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1 #!/usr/bin/env python3
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2 import os
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3 import hashlib
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4
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5 from itertools import chain
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6
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7
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8
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9 def md5checksum(filename, fail_if_missing=True):
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10 try:
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11 md5 = hashlib.md5()
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12 with open(filename, "rb") as f:
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13 for i in iter(lambda: f.read(4096), b""):
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14 md5.update(i)
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15 except FileNotFoundError as e:
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16 if not fail_if_missing:
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17 return "Not calculated!!!! File {} is missing".format(filename)
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18 else:
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19 raise e
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20
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21 return md5.hexdigest()
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22
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23
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24 class FilePath(str):
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25 '''
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26 Extension of str - it just contain additional atribute showing that the string is alsp path to file
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27 '''
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28
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29 def __new__(cls, string):
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30 obj = super(FilePath, cls).__new__(cls, string)
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31 obj.filepath = True
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32 return obj
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33
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34 def relative(self, start):
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35 ''' return path relative to start'''
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36 return os.path.relpath(self, start)
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37
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38
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39 def save_as_table(d, path, header=None, relative=True):
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40 ''' takes list of dictionaries and save csv file
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41 define header if you want to use specific order!
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42 '''
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43 pathdir = os.path.dirname(path)
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44 if not header:
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45
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46 all_keys = [i.keys() for i in d]
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47 header = set(chain(*all_keys))
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48 print("header: ---------", header)
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49 with open(path, 'w') as f:
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50 f.write("\t".join(header))
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51 f.write("\n")
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52 for i in d:
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53 istr = []
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54 for key in header:
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55 if isinstance(i[key], FilePath):
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56 if relative:
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57 istr.append('"' + str(i[key].relative(pathdir)) + '"')
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58 else:
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59 istr.append('"' + str(i[key]) + '"')
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60 else:
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61 if isinstance(i[key], str):
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62 istr.append('"' + str(i[key] + '"'))
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63 else:
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64 istr.append(str(i[key]))
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65
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66 f.write("\t".join(istr))
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67 f.write("\n")
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68
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69
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70 def export_tandem_consensus(clusters_info, path, rank=1, n=1):
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71 ''' export tr consensu to file'''
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72 print("exporting fasta files")
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73 print(clusters_info)
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74 s = None
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75 with open(path, 'w') as f:
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76 for cl in clusters_info:
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77 print(cl)
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78 print(dir(cl))
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79 if cl.TR_consensus and rank == cl.tandem_rank:
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80 s = ">CL{index}_TR_{n}_x_{L}nt\n{sequence}\n".format(
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81 index=cl.index,
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82 n=n,
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83 L=cl.TR_monomer_length,
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84 sequence=n * cl.TR_consensus.replace('<pre>', ''))
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85 f.write(s)
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86 if s:
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87 return path
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88 else:
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89 return None
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90
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91
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92 def file_len(filename):
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93 '''count number of lines in file'''
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94 with open(filename) as f:
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95 i = 0
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96 for i in f:
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97 i += i
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98 return i
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99
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100 def go2line(f, L):
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101 ''' find line L in file object f '''
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102 f.seek(0)
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103 if L == 0:
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104 return
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105 i = 0
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106 pos = f.tell()
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107 for line in f:
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108 i += 1
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109 if i == L:
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110 f.seek(pos)
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111 return
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112 else:
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113 pos = pos + len(line)
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114
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115 def format_query(x):
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116 '''
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117 make list for query in format ("x","y","x",...)
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118 '''
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119 out = '("'+ '","'.join(
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120 map(str, x)
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121 ) + '")'
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122 return out
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