text: #!/usr/bin/env python2
  import sys
  
  InputFileName = sys.argv[1]
  AlnFileName = sys.argv[2]
  
  def Die(s):
  	print >> sys.stderr
  	print >> sys.stderr, sys.argv
  	print >> sys.stderr, "**ERROR**", s
  	sys.exit(1)
  
  def ReadSeqs(FileName):
  	Seqs = {}
  	Id = ""
  	File = open(FileName)
  	while 1:
  		Line = File.readline()
  		if len(Line) == 0:
  			return Seqs
  		if len(Line) == 0:
  			continue
  		if Line[0] == ">":
  			Id = Line[1:][:-1]
  			Seqs[Id] = ""
  		else:
  			if Id == "":
  				Die("FASTA file '%s' does not start with '>'" % FileName)
  			Seqs[Id] = Seqs[Id] + Line[:-1]
  
  def ReadSeqs2(FileName):
  	Seqs = []
  	Labels = []
  	File = open(FileName)
  	while 1:
  		Line = File.readline()
  		if len(Line) == 0:
  			return Labels, Seqs
  		Line = Line.strip()
  		if len(Line) == 0:
  			continue
  		if Line[0] == ">":
  			Id = Line[1:]
  			Labels.append(Id)
  			Seqs.append("")
  		else:
  			i = len(Seqs)-1
  			Seqs[i] = Seqs[i] + Line
  
  InLabels, InSeqs = ReadSeqs2(InputFileName)
  AlnSeqs = ReadSeqs(AlnFileName)
  
  for Label in InLabels:
  	if Label not in AlnSeqs.keys():
  		Die("Not found in alignment: " + Label)
  	print ">" + Label
  	print AlnSeqs[Label]
  