Package Bio :: Package Sequencing :: Package Applications :: Module _Novoalign :: Class NovoalignCommandline
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Class NovoalignCommandline

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                     object --+    
Application.AbstractCommandline --+

Command line wrapper for novoalign by Novocraft.

See - novoalign is a short read alignment program.


>>> 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 with 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' # limited valid values
>>> novoalign_cline.fragment = '250 20' # must be given as a string
>>> 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

Instance Methods [hide private]
__init__(self, cmd='novoalign', **kwargs)
Initialize the class.
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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__

Class Variables [hide private]

Inherited from Application.AbstractCommandline: parameters

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, cmd='novoalign', **kwargs)

source code 
Initialize the class.
Overrides: object.__init__