Class NcbipsiblastCommandline
source code
object --+
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Application.AbstractCommandline --+
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_NcbiblastCommandline --+
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_Ncbiblast2SeqCommandline --+
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NcbipsiblastCommandline
Wrapper for the NCBI BLAST+ program psiblast.
With the release of BLAST+ (BLAST rewritten in C++ instead of C), the
NCBI replaced the old blastpgp tool with a similar tool psiblast. This
wrapper therefore replaces BlastpgpCommandline, the wrapper for
blastpgp.
>>> from Bio.Blast.Applications import NcbipsiblastCommandline
>>> cline = NcbipsiblastCommandline(help=True)
>>> cline
NcbipsiblastCommandline(cmd='psiblast', help=True)
>>> print cline
psiblast -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=' psiblast ' ,
**kwargs)
Create a new instance of a command line wrapper object. |
source code
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Inherited from Application.AbstractCommandline :
__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=' psiblast ' ,
**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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Make sure the required parameters have been set (PRIVATE).
No return value - it either works or raises a ValueError.
This is a separate method (called from __str__) so that subclasses may
override it.
- Overrides:
Application.AbstractCommandline._validate
- (inherited documentation)
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