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

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                     object --+    
Application.AbstractCommandline --+

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 for more details


>>> from Bio.Sequencing.Applications import SamtoolsFixmateCommandline
>>> in_bam = "/path/to/in.nameSrt.bam"
>>> out_bam = "/path/to/out.bam"
>>> fixmate_cmd = SamtoolsFixmateCommandline(input_bam=in_bam,
...                                          out_bam=out_bam)
>>> print(fixmate_cmd)
samtools fixmate /path/to/in.nameSrt.bam /path/to/out.bam
Instance Methods [hide private]
__init__(self, cmd='samtools', **kwargs)
Initialize the class.
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__

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__