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

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                     object --+    
                              |    
Application.AbstractCommandline --+
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                                 BwaSamseCommandline

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

Generate alignments in the SAM format given single-end reads. Equvialent to:

   $ bwa samse [-n maxOcc] <in.db.fasta> <in.sai> <in.fq> > <out.sam>

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

Example:

>>> from Bio.Sequencing.Applications import BwaSamseCommandline
>>> reference_genome = "/path/to/reference_genome.fasta"
>>> read_file = "/path/to/read_1.fq"
>>> sai_file = "/path/to/read_1.sai"
>>> output_sam_file = "/path/to/read_1.sam"
>>> samse_cmd = BwaSamseCommandline(reference=reference_genome,
...                                 read_file=read_file, sai_file=sai_file)
>>> print(samse_cmd)
bwa samse /path/to/reference_genome.fasta /path/to/read_1.sai /path/to/read_1.fq

You would typically run the command line using samse_cmd(stdout=output_sam_file) 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)

source code 
Create a new instance of a command line wrapper object.

Overrides: object.__init__
(inherited documentation)