-2

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.

Mossig Stamboulian
  • 17
  • 5
  • Your best option is to use jfatcat through a subprocess. Biopython do this all over the place (wrappers for blast, clustal, muscle, Tcoffee, etc) http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec91 – xbello Jul 29 '14 at 19:24
  • is there any documentation provided concerning the wrappers for Jfatcat and Jce (combinatorial extensions) I'm assuming it's within the PDB tools in Biopython... as in Bio.PDB.---- but I cant seem to find it. Thanks. – Mossig Stamboulian Jul 30 '14 at 16:18

1 Answers1

0

[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.

xbello
  • 7,223
  • 3
  • 28
  • 41