[Octave-cvsupdate] SF.net SVN: octave: [4838] trunk/octave-forge/main/bioinfo/inst/cleave.m

[<ws...@us...>]

Revision: 4838
          http://octave.svn.sourceforge.net/octave/?rev=4838&view=rev
Author:   wsloand
Date:     2008-03-31 14:52:55 -0700 (Mon, 31 Mar 2008)

Log Message:
-----------
new function: cleave.m (really true this time)

Added Paths:
-----------
    trunk/octave-forge/main/bioinfo/inst/cleave.m

Added: trunk/octave-forge/main/bioinfo/inst/cleave.m
===================================================================
--- trunk/octave-forge/main/bioinfo/inst/cleave.m	                        (rev 0)
+++ trunk/octave-forge/main/bioinfo/inst/cleave.m	2008-03-31 21:52:55 UTC (rev 4838)
@@ -0,0 +1,85 @@
+## Copyright (C) 2008 Bill Denney
+##
+## This software is free software; you can redistribute it and/or modify it
+## under the terms of the GNU General Public License as published by
+## the Free Software Foundation; either version 3 of the License, or (at
+## your option) any later version.
+##
+## This software is distributed in the hope that it will be useful, but
+## WITHOUT ANY WARRANTY; without even the implied warranty of
+## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+## General Public License for more details.
+##
+## You should have received a copy of the GNU General Public License
+## along with this software; see the file COPYING.  If not, see
+## <http://www.gnu.org/licenses/>.
+
+## -*- texinfo -*-
+## @deftypefn {Function File} {@var{fragments} =} cleave (@var{sequence}, @var{pattern}, @var{position})
+## @deftypefnx {Function File} {[@var{fragments}, @var{cuttingsites}] =} cleave (@dots{})
+## @deftypefnx {Function File} {[@var{fragments}, @var{cuttingsites}, @var{lengths}] =} cleave (@dots{})
+## @deftypefnx {Function File} {[@dots{}] =} cleave (@dots{}, "PartialDigest", @var{prob})
+## Celave a peptide @var{sequence} using the @var{pattern} at the
+## @var{position} relative to the pattern.  The @var{sequence} is a
+## sequence of amino acids; the @var{pattern} is a regular expression to
+## find the location of the cleavage; and the @var{position} is the
+## position relative to that regular expression (0 is immediately to the
+## left of the first character, 1 is immediately to the right of the
+## first character, @dots{}).
+##
+## @multitable
+## @item Protease @tab Peptide Pattern @tab Position
+## @item Trypsin @tab [KR](?!P) @tab 1
+## @item Chymotrypsin @tab [WYF](?!P) @tab 1
+## @item Glutamine C @tab [ED](?!P)  @tab 1
+## @item Lysine C @tab [K](?!P)  @tab 1
+## @item Aspartic acid N @tab D @tab 1
+## @end multitable
+##
+## @example
+##
+## @seealso{rebasecuts, restrict, seqshowwords, regexp}
+## @end deftypefn
+
+## Author: Bill Denney <bi...@de...>
+
+function [fragments, s, lengths] = cleave (seq, pattern, pos, varargin)
+
+  if isstruct (seq)
+    seq = seq.sequence;
+  endif
+  if (rows (seq) != 1)
+    error ("seqreverse: the sequence must have a single row");
+  endif
+  if (! isempty (varargin))
+    ## FIXME: add support for partialdigest
+    error ("cleave: additional parameters are not yet supported")
+  endif
+
+  s = [0 (pos - 1 + regexp (seq, pattern))];
+  ## There is no cleavage at the end-- there was already a cleavage
+  ## there.
+  if (s(end) == length(seq))
+  s(end) = [];
+  endif
+  fragments = cell (size (s));
+  lengths = [s(2:end) length(seq)] - s;
+  for i = 1:numel (s)
+    fragments{i} = seq(s(i)+1:s(i)+lengths(i));
+  endfor
+
+endfunction
+
+## Tests
+%!test
+%! site = [0 6 7 41 46 67 74 80 92 100];
+%! len = [6 1 34 5 21 7 6 12 8 10];
+%! frag = {"MGTGGR" "R" "GAAAAPLLVAVAALLLGAAGHLYPGEVCPGMDIR" "NNLTR" \
+%!         "LHELENCSVIEGHLQILLMFK" "TRPEDFR" "DLSFPK" "LIMITDYLLLFR" \
+%!         "VYGLESLK" "DLFPNLTVIR"};
+%! seq = strcat (frag{:});
+%! [tfrag, tsite, tlen] = cleave (seq, '[KR](?!P)', 1);
+%! assert (tfrag, frag)
+%! assert (tsite, site)
+%! assert (tlen, len)
+## FIXME: This needs a test for partialdigest.


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