Source Code for Module Bio._utils

  1  # Copyright 2010 by Eric Talevich. All rights reserved. 
  2  # Copyright 2012 by Wibowo Arindrarto. All rights reserved. 
  3  # This code is part of the Biopython distribution and governed by its 
  4  # license.  Please see the LICENSE file that should have been included 
  5  # as part of this package. 
  6   
  7  """Common utility functions for various Bio submodules.""" 
  8   
  9  import os 
 10   
 11   
 12 -def iterlen(items): 
 13      """Count the number of items in an iterable. 
 14   
 15      If the argument supports len(items), and some iterators do, then 
 16      this returns len(items). Otherwise it will scan over the entries 
 17      in order to count them. 
 18   
 19      Exhausts a generator, but doesn't require creating a full list. 
 20   
 21      >>> iterlen("abcde") 
 22      5 
 23      >>> iterlen(iter("abcde")) 
 24      5 
 25      >>> iterlen(xrange(5)) 
 26      5 
 27   
 28      """ 
 29      try: 
 30          #e.g. Under Python 2, the xrange iterator defines __len__ 
 31          return len(items) 
 32      except TypeError: 
 33          for i, x in enumerate(items): 
 34              count = i 
 35          return count + 1 
 36   
 37   
 38 -def read_forward(handle): 
 39      """Reads through whitespaces, returns the first non-whitespace line.""" 
 40      while True: 
 41          line = handle.readline() 
 42          # if line has characters and stripping does not remove them, 
 43          # return the line 
 44          if line and line.strip(): 
 45              return line 
 46          # if line ends, return None 
 47          elif not line: 
 48              return line 
 49   
 50   
 51 -def trim_str(string, max_len, concat_char): 
 52      """Truncates the given string for display.""" 
 53      if len(string) > max_len: 
 54          return string[:max_len - len(concat_char)] + concat_char 
 55      return string 
 56   
 57   
 58 -def getattr_str(obj, attr, fmt=None, fallback='?'): 
 59      """Returns a string of the given object's attribute, defaulting to the 
 60      fallback value if attribute is not present.""" 
 61      if hasattr(obj, attr): 
 62          if fmt is not None: 
 63              return fmt % getattr(obj, attr) 
 64          return str(getattr(obj, attr)) 
 65      return fallback 
 66   
 67   
 68 -def find_test_dir(start_dir=None): 
 69      """Finds the absolute path of Biopython's Tests directory. 
 70   
 71      Arguments: 
 72      start_dir -- Initial directory to begin lookup (default to current dir) 
 73   
 74      If the directory is not found up the filesystem's root directory, an 
 75      exception will be raised. 
 76   
 77      """ 
 78      if not start_dir: 
 79          # no callbacks in function signatures! 
 80          # defaults to the current directory 
 81          # (using __file__ would give the installed Biopython) 
 82          start_dir = "." 
 83   
 84      target = os.path.abspath(start_dir) 
 85      while True: 
 86          if os.path.isdir(os.path.join(target, "Bio")) \ 
 87          and os.path.isdir(os.path.join(target, "Tests")): 
 88             #Good, we're in the Biopython root now 
 89             return os.path.abspath(os.path.join(target, "Tests")) 
 90          #Recurse up the tree 
 91          #TODO - Test this on Windows 
 92          new, tmp = os.path.split(target) 
 93          if target == new: 
 94              #Reached root 
 95              break 
 96          target = new 
 97      raise ValueError("Not within Biopython source tree: %r" % os.path.abspath(start_dir)) 
 98   
 99   
100 -def run_doctest(target_dir=None, *args, **kwargs): 
101      """Runs doctest for the importing module.""" 
102      import doctest 
103   
104      # default doctest options 
105      default_kwargs = { 
106          'optionflags': doctest.ELLIPSIS, 
107      } 
108      kwargs.update(default_kwargs) 
109   
110      cur_dir = os.path.abspath(os.curdir) 
111   
112      print "Runing doctests..." 
113      try: 
114          os.chdir(find_test_dir(target_dir)) 
115          doctest.testmod(*args, **kwargs) 
116      finally: 
117          # and revert back to initial directory 
118          os.chdir(cur_dir) 
119      print "Done" 
120   
121  if __name__ == "__main__": 
122      run_doctest() 
123