Class NovoalignCommandline
source code
object --+
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Application.AbstractCommandline --+
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NovoalignCommandline
Command line wrapper for novoalign by Novocraft.
See www.novocraft.com - novoalign is a short read alignment
program.
Example:
>>> from Bio.Sequencing.Applications import NovoalignCommandline
>>> novoalign_cline = NovoalignCommandline(database='some_db',
... readfile='some_seq.txt')
>>> print novoalign_cline
novoalign -d some_db -f some_seq.txt
As will all the Biopython application wrappers, you can also add or
change options after creating the object:
>>> novoalign_cline.format = 'PRBnSEQ'
>>> novoalign_cline.r_method='0.99'
>>> novoalign_cline.fragment = '250 20'
>>> novoalign_cline.miRNA = 100
>>> print novoalign_cline
novoalign -d some_db -f some_seq.txt -F PRBnSEQ -r 0.99 -i 250 20 -m 100
You would typically run the command line with novoalign_cline() or via
the Python subprocess module, as described in the Biopython tutorial.
Last checked against version: 2.05.04
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__init__(self,
cmd=' novoalign ' ,
**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=' novoalign ' ,
**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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