Class BlastpgpCommandline
source code
object --+
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Application.AbstractCommandline --+
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_BlastCommandLine --+
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_BlastAllOrPgpCommandLine --+
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BlastpgpCommandline
Create a commandline for the blastpgp program from NCBI
(OBSOLETE).
With the release of BLAST+ (BLAST rewritten in C++ instead of C), the
NCBI are replacing blastpgp with a renamed tool psiblast. This module
provides NcbipsiblastCommandline as a wrapper for the new tool
psiblast.
Like blastpgp (and blastall), this wrapper is now obsolete, and will
be deprecated and removed in a future release of Biopython.
>>> from Bio.Blast.Applications import BlastpgpCommandline
>>> cline = BlastpgpCommandline(help=True)
>>> cline
BlastpgpCommandline(cmd='blastpgp', help=True)
>>> print cline
blastpgp --help
You would typically run the command line with cline() or via the
Python subprocess module, as described in the Biopython tutorial.
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__init__(self,
cmd=' blastpgp ' ,
**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=' blastpgp ' ,
**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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