Package Bio :: Package Application
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Package Application

source code

General mechanisms to access applications in Biopython.

This module is not intended for direct use. It provides the basic objects which are subclassed by our command line wrappers, such as:

These modules provide wrapper classes for command line tools to help you construct command line strings by setting the values of each parameter. The finished command line strings are then normally invoked via the built-in Python module subprocess.

Classes [hide private]
  ApplicationError
Raised when an application returns a non-zero exit status.
  AbstractCommandline
Generic interface for constructing command line strings.
  _AbstractParameter
A class to hold information about a parameter for a commandline.
  _Option
Represent an option that can be set for a program.
  _Switch
Represent an optional argument switch for a program.
  _Argument
Represent an argument on a commandline.
  _ArgumentList
Represent a variable list of arguments on a command line, e.g.
  _StaticArgument
Represent a static (read only) argument on a commandline.
Functions [hide private]
 
_escape_filename(filename)
Escape filenames with spaces by adding quotes (PRIVATE).
source code
 
_test()
Run the Bio.Application module's doctests.
source code
Variables [hide private]
  _re_prop_name = re.compile(r'^[a-zA-Z][a-zA-Z0-9_]*$')
  _reserved_names = ['and', 'del', 'from', 'not', 'while', 'as',...
  _local_reserved_names = ['set_parameter']
  __package__ = 'Bio.Application'
Function Details [hide private]

_escape_filename(filename)

source code 

Escape filenames with spaces by adding quotes (PRIVATE).

Note this will not add quotes if they are already included:

>>> print((_escape_filename('example with spaces')))
"example with spaces"
>>> print((_escape_filename('"example with spaces"')))
"example with spaces"

Variables Details [hide private]

_reserved_names

Value:
['and',
 'del',
 'from',
 'not',
 'while',
 'as',
 'elif',
 'global',
...