Source Code for Module file_ops

 1  from os import mkdir 
 2  from re import match 
 3  from string import split 
 4  import sys 
 5   
 6 -class file_ops: 
 7 -        def __init__(self, mf): 
 8                  "Class containing the file operations" 
 9   
10                  self.mf = mf 
11   
12   
13 -        def init_log_file(self, title='Log file'): 
14                  "Initialise the log file." 
15   
16                  self.mf.log = open('log.stage' + self.mf.data.stage, 'w') 
17                  self.mf.log.write(title) 
18   
19   
20 -        def open_file(self, file_name): 
21                  "Open the file 'file' and return all the data." 
22   
23                  file = open(file_name, 'r') 
24                  lines = file.readlines() 
25                  data = [] 
26                  i = 0 
27                  for line in lines: 
28                          if i != 0: 
29                                  j = i - 1 
30                                  row = split(line) 
31                                  data.append([]) 
32                                  data[j].append(row[0]) 
33                                  data[j].append(row[1]) 
34                                  for k in range(len(row)): 
35                                          if k > 1: 
36                                                  data[j].append(float(row[k])) 
37                          i = i + 1 
38                  return data 
39   
40   
41 -        def mkdir(self, dir): 
42                  "Create the given directory, or exit if the directory exists." 
43   
44                  if self.mf.debug: 
45                          self.mf.log.write("Making directory " + dir + "\n") 
46                  try: 
47                          mkdir(dir) 
48                  except OSError: 
49                          print "Directory ./" + dir + " already exists, quitting program.\n" 
50                          sys.exit() 
51   
52   
53 -        def read_file(self, file_name, message=''): 
54                  "Attempt to read the file, or quit the program if it does not exist." 
55   
56                  try: 
57                          open(file_name, 'r') 
58                  except IOError: 
59                          sys.stdout.write(message) 
60                          sys.stdout.write("The file '" + file_name + "' does not exist, quitting program.\n\n\n") 
61                          sys.exit() 
62                  file = open(file_name, 'r') 
63                  return file 
64   
65   
66 -        def relax_data(self, file): 
67                  """Open the relaxation data in the file 'file' and return all the data. 
68   
69                  It is assumed that the file has four columns separated by whitespace.  The columns should be: 
70                          0 - Residue numbers 
71                          1 - Residue names 
72                          2 - R1, R2, or NOE values 
73                          3 - The errors 
74                  """ 
75   
76                  lines = open(file, 'r') 
77                  lines = lines.readlines() 
78                  data = [] 
79                  i = 0 
80                  for line in lines: 
81                          if i != 0: 
82                                  j = i - 1 
83                                  row = split(line) 
84                                  data.append([]) 
85                                  data[j].append(row[0]) 
86                                  data[j].append(row[1]) 
87                                  data[j].append(float(row[2])) 
88                                  data[j].append(float(row[3])) 
89                          i = i + 1 
90                  return data 
91