Class BlastallCommandline
source code
object --+
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Application.AbstractCommandline --+
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_BlastCommandLine --+
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_BlastAllOrPgpCommandLine --+
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BlastallCommandline
Create a commandline for the blastall program from NCBI
(OBSOLETE).
With the release of BLAST+ (BLAST rewritten in C++ instead of C), the
NCBI are replacing blastall with separate tools blastn, blastp, blastx,
tblastn and tblastx.
Like blastall, this wrapper is now obsolete, and will be deprecated
and removed in a future release of Biopython.
>>> from Bio.Blast.Applications import BlastallCommandline
>>> cline = BlastallCommandline(program="blastx", infile="m_cold.fasta",
... database="nr", expectation=0.001)
>>> cline
BlastallCommandline(cmd='blastall', database='nr', infile='m_cold.fasta', expectation=0.001, program='blastx')
>>> print cline
blastall -d nr -i m_cold.fasta -e 0.001 -p blastx
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=' blastall ' ,
**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=' blastall ' ,
**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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