sort_fasta.py
from Bio import SeqIO
import argparse
parser = argparse.ArgumentParser(description="Sort fasta files by label.")
parser.add_argument("--fasta", "-f")
args = parser.parse_args()
handle = open(args.fasta, "rU")
l = SeqIO.parse(handle, "fasta")
sortedList = [f for f in sorted(l, key=lambda x : x.id)]
for s in sortedList:
print s.description
print str(s.seq)