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.

This module also includes some deprecated functionality (function generic_run and class ApplicationResult) which should not be used anymore.

Classes [hide private]
  ApplicationResult
Make results of a program available through a standard interface (DEPRECATED).
  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.
Functions [hide private]
 
generic_run(commandline)
Run an application with the given commandline (DEPRECATED).
source code
 
_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]

generic_run(commandline)

source code 

Run an application with the given commandline (DEPRECATED).

This expects a pre-built commandline that derives from AbstractCommandline, and returns a ApplicationResult object to get results from a program, along with handles of the standard output and standard error.

WARNING - This will read in the full program output into memory! This may be in issue when the program writes a large amount of data to standard output.

NOTE - This function is considered to be obsolete, and we intend to deprecate it and then remove it in future releases of Biopython. We now recommend you invoke subprocess directly, using str(commandline) to turn an AbstractCommandline wrapper into a command line string. This will give you full control of the tool's input and output as well.

_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',
...