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

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                     object --+    
                              |    
Application.AbstractCommandline --+
                                  |
                                 SamtoolsViewCommandline

Command line wrapper for samtools view.

Extract/print all or sub alignments in SAM or BAM format, equivalent to:

$ samtools view [-bchuHS] [-t in.refList] [-o output] [-f reqFlag]
                [-F skipFlag] [-q minMapQ] [-l library] [-r readGroup]
                [-R rgFile] <in.bam>|<in.sam> [region1 [...]]

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

Example:

    >>> from Bio.Sequencing.Applications import SamtoolsViewCommandline
    >>> input_file = "/path/to/sam_or_bam_file"
    >>> samtools_view_cmd = SamtoolsViewCommandline(input_file=input_file)
    >>> print(samtools_view_cmd)
    samtools view /path/to/sam_or_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)