def main(iFileHandle, oFileHandle):
iFile = fasta.load_mfa_iter(iFileHandle)
oFile = smartopen(oFileHandle)
for h,s in iFile:
s = s.replace('-','')
s = s.replace('.','')
fasta.pretty(h, s, stream=oFile)
#!/usr/bin/env python
"""
fastaCleanHeader.py <input file>
"""
import sys
from optparse import OptionParser
import mungo.old.fasta as fasta
from mungo.useful import *
usage = "%prog [options] <input file>"
parser = OptionParser(usage=usage, version="%prog - Version 1")
options, args = parser.parse_args(sys.argv)
faFile = fasta.load_mfa_iter(args[1])
for h,s in faFile:
h = h.split()[0]
if '|' in h:
h = h.split('|')[1]
print '>%s' % h
print s
