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import sys
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
if(len(sys.argv) <3):
print('two arguments needed: input path, output path')
exit(2)
with open(sys.argv[1],'r') as inFile:
with open(sys.argv[2], "w") as output_handle:
SeqIO.write(list(SeqIO.parse(inFile,'stockholm')), output_handle, "fasta")