#!/opt/conda/conda-bld/biocode_1660685443970/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin/python

"""
This script can be used to transform a GFF3 file into a TBL file suitable for submitting
to NCBI.  Its encoding is meant to include prokaryotes and eukaryotes, though it was
written/tested first for eukaryotes.

Note, you'll need to modify the IDs if you're doing an update to an already existing
submission, since this generates them automatically base on your prefix.

The options:

--input_file:  Must follow the GFF3 specification

--output_base:  Will be used to write NCBI table and fasta formatted files.  TBL defined here:
                http://www.ncbi.nlm.nih.gov/genbank/eukaryotic_genome_submission_annotation

--lab_name:  A short, unique identifier, no spaces, which will form part of the exported
             protein and transcript IDs.  See the documentation for examples:
             Documentation: http://www.ncbi.nlm.nih.gov/genbank/eukaryotic_genome_submission_annotation#protein_id

--ncbi_acc_prefix:  Assigned by NCBI, this is the accession prefix for this submission.

--fasta:  NCBI has strict requirements for feature identifiers, and this script will reformat them
          unless you have already prepared them correctly.  If corrections need to be made, a new
          corresponding FASTA file will also be written, which requires this input source fasta file.
                
--go_obo:  Optional.  If your GFF3 annotation includes GO attributes, this is required because
           the GFF3 has only the ID but the TBL file also requires the descriptor and class, so
           this enables a lookup of these using the annotated GO ids.

"""

import argparse

from biocode import utils, gff, things, tbl


def main():
    parser = argparse.ArgumentParser( description='Create a TBL file for submission to NCBI from GFF3')

    ## output file to be written
    parser.add_argument('-i', '--input_file', type=str, required=True, help='Path to an input file to be read' )
    parser.add_argument('-o', '--output_base', type=str, required=True, help='Base name of output files to be created' )
    parser.add_argument('-ln', '--lab_name', type=str, required=True, help='Required by NCBI to identify the submitting group' )
    parser.add_argument('-nap', '--ncbi_acc_prefix', type=str, required=True, help='Required and assigned by NCBI' )
    parser.add_argument('-gf', '--genomic_fasta', type=str, required=False, help='FASTA file of genomic sequence, if not embedded in GFF' )
    parser.add_argument('-go', '--go_obo', type=str, required=False, help='GO terms will not be exported unless you pass the path to a GO OBO file')
    
    args = parser.parse_args()

    (assemblies, features) = gff.get_gff3_features(args.input_file)
    
    if args.genomic_fasta is not None:
        utils.add_assembly_fasta(assemblies, args.genomic_fasta)
        
    new_assemblies = dict() 

    ## We need to first check the ID format
    reformat_IDs = True

    ## maps old IDs (like tp.assembly.567468735.1) to new ones (like AAGK01000001)
    asm_id_map = dict()
    asm_num = 1

    for asm_id in assemblies:
        # pre-formatted IDs are like this: gnl|WGS:XXXX|SeqID|gb|XXXX01xxxxxx
        if asm_id.startswith('gnl|WGS:'):
            reformat_IDs = False
            break
        else:
            new_id = "gnl|WGS:{0}|SeqID|gb|{0}01{1:06d}".format(args.ncbi_acc_prefix, asm_num)
            asm_id_map[asm_id] = new_id
            asm_num += 1
            new_assemblies[new_id] = assemblies[asm_id]
            new_assemblies[new_id].id = new_id

    if reformat_IDs == True:
        assemblies = new_assemblies

    ofh = open("{0}.tbl".format(args.output_base), 'wt')
    tbl.print_tbl_from_assemblies(assemblies=assemblies, ofh=ofh, go_obo=args.go_obo, lab_name=args.lab_name)

    mset = things.AssemblySet()
    mset.load_from_dict(assemblies)
    mset.write_fasta(path="{0}.fna".format(args.output_base))

if __name__ == '__main__':
    main()







