filter_fasta.py

#!/usr/bin/python

#usage
#python rename.fasta-to-fasta.py <filein> > <fileout>

import sys
import Bio
from Bio import SeqIO

filein=open(sys.argv[1],'rb')
fileout=open(sys.argv[2], 'w')

for seq_record in SeqIO.parse(filein, format="fasta"):
   line=seq_record.description
#   print line
   line=line.split('#')
#   print line
   partial_info=line[4]
#   print partial_info
   partial=partial_info.split(';')
#   print partial
   if partial[1]=='partial=00':
      fileout.write('>%s %s\n%s\n' %(seq_record.id, seq_record.description, seq_record.seq))
#      print 'complete'
   else:
      continue

#   print name
#   print '>%s\n%s' % (name, seq_record.seq)

filein.close()
fileout.close()