Package Bio :: Package Blast :: Module Applications :: Class BlastallCommandline
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Class BlastallCommandline

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                     object --+            
                              |            
Application.AbstractCommandline --+        
                                  |        
                  _BlastCommandLine --+    
                                      |    
              _BlastAllOrPgpCommandLine --+
                                          |
                                         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.

Instance Methods [hide private]
 
__init__(self, cmd='blastall', **kwargs)
Create a new instance of a command line wrapper object.
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Inherited from _BlastCommandLine (private): _validate

Inherited from Application.AbstractCommandline: __call__, __repr__, __setattr__, __str__, set_parameter

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __sizeof__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, cmd='blastall', **kwargs)
(Constructor)

source code 
Create a new instance of a command line wrapper object.

Overrides: object.__init__
(inherited documentation)