<commit_before><commit_msg>base form of converter<commit_after>#!/usr/bin/env python 
"""
Convert data from GFF and associated genome sequence in fasta file into GenBank.

Usage: 
python gff_to_gbk.py in.gff in.fasta out.gbk 

Requirements:
    BioPython:- http://biopython.org/
    helper.py : https://github.com/vipints/GFFtools-GX/blob/master/helper.py

Copyright (C) 
    2010-2012 <NAME> Laboratory of the Max Planck Society, Tubingen, Germany.
    2012-2014 Memorial Sloan Kettering Cancer Center New York City, USA.
"""

import sys
import helper

from Bio import SeqIO
from Bio.Alphabet import generic_dna

def __main__():
    """
    """

    try:
        gff_fname = sys.argv[1]
        fasta_fname = sys.argv[2]
        gb_fname = sys.argv[3]
    except: 
        print __doc__
        sys.exit(-1)

    fasta_fh = helper.open_file(fasta_fname) 

    fasta_rec = SeqIO.to_dict(SeqIO.parse(fasta_fh, "fasta", generic_dna))
    fasta_fh.close()

    #
    #from Core import GFF
    #gff_rec = GFF.parse(gff_fname, fasta_rec)
    #gb_fh=open(gb_fname, "w")
    #SeqIO.write(gff_rec, gb_fh, "genbank")
    #gb_fh.close()
    #

if __name__=="__main__":
    __main__()

{'fraction_non_alphanumeric': 0.11584327086882454, 'fraction_numerical': 0.017035775127768313, 'mean_word_length': 3.0940766550522647, 'pattern_counts': {'":': 1, '<': 4, '<?xml version=': 0, '>': 4, 'https://': 1, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4173854', 'n_tokens_mistral': 477, 'n_tokens_neox': 438, 'n_words': 99}