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

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                     object --+    
Application.AbstractCommandline --+

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

Run a BWA alignment, equivalent to:

$ bwa aln [...] <in.db.fasta> <in.query.fq> > <out.sai>

See for details.


>>> from Bio.Sequencing.Applications import BwaAlignCommandline
>>> reference_genome = "/path/to/reference_genome.fasta"
>>> read_file = "/path/to/read_1.fq"
>>> output_sai_file = "/path/to/read_1.sai"
>>> align_cmd = BwaAlignCommandline(reference=reference_genome, read_file=read_file)
>>> print(align_cmd)
bwa aln /path/to/reference_genome.fasta /path/to/read_1.fq

You would typically run the command line using align_cmd(stdout=output_sai_file) or via the Python subprocess module, as described in the Biopython tutorial.

Instance Methods [hide private]
__init__(self, cmd='bwa', **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='bwa', **kwargs)

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Initialize the class.
Overrides: object.__init__