Written for https://www.biostars.org/p/223495

FilterFasta.py

import sys, os, glob
from Bio import SeqIO

def getfiles():
  files = glob.glob("*.csv") + glob.glob(".tfa")
  print("Found {} files to filter".format(len(files)))
  return(files)
         
def filter(inputfile):
  countAll = 0
  countGood = 0
  goodproteins=[]
  for record in SeqIO.parse(sys.argv[1],'fasta'):
    countAll += 1 #For each record in the file, increment countAll
    if len(record.seq) > 20:
      countGood += 1 #For each good record in the file, increment countGood
      goodproteins.append(record)
  SeqIO.write(goodproteins,filtered_file,"fasta")
  print("Filtering retained {} out of {} sequences in this file".format(countGood, countAll))

def main():
  if sys.argv[1] == 'dir': #Alternatively, could check if the path in sys.argv[1] is a file or a directory and act accordingly
      files = getfiles()
  else:
      if os.path.isfile(sys.argv[1]):
        files = [sys.argv[1]]
      else:
        sys.exit("Invalid input!")
  for input in files:
    filter(input)
    
main()