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

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                     object --+    
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Application.AbstractCommandline --+
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                                 SamtoolsTargetcutCommandline

Command line wrapper for samtools targetcut.

This command identifies target regions by examining the continuity of read depth, computes haploid consensus sequences of targets and outputs a SAM with each sequence corresponding to a target, equivalent to:

$ samtools targetcut [-Q minBaseQ] [-i inPenalty] [-0 em0]
                     [-1 em1] [-2 em2] [-f ref] <in.bam>

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

Example:

>>> from Bio.Sequencing.Applications import SamtoolsTargetcutCommandline
>>> input_bam = "/path/to/aln.bam"
>>> samtools_targetcut_cmd = SamtoolsTargetcutCommandline(input_bam=input_bam)
>>> print(samtools_targetcut_cmd)
samtools targetcut /path/to/aln.bam
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)