Package Bio :: Package Sequencing :: Package Applications :: Module _samtools :: Class SamtoolsMergeCommandline
[hide private]
[frames] | no frames]

Class SamtoolsMergeCommandline

source code

                     object --+    
                              |    
Application.AbstractCommandline --+
                                  |
                                 SamtoolsMergeCommandline

Command line wrapper for samtools merge.

Merge multiple sorted alignments, equivalent to:

$ samtools merge [-nur1f] [-h inh.sam] [-R reg]
                 <out.bam> <in1.bam> <in2.bam> [...]

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

Example

>>> from Bio.Sequencing.Applications import SamtoolsMergeCommandline
>>> out_bam = "/path/to/out_bam"
>>> in_bam = ["/path/to/input_bam1", "/path/to/input_bam2"]
>>> samtools_merge_cmd = SamtoolsMergeCommandline(                                                      out_bam=out_bam,                                                      input_bam=in_bam)
>>> print(samtools_merge_cmd)
samtools merge /path/to/out_bam /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.
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__

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)