Class RpsBlastCommandline
source code
object --+
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Application.AbstractCommandline --+
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_BlastCommandLine --+
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RpsBlastCommandline
Create a commandline for the classic rpsblast program from NCBI
(OBSOLETE).
With the release of BLAST+ (BLAST rewritten in C++ instead of C), the
NCBI are replacing the old rpsblast with a new version of the same name
plus a second tool rpstblastn, both taking different command line
arguments. This module provides NcbirpsblastCommandline and
NcbirpsblasntCommandline as wrappers for the new tools.
Like the old rpsblast (and blastall), this wrapper is now obsolete,
and will be deprecated and removed in a future release of Biopython.
>>> from Bio.Blast.Applications import RpsBlastCommandline
>>> cline = RpsBlastCommandline(help=True)
>>> cline
RpsBlastCommandline(cmd='rpsblast', help=True)
>>> print cline
rpsblast --help
You would typically run the command line with the Python subprocess
module, as described in the Biopython tutorial.
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__init__(self,
cmd=' rpsblast ' ,
**kwargs)
Create a new instance of a command line wrapper object. |
source code
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Inherited from Application.AbstractCommandline :
__call__ ,
__repr__ ,
__setattr__ ,
__str__ ,
set_parameter
Inherited from object :
__delattr__ ,
__format__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__sizeof__ ,
__subclasshook__
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Inherited from object :
__class__
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__init__(self,
cmd=' rpsblast ' ,
**kwargs)
(Constructor)
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Create a new instance of a command line wrapper object.
- Overrides:
object.__init__
- (inherited documentation)
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