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

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                     object --+    
Application.AbstractCommandline --+

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 for more details


>>> 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)
Initialize the class.
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__

Class Variables [hide private]

Inherited from Application.AbstractCommandline: parameters

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, cmd='samtools', **kwargs)

source code 
Initialize the class.
Overrides: object.__init__