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

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                     object --+    
                              |    
Application.AbstractCommandline --+
                                  |
                                 SamtoolsFixmateCommandline

Command line wrapper for samtools fixmate.

Fill in mate coordinates, ISIZE and mate related flags from a name-sorted alignment, equivalent to:

$ samtools fixmate <in.nameSrt.bam> <out.bam>

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

Example:

>>> from Bio.Sequencing.Applications import SamtoolsFixmateCommandline
>>> in_bam = "/path/to/in.nameSrt.bam"
>>> out_bam = "/path/to/out.bam"
>>> samtools_fixmate_cmd = SamtoolsFixmateCommandline(                                                              input_bam=in_bam,                                                              out_bam=out_bam)
>>> print(samtools_fixmate_cmd)
samtools fixmate /path/to/in.nameSrt.bam /path/to/out.bam
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)

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Create a new instance of a command line wrapper object.

Overrides: object.__init__
(inherited documentation)