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General mechanisms to access applications in biopython.
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ApplicationResult Make results of a program available through a standard interface. |
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AbstractCommandline Generic interface for running applications from biopython. |
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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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_Argument Represent an argument on a commandline. |
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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. |
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