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object --+ | Application.AbstractCommandline --+ | 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 agains version: 1.12
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Create a new instance of a command line wrapper object.
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