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

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                     object --+    
                              |    
Application.AbstractCommandline --+
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                                 SamtoolsSortCommandline

Command line wrapper for samtools sort.

Concatenate BAMs, equivalent to:

$ samtools sort [-no] [-m maxMem] <in.bam> <out.prefix>

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

Example

>>> from Bio.Sequencing.Applications import SamtoolsSortCommandline
>>> input_bam = "/path/to/input_bam"
>>> out_prefix = "/path/to/out_prefix"
>>> samtools_sort_cmd = SamtoolsSortCommandline(                                                    input_bam=input_bam,                                                    out_prefix=out_prefix)
>>> print(samtools_sort_cmd)
samtools sort /path/to/input_bam /path/to/out_prefix
Instance Methods [hide private]
 
__init__(self, cmd='samtools', **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='samtools', **kwargs)
(Constructor)

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