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

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                     object --+    
                              |    
Application.AbstractCommandline --+
                                  |
                                 SamtoolsReheaderCommandline

Command line wrapper for samtools reheader.

Replace the header in in.bam with the header in in.header.sam, equivalent to:

$ samtools reheader <in.header.sam> <in.bam>

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

Example:

>>> from Bio.Sequencing.Applications import SamtoolsReheaderCommandline
>>> input_header = "/path/to/header_sam_file"
>>> input_bam = "/path/to/input_bam_file"
>>> samtools_reheader_cmd = SamtoolsReheaderCommandline(                                        input_header=input_header,                                        input_bam=input_bam)
>>> print(samtools_reheader_cmd)
samtools reheader /path/to/header_sam_file /path/to/input_bam_file
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)