Search code examples
python-2.7alignmentbiopython

Structure structure alignment using combinatorial extensions

I am trying to find a tool that performs structure structure alignment for two sequences given their residues using combinatorial extensions (CE). I found a tool based on combinatorial extensions provided by the protein data bank: http://source.rcsb.org/jfatcatserver/ However I was wondering if there is any python module or a class for structure to structure alignment that I can implement. I have found the structure Alignment tool from Bio.PDB, but is poorly documented. is there any python module or library that implements this method? Thanks.

Solution

  • [Doesn't fit as a comment]

    I doubt that wrap exists. You'll have to scratch your own itch here: experiment with the command in a console, and then put it in a subprocess.Popen(). The wrappers won't save you from work, e.g.

    from Bio.Align.Applications import MuscleCommandline

muscle_cline = MuscleCommandline(input="opuntia.fasta")
stdout, stderr = muscle_cline()

align = AlignIO.read(stdout, "fasta")

    Is about the same as:

    import subprocess

proc = subprocess.Popen(["muscle", "-in", "opuntia.fasta"],
                        stdout=subprocess.PIPE,
                        stderr=subprocess.PIPE)

align = AlignIO.read(proc.stdout, "fasta")

    Maybe if you put this code inside a bigger app (like the external commands in Bioedit), you can assert that the user input fits the values that the wrapped command expects, or if a required flag is present... that's where the wrappers shine.