text: import sys
  import numpy as np
  from Bio import SeqIO
  
  def getData(inFile, fragLen, stride=1):
  
  	seqs = [line for line in SeqIO.parse(inFile, 'fasta')]
  	names = [(s.id, len(s)) for s in seqs]
  
  	allData = []
  	seqIdx = 0
  
  	for s in seqs:
  		seq = str(s.seq).upper()
  		frags = fragment(seq, fragLen, stride)
  		for f in frags:
  			allData.append([seqIdx, f.upper()])
  		seqIdx += 1
  
  	
  	return np.array(allData), np.array(names)
  
  def fragment(seq, fragLen, stride):
  
  	# If seq is too short, pad with X (unknown amino acid)
  	if len(seq) < fragLen:
  		print('padded sequence len ', len(seq))
  		seq = seq.ljust(fragLen, 'X')
  
  	frags = []
  
  	for i in range(0, len(seq) - fragLen + 1, stride):
  		f = seq[i:i+fragLen]
  		frags.append(f)
  
  	return frags
  
  if __name__ == "__main__":
  
  	try: inFile = sys.argv[1]
  	except: inFile = 'sample_data/3PGK_PROTEIN.fasta'
  
  	try: fragLen = int(sys.argv[2])
  	except: fragLen = 14
  
  	data, names = getData(data, fragLen)
  
  	np.savetxt('temp/data', data, fmt='%s')
  	np.savetxt('temp/names', names, fmt='%s')
  
  