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Package Bio :: Package Application :: Class AbstractCommandline |
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AlignAceCommandline
,
BlastallCommandline
,
CompareAceCommandline
,
EConsenseCommandline
,
EInvertedCommandline
,
ENeighborCommandline
,
EProtDistCommandline
,
EProtParsCommandline
,
ESeqBootCommandline
,
Est2GenomeCommandline
,
ETandemCommandline
,
FastacmdCommandline
,
FuzznucCommandline
,
PalindromeCommandline
,
Primer3Commandline
,
PrimerSearchCommandline
,
TranalignCommandline
,
WaterCommandline
Generic interface for running applications from biopython.
This class shouldn't be called directly; it should be subclassed to provide an implementation for a specific application.Method Summary | |
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__init__(self)
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Make the commandline with the currently set options. | |
Set a commandline option for a program. | |
Check whether the given value is valid. |
Method Details |
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__str__(self)
Make the commandline with the currently set options.
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set_parameter(self, name, value=None)Set a commandline option for a program. |
_check_value(self, value, name, check_function)Check whether the given value is valid. This uses the passed function 'check_function', which can either return a [0, 1] (bad, good) value or raise an error. Either way this function will raise an error if the value is not valid, or finish silently otherwise. |
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