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

Class SamtoolsMpileupCommandline

source code

                     object --+    
                              |    
Application.AbstractCommandline --+
                                  |
                                 SamtoolsMpileupCommandline

Command line wrapper for samtools mpileup.

Generate BCF or pileup for one or multiple BAM files, equivalent to:

$ samtools mpileup [-EBug] [-C capQcoef] [-r reg] [-f in.fa]
                   [-l list] [-M capMapQ] [-Q minBaseQ]
                   [-q minMapQ] in.bam [in2.bam [...]]

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

Example:

>>> from Bio.Sequencing.Applications import SamtoolsMpileupCommandline
>>> input = ["/path/to/sam_or_bam_file"]
>>> samtools_mpileup_cmd = SamtoolsMpileupCommandline(input_file=input)
>>> print(samtools_mpileup_cmd)
samtools mpileup /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.
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)