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

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                     object --+    
                              |    
Application.AbstractCommandline --+
                                  |
                                 SamtoolsFaidxCommandline

Command line wrapper for samtools faidx.

Retrieve and print stats in the index file, equivalent to:

$ samtools faidx <ref.fasta> [region1 [...]]

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

Example:

>>> from Bio.Sequencing.Applications import SamtoolsFaidxCommandline
>>> reference = "/path/to/reference.fasta"
>>> samtools_faidx_cmd = SamtoolsFaidxCommandline(reference=reference)
>>> print(samtools_faidx_cmd)
samtools faidx /path/to/reference.fasta
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)