Class XXmotifCommandline

source code

                     object --+    
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Application.AbstractCommandline --+
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                                 XXmotifCommandline

Command line wrapper for XXmotif.

http://xxmotif.genzentrum.lmu.de/

Example:

>>> from Bio.Motif.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.

Citations:

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

Create a new instance of a command line wrapper object.