove.')

  with open(args.outputFile, "w") as fileOut:
    for seq_record in SeqIO.parse(args.inputFile, "fasta"):
      if args.sampleName not in seq_record.id:
        fileOut.write(seq_record.format("fasta"))

if __name__ == '__main__':
  main()

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