Package Bio :: Package Sequencing :: Package Applications :: Module _bwa :: Class BwaIndexCommandline
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Class BwaIndexCommandline

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                     object --+    
                              |    
Application.AbstractCommandline --+
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                                 BwaIndexCommandline

Command line wrapper for Burrows Wheeler Aligner (BWA) index.

Index database sequences in the FASTA format, equivalent to:

   $ bwa index [-p prefix] [-a algoType] [-c] <in.db.fasta>

See http://bio-bwa.sourceforge.net/bwa.shtml for details.

Example:

>>> from Bio.Sequencing.Applications import BwaIndexCommandline
>>> reference_genome = "/path/to/reference_genome.fasta"
>>> index_cmd = BwaIndexCommandline(infile=reference_genome, algorithm="bwtsw")
>>> print(index_cmd)
bwa index -a bwtsw /path/to/reference_genome.fasta

You would typically run the command using index_cmd() or via the Python subprocess module, as described in the Biopython tutorial.

Instance Methods [hide private]
 
__init__(self, cmd='bwa', **kwargs)
Create a new instance of a command line wrapper object.
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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__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, cmd='bwa', **kwargs)
(Constructor)

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Create a new instance of a command line wrapper object.

Overrides: object.__init__
(inherited documentation)