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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.
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ApplicationError Raised when an application returns a non-zero exit status. |
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ApplicationResult Make results of a program available through a standard interface (DEPRECATED). |
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AbstractCommandline Generic interface for constructing command line strings. |
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_AbstractParameter A class to hold information about a parameter for a commandline. |
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_Option Represent an option that can be set for a program. |
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_Switch Represent an optional argument switch for a program. |
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_Argument Represent an argument on a commandline. |
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_re_prop_name = re.compile(r'
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_reserved_names =
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_local_reserved_names =
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__package__ =
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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 deprecated, and we intend to 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 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" |
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_reserved_names
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