--- a/SeqSero2S/bin/SeqSero2_update_kmer_database.py	Fri May 15 17:55:16 2026 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,113 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-import os,subprocess
-import pickle
-
-### SeqSero Kmer
-def parse_args():
-    "Parse the input arguments, use '-h' for help."
-    parser = argparse.ArgumentParser(usage='Just type "SeqSero2_update_kmer_database.py", it will update kmer database automatically')
-    return parser.parse_args()
-
-def reverse_complement(sequence):
-    complement = {
-        'A': 'T',
-        'C': 'G',
-        'G': 'C',
-        'T': 'A',
-        'N': 'N',
-        'M': 'K',
-        'R': 'Y',
-        'W': 'W',
-        'S': 'S',
-        'Y': 'R',
-        'K': 'M',
-        'V': 'B',
-        'H': 'D',
-        'D': 'H',
-        'B': 'V'
-    }
-    return "".join(complement[base] for base in reversed(sequence))
-
-def multifasta_dict(multifasta):
-    multifasta_list = [
-        line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0
-    ]
-    headers = [i for i in multifasta_list if i[0] == '>']
-    multifasta_dict = {}
-    for h in headers:
-        start = multifasta_list.index(h)
-        for element in multifasta_list[start + 1:]:
-            if element[0] == '>':
-                break
-            else:
-                if h[1:] in multifasta_dict:
-                    multifasta_dict[h[1:]] += element
-                else:
-                    multifasta_dict[h[1:]] = element
-    return multifasta_dict
-
-def createKmerDict_reads(list_of_strings, kmer):
-    kmer_table = {}
-    for string in list_of_strings:
-        sequence = string.strip('\n')
-        for i in range(len(sequence) - kmer + 1):
-            new_mer = sequence[i:i + kmer].upper()
-            new_mer_rc = reverse_complement(new_mer)
-            if new_mer in kmer_table:
-                kmer_table[new_mer.upper()] += 1
-            else:
-                kmer_table[new_mer.upper()] = 1
-            if new_mer_rc in kmer_table:
-                kmer_table[new_mer_rc.upper()] += 1
-            else:
-                kmer_table[new_mer_rc.upper()] = 1
-    return kmer_table
-
-def multifasta_to_kmers_dict(multifasta):
-    multi_seq_dict = multifasta_dict(multifasta)
-    lib_dict = {}
-    for h in multi_seq_dict:
-        lib_dict[h] = set(
-            [k for k in createKmerDict_reads([multi_seq_dict[h]], 27)])
-    return lib_dict
-
-def get_salmid_invA_database(ex_dir):
-  # read invA kmer and return it
-  a = open(ex_dir + '/invA_mers_dict', 'rb')
-  invA_dict = pickle.load(a)
-  try:
-    del invA_dict['version']
-  except:
-    pass
-  return invA_dict
-
-def get_salmid_rpoB_database(ex_dir):
-  # read invA kmer and return it
-  a = open(ex_dir + '/rpoB_mers_dict', 'rb')
-  rpoB_dict = pickle.load(a)
-  try:
-    del rpoB_dict['version']
-  except:
-    pass
-  return rpoB_dict
-
-def main():
-  args = parse_args()
-  ex_dir = os.path.dirname(os.path.realpath(__file__))
-  lib_dict = multifasta_to_kmers_dict(ex_dir + '/H_and_O_and_specific_genes.fasta')
-  invA_dict=get_salmid_invA_database(ex_dir)
-  #rpoB_dict=get_salmid_rpoB_database(ex_dir)
-  lib_dict_new = lib_dict.copy()
-  #print(len(lib_dict_new))
-  lib_dict_new.update(invA_dict)
-  #print(len(lib_dict_new))
-  #lib_dict_new.update(rpoB_dict)
-  #print(len(lib_dict_new))
-  f = open(ex_dir + '/antigens.pickle', "wb")
-  pickle.dump(lib_dict_new, f)
-  f.close()
-
-if __name__ == '__main__':
-  main()