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

Class SamtoolsCalmdCommandline

source code

                     object --+    
                              |    
Application.AbstractCommandline --+
                                  |
                                 SamtoolsCalmdCommandline

Command line wrapper for samtools calmd.

Generate the MD tag, equivalent to:

$ samtools calmd [-EeubSr] [-C capQcoef] <aln.bam> <ref.fasta>

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

Example:

>>> from Bio.Sequencing.Applications import SamtoolsCalmdCommandline
>>> input_bam = "/path/to/aln.bam"
>>> reference_fasta = "/path/to/reference.fasta"
>>> samtools_calmd_cmd = SamtoolsCalmdCommandline(                                                      input_bam=input_bam,                                                      reference=reference_fasta)
>>> print(samtools_calmd_cmd)
samtools calmd /path/to/aln.bam /path/to/reference.fasta
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)