Table of Contents

Module: __init__ Bio/Application/__init__.py

General mechanisms to access applications in biopython.

Imported modules   
from Bio import File
import StringIO
import os
import popen2
Functions   
_file_exists
generic_run
  _file_exists  
_file_exists ( self,  filename )

Make sure that a passed filename exists.

--- general functions to check for valid parameters

Exceptions   
ValueError( "File %s does not exist." % filename )
  generic_run  
generic_run ( commandline )

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.

Classes   
AbstractCommandline

Generic interface for running applications from biopython.

ApplicationResult

Make results of a program available through a standard interface.

_AbstractParameter

A class to hold information about a parameter for a commandline.

_Argument

Represent an argument on a commandline.

_Option

Represent an option that can be set for a program.

Table of Contents

This document was automatically generated on Mon Jul 1 12:03:08 2002 by HappyDoc version 2.0.1