Package Bio :: Package Sequencing :: Package Applications :: Module _samtools :: Class SamtoolsPhaseCommandline
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Class SamtoolsPhaseCommandline

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                     object --+    
                              |    
Application.AbstractCommandline --+
                                  |
                                 SamtoolsPhaseCommandline

Command line wrapper for samtools phase.

Call and phase heterozygous SNPs, equivalent to:

$ samtools phase [-AF] [-k len] [-b prefix]
                 [-q minLOD] [-Q minBaseQ] <in.bam>

See http://samtools.sourceforge.net/samtools.shtml for more details

Example:

>>> from Bio.Sequencing.Applications import SamtoolsPhaseCommandline
>>> input_bam = "/path/to/in.bam"
>>> samtools_phase_cmd = SamtoolsPhaseCommandline(input_bam=input_bam)
>>> print(samtools_phase_cmd)
samtools phase /path/to/in.bam
Instance Methods [hide private]
 
__init__(self, cmd='samtools', **kwargs)
Create a new instance of a command line wrapper object.
source code

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='samtools', **kwargs)
(Constructor)

source code 
Create a new instance of a command line wrapper object.
Overrides: object.__init__
(inherited documentation)