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

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                     object --+    
Application.AbstractCommandline --+

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 for more details


>>> 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)
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='samtools', **kwargs)

source code 
Initialize the class.
Overrides: object.__init__