Package Bio :: Package Emboss :: Module Applications :: Class Primer3Commandline
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Class Primer3Commandline

source code

                     object --+            
                              |            
Application.AbstractCommandline --+        
                                  |        
          _EmbossMinimalCommandLine --+    
                                      |    
                     _EmbossCommandLine --+
                                          |
                                         Primer3Commandline

Commandline object for the Primer3 interface from EMBOSS.

The precise set of supported arguments depends on your version of EMBOSS. This version accepts arguments current at EMBOSS 6.1.0, but in order to remain backwards compatible also support the old argument names as well.

e.g. Using EMBOSS 6.1.0 or later,

>>> cline = Primer3Commandline(sequence="mysequence.fas", auto=True, hybridprobe=True)
>>> cline.explainflag = True
>>> cline.osizeopt=20
>>> cline.psizeopt=200
>>> cline.outfile = "myresults.out"
>>> cline.bogusparameter = 1967     # Invalid parameter
Traceback (most recent call last):
    ...
ValueError: Option name bogusparameter was not found.
>>> print(cline)
eprimer3 -auto -outfile=myresults.out -sequence=mysequence.fas -hybridprobe=True -psizeopt=200 -osizeopt=20 -explainflag=True

The equivalent for anyone still using an older version of EMBOSS would be:

>>> cline = Primer3Commandline(sequence="mysequence.fas", auto=True, hybridprobe=True)
>>> cline.explainflag = True
>>> cline.oligosize=20              # Old EMBOSS, instead of osizeopt
>>> cline.productosize=200          # Old EMBOSS, instead of psizeopt
>>> cline.outfile = "myresults.out"
>>> print(cline)
eprimer3 -auto -outfile=myresults.out -sequence=mysequence.fas -hybridprobe=True -productosize=200 -oligosize=20 -explainflag=True
Instance Methods [hide private]
 
__init__(self, cmd='eprimer3', **kwargs)
Create a new instance of a command line wrapper object.
source code

Inherited from _EmbossCommandLine (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='eprimer3', **kwargs)
(Constructor)

source code 
Create a new instance of a command line wrapper object.
Overrides: object.__init__
(inherited documentation)