text: #!/usr/bin/env python
  """Convert a GFF and associated FASTA file into GenBank format.
  code from "https://github.com/chapmanb/bcbb/blob/master/gff/Scripts/gff/gff_to_genbank.py"
  Usage:
      gff_to_genbank.py <GFF annotation file> [<FASTA sequence file> <molecule type>]
   FASTA sequence file: input sequences matching records in GFF. Optional if sequences
     are in the GFF
   molecule type: type of molecule in the GFF file. Defaults to DNA, the most common case.
  """
  from __future__ import print_function
  
  import sys
  import os
  
  from Bio import SeqIO
  
  from BCBio import GFF
  
  
  def main(gff_file, fasta_file=None, molecule_type="DNA"):
      out_file = "%s.gb" % os.path.splitext(gff_file)[0]
      if fasta_file:
          fasta_input = SeqIO.to_dict(SeqIO.parse(fasta_file, "fasta"))
      else:
          fasta_input = {}
      gff_iter = GFF.parse(gff_file, fasta_input)
      SeqIO.write(_check_gff(_fix_ncbi_id(gff_iter), molecule_type), out_file, "genbank")
  
  
  def _fix_ncbi_id(fasta_iter):
      """GenBank identifiers can only be 16 characters; try to shorten NCBI.
      """
      for rec in fasta_iter:
          if len(rec.name) > 16 and rec.name.find("|") > 0:
              new_id = [x for x in rec.name.split("|") if x][-1]
              print("Warning: shortening NCBI name %s to %s" % (rec.id, new_id))
              rec.id = new_id
              rec.name = new_id
          yield rec
  
  
  def _check_gff(gff_iterator, molecule_type):
      """Check GFF files before feeding to SeqIO to be sure they have sequences.
      """
      for rec in gff_iterator:
          if "molecule_type" not in rec.annotations:
              rec.annotations["molecule_type"] = molecule_type
          yield _flatten_features(rec)
  
  
  def _flatten_features(rec):
      """Make sub_features in an input rec flat for output.
      GenBank does not handle nested features, so we want to make
      everything top level.
      """
      out = []
      for f in rec.features:
          cur = [f]
          while len(cur) > 0:
              nextf = []
              for curf in cur:
                  out.append(curf)
                  if len(curf.sub_features) > 0:
                      nextf.extend(curf.sub_features)
              cur = nextf
      rec.features = out
      return rec
  
  
  if __name__ == "__main__":
      main(*sys.argv[1:])
  