Mercurial > repos > jpayne > seqsero_v2

comparison SeqSero2/SeqSero2_update_kmer_database.py @ 1:fae43708974d

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planemo upload
author jpayne
date Fri, 09 Nov 2018 11:30:45 -0500
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0:4ff2aee11e5b 1:fae43708974d
1 #!/usr/bin/env python3
2
3 import argparse
4 import os,subprocess
5 import pickle
6
7 ### SeqSero Kmer
8 def parse_args():
9 "Parse the input arguments, use '-h' for help."
10 parser = argparse.ArgumentParser(usage='Just type "SeqSero2_update_kmer_database.py", it will update kmer database automatically')
11 return parser.parse_args()
12
13 def reverse_complement(sequence):
14 complement = {
15 'A': 'T',
16 'C': 'G',
17 'G': 'C',
18 'T': 'A',
19 'N': 'N',
20 'M': 'K',
21 'R': 'Y',
22 'W': 'W',
23 'S': 'S',
24 'Y': 'R',
25 'K': 'M',
26 'V': 'B',
27 'H': 'D',
28 'D': 'H',
29 'B': 'V'
30 }
31 return "".join(complement[base] for base in reversed(sequence))
32
33 def multifasta_dict(multifasta):
34 multifasta_list = [
35 line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0
36 ]
37 headers = [i for i in multifasta_list if i[0] == '>']
38 multifasta_dict = {}
39 for h in headers:
40 start = multifasta_list.index(h)
41 for element in multifasta_list[start + 1:]:
42 if element[0] == '>':
43 break
44 else:
45 if h[1:] in multifasta_dict:
46 multifasta_dict[h[1:]] += element
47 else:
48 multifasta_dict[h[1:]] = element
49 return multifasta_dict
50
51 def createKmerDict_reads(list_of_strings, kmer):
52 kmer_table = {}
53 for string in list_of_strings:
54 sequence = string.strip('\n')
55 for i in range(len(sequence) - kmer + 1):
56 new_mer = sequence[i:i + kmer].upper()
57 new_mer_rc = reverse_complement(new_mer)
58 if new_mer in kmer_table:
59 kmer_table[new_mer.upper()] += 1
60 else:
61 kmer_table[new_mer.upper()] = 1
62 if new_mer_rc in kmer_table:
63 kmer_table[new_mer_rc.upper()] += 1
64 else:
65 kmer_table[new_mer_rc.upper()] = 1
66 return kmer_table
67
68 def multifasta_to_kmers_dict(multifasta):
69 multi_seq_dict = multifasta_dict(multifasta)
70 lib_dict = {}
71 for h in multi_seq_dict:
72 lib_dict[h] = set(
73 [k for k in createKmerDict_reads([multi_seq_dict[h]], 27)])
74 return lib_dict
75
76 def get_salmid_invA_database(ex_dir):
77 # read invA kmer and return it
78 a = open(ex_dir + '/invA_mers_dict', 'rb')
79 invA_dict = pickle.load(a)
80 try:
81 del invA_dict['version']
82 except:
83 pass
84 return invA_dict
85
86 def get_salmid_rpoB_database(ex_dir):
87 # read invA kmer and return it
88 a = open(ex_dir + '/rpoB_mers_dict', 'rb')
89 rpoB_dict = pickle.load(a)
90 try:
91 del rpoB_dict['version']
92 except:
93 pass
94 return rpoB_dict
95
96 def main():
97 args = parse_args()
98 ex_dir = os.path.dirname(os.path.realpath(__file__))
99 lib_dict = multifasta_to_kmers_dict(ex_dir + '/H_and_O_and_specific_genes.fasta')
100 invA_dict=get_salmid_invA_database(ex_dir)
101 #rpoB_dict=get_salmid_rpoB_database(ex_dir)
102 lib_dict_new = lib_dict.copy()
103 #print(len(lib_dict_new))
104 lib_dict_new.update(invA_dict)
105 #print(len(lib_dict_new))
106 #lib_dict_new.update(rpoB_dict)
107 #print(len(lib_dict_new))
108 f = open(ex_dir + '/antigens.pickle', "wb")
109 pickle.dump(lib_dict_new, f)
110 f.close()
111
112 if __name__ == '__main__':
113 main()