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annotate SeqSero2S/bin/SeqSero2_update_kmer_database.py @ 19:cfc91e1d2c9b draft

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planemo upload commit 936a627c4fc706080f07ec678f89e8256a7e7895
author jpayne
date Fri, 15 May 2026 17:50:45 +0000
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19
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1 #!/usr/bin/env python3
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2
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3 import argparse
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4 import os,subprocess
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5 import pickle
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6
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7 ### SeqSero Kmer
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8 def parse_args():
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9 "Parse the input arguments, use '-h' for help."
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10 parser = argparse.ArgumentParser(usage='Just type "SeqSero2_update_kmer_database.py", it will update kmer database automatically')
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11 return parser.parse_args()
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12
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13 def reverse_complement(sequence):
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14 complement = {
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15 'A': 'T',
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16 'C': 'G',
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17 'G': 'C',
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18 'T': 'A',
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19 'N': 'N',
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20 'M': 'K',
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21 'R': 'Y',
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22 'W': 'W',
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23 'S': 'S',
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24 'Y': 'R',
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25 'K': 'M',
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26 'V': 'B',
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27 'H': 'D',
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28 'D': 'H',
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29 'B': 'V'
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30 }
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31 return "".join(complement[base] for base in reversed(sequence))
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32
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33 def multifasta_dict(multifasta):
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34 multifasta_list = [
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35 line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0
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36 ]
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37 headers = [i for i in multifasta_list if i[0] == '>']
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38 multifasta_dict = {}
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39 for h in headers:
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40 start = multifasta_list.index(h)
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41 for element in multifasta_list[start + 1:]:
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42 if element[0] == '>':
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43 break
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44 else:
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45 if h[1:] in multifasta_dict:
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46 multifasta_dict[h[1:]] += element
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47 else:
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48 multifasta_dict[h[1:]] = element
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49 return multifasta_dict
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50
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51 def createKmerDict_reads(list_of_strings, kmer):
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52 kmer_table = {}
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53 for string in list_of_strings:
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54 sequence = string.strip('\n')
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55 for i in range(len(sequence) - kmer + 1):
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56 new_mer = sequence[i:i + kmer].upper()
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57 new_mer_rc = reverse_complement(new_mer)
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58 if new_mer in kmer_table:
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59 kmer_table[new_mer.upper()] += 1
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60 else:
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61 kmer_table[new_mer.upper()] = 1
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62 if new_mer_rc in kmer_table:
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63 kmer_table[new_mer_rc.upper()] += 1
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64 else:
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65 kmer_table[new_mer_rc.upper()] = 1
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66 return kmer_table
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67
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68 def multifasta_to_kmers_dict(multifasta):
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69 multi_seq_dict = multifasta_dict(multifasta)
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70 lib_dict = {}
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71 for h in multi_seq_dict:
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72 lib_dict[h] = set(
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73 [k for k in createKmerDict_reads([multi_seq_dict[h]], 27)])
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74 return lib_dict
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75
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76 def get_salmid_invA_database(ex_dir):
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77 # read invA kmer and return it
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78 a = open(ex_dir + '/invA_mers_dict', 'rb')
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79 invA_dict = pickle.load(a)
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80 try:
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81 del invA_dict['version']
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82 except:
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83 pass
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84 return invA_dict
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85
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86 def get_salmid_rpoB_database(ex_dir):
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87 # read invA kmer and return it
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88 a = open(ex_dir + '/rpoB_mers_dict', 'rb')
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89 rpoB_dict = pickle.load(a)
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90 try:
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91 del rpoB_dict['version']
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92 except:
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93 pass
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94 return rpoB_dict
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95
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96 def main():
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97 args = parse_args()
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98 ex_dir = os.path.dirname(os.path.realpath(__file__))
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99 lib_dict = multifasta_to_kmers_dict(ex_dir + '/H_and_O_and_specific_genes.fasta')
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100 invA_dict=get_salmid_invA_database(ex_dir)
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101 #rpoB_dict=get_salmid_rpoB_database(ex_dir)
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102 lib_dict_new = lib_dict.copy()
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103 #print(len(lib_dict_new))
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104 lib_dict_new.update(invA_dict)
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105 #print(len(lib_dict_new))
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106 #lib_dict_new.update(rpoB_dict)
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107 #print(len(lib_dict_new))
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108 f = open(ex_dir + '/antigens.pickle', "wb")
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109 pickle.dump(lib_dict_new, f)
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110 f.close()
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111
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112 if __name__ == '__main__':
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113 main()