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:

 - Bio.Align.Applications
 - Bio.Blast.Applications
 - Bio.Emboss.Applications
 - Bio.Sequencing.Applications

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]
Raised when an application returns a non-zero exit status.
Generic interface for constructing command line strings.
A class to hold information about a parameter for a commandline.
Represent an option that can be set for a program.
Represent an optional argument switch for a program.
Represent an argument on a commandline.
Represent a static (read only) argument on a commandline.
Functions [hide private]
Escape filenames with spaces by adding quotes (PRIVATE).
source code
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]


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]