<commit_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, overwrite, 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, overwrite, locus, vsubtype, authors, path, auth_key)

if __name__=="__main__":<commit_msg>Got rid of subtype field for Zika upload<commit_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, overwrite, 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
        '''
        self.virus_optional_fields = ['division', 'location']
        self.updateable_virus_fields = ['date', 'country', 'division', 'location', 'virus']
        vdb_upload.__init__(self, fasta_fields, fasta_fname, database, virus, source, overwrite, locus, vsubtype, authors, path, auth_key)

if __name__=="__main__":
{'fraction_non_alphanumeric': 0.09456740442655935, 'fraction_numerical': 0.0, 'mean_word_length': 4.944223107569721, 'pattern_counts': {'":': 2, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, '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': '3172269', 'n_tokens_mistral': 478, 'n_tokens_neox': 458, 'n_words': 145}