Package Bio :: Package motifs :: Package applications :: Module _xxmotif :: Class XXmotifCommandline
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Class XXmotifCommandline

source code

                     object --+    
Application.AbstractCommandline --+

Command line wrapper for XXmotif.


>>> from Bio.motifs.applications import XXmotifCommandline
>>> out_dir = "results"
>>> in_file = "sequences.fasta"
>>> xxmotif_cline = XXmotifCommandline(outdir=out_dir, seqfile=in_file, revcomp=True)
>>> print(xxmotif_cline)
XXmotif results sequences.fasta --revcomp

You would typically run the command line with xxmotif_cline() or via
the Python subprocess module, as described in the Biopython tutorial.


Luehr S, Hartmann H, and Söding J. The XXmotif web server for eXhaustive,
weight matriX-based motif discovery in nucleotide sequences,
Nucleic Acids Res. 40: W104-W109 (2012).

Hartmann H, Guthoehrlein EW, Siebert M., Luehr S, and Söding J. P-value
based regulatory motif discovery using positional weight matrices
(to be published)

Last checked against version: 1.3

Instance Methods [hide private]
__init__(self, cmd='XXmotif', **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__

Class Variables [hide private]

Inherited from Application.AbstractCommandline: parameters

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

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

source code 
Create a new instance of a command line wrapper object.
Overrides: object.__init__
(inherited documentation)