Package Bio :: Package Application
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Package Application

source code

General mechanisms to access applications in biopython.

Classes [hide private]
  ApplicationResult
Make results of a program available through a standard interface.
  AbstractCommandline
Generic interface for running applications from biopython.
  _AbstractParameter
A class to hold information about a parameter for a commandline.
  _Option
Represent an option that can be set for a program.
  _Argument
Represent an argument on a commandline.
Functions [hide private]
 
generic_run(commandline)
Run an application with the given commandline.
source code
Variables [hide private]
  __package__ = 'Bio.Application'
Function Details [hide private]

generic_run(commandline)

source code 

Run an application with the given commandline.

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 write a large amount of data to standard output.