Class Primer3Commandline
source code
object --+
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Application.AbstractCommandline --+
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_EmbossMinimalCommandLine --+
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_EmbossCommandLine --+
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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
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
>>> cline.productosize=200
>>> cline.outfile = "myresults.out"
>>> print cline
eprimer3 -auto -outfile=myresults.out -sequence=mysequence.fas -hybridprobe=True -productosize=200 -oligosize=20 -explainflag=True
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__init__(self,
cmd=' eprimer3 ' ,
**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=' eprimer3 ' ,
**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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