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

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                     object --+    
                              |    
Application.AbstractCommandline --+
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                                 SamtoolsCatCommandline

Command line wrapper for samtools cat.

Concatenate BAMs, equivalent to:

$ samtools cat [-h header.sam] [-o out.bam] <in1.bam> <in2.bam> [ ... ]

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

Example:

>>> from Bio.Sequencing.Applications import SamtoolsCatCommandline
>>> input_bam1 = "/path/to/input_bam1"
>>> input_bam2 = "/path/to/input_bam2"
>>> input_bams = [input_bam1, input_bam2]
>>> samtools_cat_cmd = SamtoolsCatCommandline(input_bam=input_bams)
>>> print(samtools_cat_cmd)
samtools cat /path/to/input_bam1 /path/to/input_bam2
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)