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.


Last checked against version: 1.3


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, Genome Res. 23: 181–194 (2013)


>>> 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.

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

source code 
Initialize the class.
Overrides: object.__init__