Author: bugman
Date: Wed Jan 21 12:15:53 2015
New Revision: 27254
URL: http://svn.gna.org/viewcvs/relax?rev=27254&view=rev
Log:
Created the lib.sequence_alignment.substitution_matrices module.
This is for storing substitution matrices for use in sequence alignment. The
module currently only
includes the BLOSSUM62 matrix.
Added:
trunk/lib/sequence_alignment/substitution_matrices.py
Modified:
trunk/lib/sequence_alignment/__init__.py
Modified: trunk/lib/sequence_alignment/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/sequence_alignment/__init__.py?rev=27254&r1=27253&r2=27254&view=diff
==============================================================================
--- trunk/lib/sequence_alignment/__init__.py (original)
+++ trunk/lib/sequence_alignment/__init__.py Wed Jan 21 12:15:53 2015
@@ -23,5 +23,6 @@
"""The relax-lib sequence alignment package - a library of functions for
aligning proteins, DNA, RNA or other molecules."""
__all__ = [
- 'needleman_wunsch'
+ 'needleman_wunsch',
+ 'substitution_matrices'
]
Added: trunk/lib/sequence_alignment/substitution_matrices.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/sequence_alignment/substitution_matrices.py?rev=27254&view=auto
==============================================================================
--- trunk/lib/sequence_alignment/substitution_matrices.py (added)
+++ trunk/lib/sequence_alignment/substitution_matrices.py Wed Jan 21
12:15:53 2015
@@ -0,0 +1,55 @@
+###############################################################################
+#
#
+# Copyright (C) 2015 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax (http://www.nmr-relax.com).
#
+#
#
+# This program 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 program 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 program. If not, see <http://www.gnu.org/licenses/>.
#
+#
#
+###############################################################################
+
+# Module docstring.
+"""Substitution matrices for use in sequence alignment."""
+
+# Python module imports.
+from numpy import array, int16
+
+
+BLOSSUM62_SEQ = ['ARNDCQEGHILKMFPSTWYVBZX*']
+BLOSSUM62 = array([
+ [ 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3,
-2, 0, -2, -1, 0, -4],
+ [-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3,
-2, -3, -1, 0, -1, -4],
+ [-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4,
-2, -3, 3, 0, -1, -4],
+ [-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4,
-3, -3, 4, 1, -1, -4],
+ [ 0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2,
-2, -1, -3, -3, -2, -4],
+ [-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2,
-1, -2, 0, 3, -1, -4],
+ [-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3,
-2, -2, 1, 4, -1, -4],
+ [ 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2,
-3, -3, -1, -2, -1, -4],
+ [-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2,
2, -3, 0, 0, -1, -4],
+ [-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3,
-1, 3, -3, -3, -1, -4],
+ [-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2,
-1, 1, -4, -3, -1, -4],
+ [-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3,
-2, -2, 0, 1, -1, -4],
+ [-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1,
-1, 1, -3, -1, -1, -4],
+ [-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1,
3, -1, -3, -3, -1, -4],
+ [-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4,
-3, -2, -2, -1, -2, -4],
+ [ 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3,
-2, -2, 0, 0, 0, -4],
+ [ 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2,
-2, 0, -1, -1, 0, -4],
+ [-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11,
2, -3, -4, -3, -2, -4],
+ [-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2,
7, -1, -3, -2, -1, -4],
+ [ 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3,
-1, 4, -3, -2, -1, -4],
+ [-2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4,
-3, -3, 4, 1, -1, -4],
+ [-1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3,
-2, -2, 1, 4, -1, -4],
+ [ 0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2,
-1, -1, -1, -1, -1, -4],
+ [-4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,
-4, -4, -4, -4, -4, 1]
+], int16)
r27254 - in /trunk/lib/sequence_alignment: __init__.py substitution_matrices.py