Mercurial > repos > estrain > ss2v102

comparison SeqSero2_package.py @ 7:46b848d28b95

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author estrain
date Thu, 03 Oct 2019 06:20:42 -0400
parents ffc351049e31
children 558823a8c53a
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6:ffc351049e31 7:46b848d28b95
1387 ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019: change ex_dir for packaging 1387 ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019: change ex_dir for packaging
1388 #output_mode = args.mode 1388 #output_mode = args.mode
1389 for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath) 1389 for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath)
1390 input_file = for_fq #-k will just use forward because not all reads were used 1390 input_file = for_fq #-k will just use forward because not all reads were used
1391 os.chdir(make_dir) 1391 os.chdir(make_dir)
1392 f = open(dir_path + '/seqsero2_db/antigens.pickle', 'rb') 1392 f = open(dirpath + '/seqsero2_db/antigens.pickle', 'rb')
1393 lib_dict = pickle.load(f) 1393 lib_dict = pickle.load(f)
1394 f.close 1394 f.close
1395 input_Ks=get_input_K(input_file,lib_dict,data_type,k_size) 1395 input_Ks=get_input_K(input_file,lib_dict,data_type,k_size)
1396 O_dict,H_dict,Special_dict=get_kmer_dict(lib_dict,input_Ks) 1396 O_dict,H_dict,Special_dict=get_kmer_dict(lib_dict,input_Ks)
1397 highest_O,highest_fliC,highest_fljB=call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir) 1397 highest_O,highest_fliC,highest_fljB=call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir)