Package Bio :: Module _utils

Module _utils

Common utility functions for various Bio submodules.

Functions

[hide private]

iterlen(items)
Count the number of items in an iterable.

source code

read_forward(handle)
Reads through whitespaces, returns the first non-whitespace line.

source code

trim_str(string, max_len, concat_char)
Truncates the given string for display.

source code

getattr_str(obj, attr, fmt=None, fallback='?')
Returns a string of the given object's attribute, defaulting to the fallback value if attribute is not present. source code

find_test_dir(start_dir=None)
Finds the absolute path of Biopython's Tests directory.

source code

run_doctest(target_dir=None, *args, **kwargs)
Runs doctest for the importing module.

source code

Function Details

[hide private]

iterlen(items)

source code

Count the number of items in an iterable.

If the argument supports len(items), and some iterators do, then
this returns len(items). Otherwise it will scan over the entries
in order to count them.

Exhausts a generator, but doesn't require creating a full list.

>>> iterlen("abcde")
5
>>> iterlen(iter("abcde"))
5
>>> iterlen(xrange(5))
5

find_test_dir(start_dir=None)

source code

Finds the absolute path of Biopython's Tests directory.

Arguments:
start_dir -- Initial directory to begin lookup (default to current dir)

If the directory is not found up the filesystem's root directory, an
exception will be raised.