Class ProbconsCommandline

source code

                     object --+    
                              |    
Application.AbstractCommandline --+
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                                 ProbconsCommandline

Command line wrapper for the multiple alignment program PROBCONS.

http://probcons.stanford.edu/

Example:

To align a FASTA file (unaligned.fasta) with the output in ClustalW format, and otherwise default settings, use:

>>> from Bio.Align.Applications import ProbconsCommandline
>>> probcons_cline = ProbconsCommandline(input="unaligned.fasta",
...                                      clustalw=True)
>>> print probcons_cline
probcons -clustalw unaligned.fasta

You would typically run the command line with probcons_cline() or via the Python subprocess module, as described in the Biopython tutorial. Note that PROBCONS will write the alignment to stdout, which you may want to save to a file and then parse, e.g.:

   stdout, stderr = probcons_cline()
   handle = open("aligned.aln", "w")
   handle.write(stdout)
   handle.close()
   from Bio import AlignIO
   align = AlignIO.read("aligned.fasta", "clustalw")

Alternatively, to parse the output with AlignIO directly you can use StringIO to turn the string into a handle:

   stdout, stderr = probcons_cline()
   from StringIO import StringIO
   from Bio import AlignIO
   align = AlignIO.read(StringIO(stdout), "clustalw")

Citations:

Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340.

Last checked against version: 1.12

Create a new instance of a command line wrapper object.