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comparison lib/utils.py @ 0:f6ebec6e235e draft

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author petrn
date Thu, 19 Dec 2019 13:46:43 +0000
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-1:000000000000 0:f6ebec6e235e
1 #!/usr/bin/env python3
2 import os
3 import hashlib
4
5 from itertools import chain
6
7
8
9 def md5checksum(filename, fail_if_missing=True):
10 try:
11 md5 = hashlib.md5()
12 with open(filename, "rb") as f:
13 for i in iter(lambda: f.read(4096), b""):
14 md5.update(i)
15 except FileNotFoundError as e:
16 if not fail_if_missing:
17 return "Not calculated!!!! File {} is missing".format(filename)
18 else:
19 raise e
20
21 return md5.hexdigest()
22
23
24 class FilePath(str):
25 '''
26 Extension of str - it just contain additional atribute showing that the string is alsp path to file
27 '''
28
29 def __new__(cls, string):
30 obj = super(FilePath, cls).__new__(cls, string)
31 obj.filepath = True
32 return obj
33
34 def relative(self, start):
35 ''' return path relative to start'''
36 return os.path.relpath(self, start)
37
38
39 def save_as_table(d, path, header=None, relative=True):
40 ''' takes list of dictionaries and save csv file
41 define header if you want to use specific order!
42 '''
43 pathdir = os.path.dirname(path)
44 if not header:
45
46 all_keys = [i.keys() for i in d]
47 header = set(chain(*all_keys))
48 print("header: ---------", header)
49 with open(path, 'w') as f:
50 f.write("\t".join(header))
51 f.write("\n")
52 for i in d:
53 istr = []
54 for key in header:
55 if isinstance(i[key], FilePath):
56 if relative:
57 istr.append('"' + str(i[key].relative(pathdir)) + '"')
58 else:
59 istr.append('"' + str(i[key]) + '"')
60 else:
61 if isinstance(i[key], str):
62 istr.append('"' + str(i[key] + '"'))
63 else:
64 istr.append(str(i[key]))
65
66 f.write("\t".join(istr))
67 f.write("\n")
68
69
70 def export_tandem_consensus(clusters_info, path, rank=1, n=1):
71 ''' export tr consensu to file'''
72 print("exporting fasta files")
73 print(clusters_info)
74 s = None
75 with open(path, 'w') as f:
76 for cl in clusters_info:
77 print(cl)
78 print(dir(cl))
79 if cl.TR_consensus and rank == cl.tandem_rank:
80 s = ">CL{index}_TR_{n}_x_{L}nt\n{sequence}\n".format(
81 index=cl.index,
82 n=n,
83 L=cl.TR_monomer_length,
84 sequence=n * cl.TR_consensus.replace('<pre>', ''))
85 f.write(s)
86 if s:
87 return path
88 else:
89 return None
90
91
92 def file_len(filename):
93 '''count number of lines in file'''
94 with open(filename) as f:
95 i = 0
96 for i in f:
97 i += i
98 return i
99
100 def go2line(f, L):
101 ''' find line L in file object f '''
102 f.seek(0)
103 if L == 0:
104 return
105 i = 0
106 pos = f.tell()
107 for line in f:
108 i += 1
109 if i == L:
110 f.seek(pos)
111 return
112 else:
113 pos = pos + len(line)
114
115 def format_query(x):
116 '''
117 make list for query in format ("x","y","x",...)
118 '''
119 out = '("'+ '","'.join(
120 map(str, x)
121 ) + '")'
122 return out