Mercurial > repos > jpayne > seqsero_v2
view SeqSero2/SeqSero2_update_kmer_database.py @ 11:f6f0702de3b4
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author | jpayne |
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date | Tue, 13 Aug 2019 08:40:57 -0400 (2019-08-13) |
parents | fae43708974d |
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#!/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()