import os, re, time, datetime, csv, sys
import rethinkdb as r
from Bio import SeqIO
from vdb_upload import vdb_upload
from vdb_upload import parser

class Zika_vdb_upload(vdb_upload):

    def __init__(self,  fasta_fields, fasta_fname, database, virus, source, locus=None, vsubtype=None, authors=None, path=None, auth_key=None):
        '''
        :param fasta_fields: Dictionary defining position in fasta field to be included in database
        '''
        vdb_upload.__init__(self, fasta_fields, fasta_fname, database, virus, source, locus, vsubtype, authors, path, auth_key)

if __name__=="__main__":
    args = parser.parse_args()
    fasta_fields = {0:'accession', 1:'strain', 2:'date', 4:'country', 5:'division', 6:'location'}
    run = Zika_vdb_upload(fasta_fields, fasta_fname=args.fname, database=args.database, virus=args.virus, source=args.source, locus=args.locus, vsubtype=args.subtype, authors=args.authors, path=args.path)
    run.upload()
import os, re, time, datetime, csv, sys
import rethinkdb as r
from Bio import SeqIO
from vdb_upload import vdb_upload
from vdb_upload import parser

class Zika_vdb_upload(vdb_upload):

    def __init__(self,  fasta_fields, fasta_fname, database, virus, source, locus=None, vsubtype=None, authors=None, path=None, auth_key=None):
        '''
        :param fasta_fields: Dictionary defining position in fasta field to be included in database
        '''
        vdb_upload.__init__(self, fasta_fields, fasta_fname, database, virus, source, locus, vsubtype, authors, path, auth_key)

if __name__=="__main__":
    args = parser.parse_args()
    fasta_fields = {0:'accession', 2:'strain', 4:'date', 6:'country'}
    #  0        1          2                            3  4       5     6
    # >KU647676|Zika_virus|MRS_OPY_Martinique_PaRi_2015|NA|2015_12|Human|Martinique
    run = Zika_vdb_upload(fasta_fields, fasta_fname=args.fname, database=args.database, virus=args.virus, source=args.source, locus=args.locus, vsubtype=args.subtype, authors=args.authors, path=args.path)
    run.upload()
Modify Zika fasta fields to match default VIPRBRC ordering.
Modify Zika fasta fields to match default VIPRBRC ordering.

  import os, re, time, datetime, csv, sys
  import rethinkdb as r
  from Bio import SeqIO
  from vdb_upload import vdb_upload
  from vdb_upload import parser
  
  class Zika_vdb_upload(vdb_upload):
  
      def __init__(self,  fasta_fields, fasta_fname, database, virus, source, locus=None, vsubtype=None, authors=None, path=None, auth_key=None):
          '''
          :param fasta_fields: Dictionary defining position in fasta field to be included in database
          '''
          vdb_upload.__init__(self, fasta_fields, fasta_fname, database, virus, source, locus, vsubtype, authors, path, auth_key)
  
  if __name__=="__main__":
      args = parser.parse_args()
-     fasta_fields = {0:'accession', 1:'strain', 2:'date', 4:'country', 5:'division', 6:'location'}
+     fasta_fields = {0:'accession', 2:'strain', 4:'date', 6:'country'}
+     #  0        1          2                            3  4       5     6
+     # >KU647676|Zika_virus|MRS_OPY_Martinique_PaRi_2015|NA|2015_12|Human|Martinique
      run = Zika_vdb_upload(fasta_fields, fasta_fname=args.fname, database=args.database, virus=args.virus, source=args.source, locus=args.locus, vsubtype=args.subtype, authors=args.authors, path=args.path)
      run.upload()
Modify Zika fasta fields to match default VIPRBRC ordering.
## Code Before:
import os, re, time, datetime, csv, sys
import rethinkdb as r
from Bio import SeqIO
from vdb_upload import vdb_upload
from vdb_upload import parser

class Zika_vdb_upload(vdb_upload):

    def __init__(self,  fasta_fields, fasta_fname, database, virus, source, locus=None, vsubtype=None, authors=None, path=None, auth_key=None):
        '''
        :param fasta_fields: Dictionary defining position in fasta field to be included in database
        '''
        vdb_upload.__init__(self, fasta_fields, fasta_fname, database, virus, source, locus, vsubtype, authors, path, auth_key)

if __name__=="__main__":
    args = parser.parse_args()
    fasta_fields = {0:'accession', 1:'strain', 2:'date', 4:'country', 5:'division', 6:'location'}
    run = Zika_vdb_upload(fasta_fields, fasta_fname=args.fname, database=args.database, virus=args.virus, source=args.source, locus=args.locus, vsubtype=args.subtype, authors=args.authors, path=args.path)
    run.upload()
## Instruction:
Modify Zika fasta fields to match default VIPRBRC ordering.
## Code After:
import os, re, time, datetime, csv, sys
import rethinkdb as r
from Bio import SeqIO
from vdb_upload import vdb_upload
from vdb_upload import parser

class Zika_vdb_upload(vdb_upload):

    def __init__(self,  fasta_fields, fasta_fname, database, virus, source, locus=None, vsubtype=None, authors=None, path=None, auth_key=None):
        '''
        :param fasta_fields: Dictionary defining position in fasta field to be included in database
        '''
        vdb_upload.__init__(self, fasta_fields, fasta_fname, database, virus, source, locus, vsubtype, authors, path, auth_key)

if __name__=="__main__":
    args = parser.parse_args()
    fasta_fields = {0:'accession', 2:'strain', 4:'date', 6:'country'}
    #  0        1          2                            3  4       5     6
    # >KU647676|Zika_virus|MRS_OPY_Martinique_PaRi_2015|NA|2015_12|Human|Martinique
    run = Zika_vdb_upload(fasta_fields, fasta_fname=args.fname, database=args.database, virus=args.virus, source=args.source, locus=args.locus, vsubtype=args.subtype, authors=args.authors, path=args.path)
    run.upload()