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

Create a new instance of a command line wrapper object.