Modified gbk2tbl.py from https://github.com/wanyuac/BINF_toolkit/#gbk2tbl to work with Python 3+

gbk2tbl.py

#!/usr/bin/env python
'''
This script converts a GenBank file (.gbk or .gb) from Stdin into a Sequin feature table (.tbl), which is an input file of tbl2asn used for creating an ASN.1 file (.sqn).

Package requirement: BioPython and argparse

Usage:
    Simple command:
        python gbk2tbl.py --mincontigsize 200 --prefix any_prefix --modifiers modifier_file.txt < annotation.gbk
        cat annotation.gbk | python gbk2tbl.py --mincontigsize 200 --prefix any_prefix --modifiers modifier_file.txt  # pipeline form
    Redirecting error messages to a text file (optional):
        python gbk2tbl.py --mincontigsize 200 --prefix any_prefix --modifiers modifier_file.txt < annotation.gbk 2> stderr.txt
        cat annotation.gbk | python gbk2tbl.py --mincontigsize 200 --prefix any_prefix --modifiers modifier_file.txt 2> stderr.txt
    Note that this script reads the GenBank file through the stdin ("< annotation.gbk") and you may want to redirect the stderr to a file via "> stderr.txt" (redirection).

Inputs:
    A GenBank file, which ought to be passed to the script through the standard input (stdin).
    A modifier file: a plain text file containing modifiers for every FASTA definition line.
        All modifiers must be written in a single line and are separated by a single space character.
        No space should be placed besides the '=' sign. Check http://www.ncbi.nlm.nih.gov/Sequin/modifiers.html for choosing a proper format for modifiers.
        For example: [organism=Serratia marcescens subsp. marcescens] [sub-species=marcescens] [strain=AH0650_Sm1] [topology=linear] [moltype=DNA] [tech=wgs] [gcode=11] [country=Australia] [isolation-source=sputum]
        This line will be copied and printed along with the record name as the definition line of every contig sequence.

Outputs:
    any_prefix.tbl: the Sequin feature table
    any_prefix.fsa: the corresponding fasta file
    These files are inputs for tbl2asn which generates ASN.1 files (*.sqn).

Arguments:
    --mincontigsize: the minimum contig size, default = 200 in accordance with NCBI's regulation
    --prefix: the prefix of output filenames, default = 'seq'
    --modifiers: the filename of the modifier file, default = 'modifiers.txt'
      
Development notes:
    This script is derived from the one developed by SEQanswers users nickloman (https://gist.github.com/nickloman/2660685/genbank_to_tbl.py) and ErinL who modified nickloman's script and put it
    on the forum post (http://seqanswers.com/forums/showthread.php?t=19975).

Author of this version: Yu Wan ([email protected], https://github.com/wanyuac)
Edition history: 20 June 2015 - 11 July 2015

Dependency: Python 2.x. This script does not work under Python 3. A syntax error arises when Python 3 is used. Nonetheless, it is not
difficult to adapt this script into the Python 3 version (to-do).

Licence: GNU GPL 2.1

Some notes about the FASTA header modifiers:
    [topology=?]: the molecular topology (circular/linear) of the sequence if this information is not contained in records
        contigs: linear (the default value)
        finished genomes of plasmids and bacterial chromosomes: circular
    An example of the content of the modifier file:
        [organism=Serratia marcescens subsp. marcescens] [sub-species=marcescens] [strain=AH0650_Sm1]
'''

import sys
from Bio import SeqIO
from argparse import ArgumentParser

def parse_args():
# Extract arguments from the command line
    parser = ArgumentParser(description= 'Read arguments: species, strain, BioProject, prefix')
    parser.add_argument('-s', '--mincontigsize', type = int, required = False, default = 200, help = 'The minimum contig length')
    parser.add_argument('-p', '--prefix', type = str, required = False, default = 'seq', help = 'The prefix of output filenames')
    parser.add_argument('-m', '--modifiers', type = str, required = True, default = 'modifiers.txt', help = 'The text file containing a single line of FASTA head modifiers')
    return parser.parse_args()

def read_modifiers(file):
    '''This function only reads the first line of the modifier file. 
    So please ensure that all modifiers are put in the first line.
    '''
    with open(file, 'rU') as f:
        return f.readline()

allowed_qualifiers = ['locus_tag', 'gene', 'product', 'pseudo', 'protein_id', 'gene_desc', 'old_locus_tag', 'note', 'inference', 'organism', 'mol_type', 'strain', 'sub_species', 'isolation-source', 'country']
'''
These are selected qualifiers because we do not want to see qualifiers such as 'translation', 'transl_table', or 'codon_start' in the feature table.
Qualifiers 'organism', 'mol_type', 'strain', 'sub_species', 'isolation-source', 'country' belong to the feature 'source'.
'''

def main():
    args = parse_args()  # read arguments
    contig_num = 0
    modifiers = read_modifiers(args.modifiers)  # read the modifiers from a text file
    with open(args.prefix + '.fsa', 'w') as fasta_fh, open(args.prefix + '.tbl', 'w') as feature_fh:
        for rec in SeqIO.parse(sys.stdin, 'genbank'):  # for every SeqRecord object in the list 'records'
            if len(rec) <= args.mincontigsize:  # filter out small contigs
                print('skipping small contig %s' % (rec.id), file=sys.stderr)
                continue  # start a new 'for' loop
            contig_num += 1
            print(rec.name)  # print the contig name to STDOUT
            
            # write the fasta file 
            rec.description = modifiers
            SeqIO.write([rec], fasta_fh, 'fasta')  # Prints this contig's sequence to the fasta file. The sequence header will be rec.description.

            # write the feature table
            print('>Feature %s' % (rec.name), file=feature_fh)  # write the first line of this record in the feature table: the LOCUS name
            for f in rec.features:
                # print the coordinates
                if f.strand == 1:
                    feature_fh.write(f'{f.location.nofuzzy_start + 1}\t{f.location.nofuzzy_end}\t{f.type}\n')
                else:
                    feature_fh.write(f'{f.location.nofuzzy_end}\t{f.location.nofuzzy_start}\t{f.type}\n')

                if (f.type == 'CDS') and ('product' not in f.qualifiers):
                    f.qualifiers['product'] = 'hypothetical protein'
                for key, values in f.qualifiers.items():
                    '''
                    Apply the iteritems() method of the dictionary f.qualifiers for (key, values) pairs
                    iteritems() is a generator that yields 2-tuples for a dictionary. It saves time and memory but is slower than the items() method.
                    '''
                    if key not in allowed_qualifiers:
                        continue  # start a new 'for' loop of f, skipping the following 'for' statement of v
                    for v in values:  # else, write all values under this key (qualifier's name)
                        feature_fh.write(f'\t\t\t{key}\t{v}\n')
    print(str(contig_num) + ' records have been converted.')

# call the main function
if __name__ == '__main__':
    main()