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15 Nov 00 Brad

* Added SubsMat tests, sample files and expected outputs.
* Updated alignment test to use SubsMat.FreqTable.
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1 parent 19dc341 commit 431dec3764614ed021d7467d8a4b1b9fcc960822 chapmanb committed Nov 15, 2000
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20 Tests/SubsMat/aaDistrib.txt
@@ -0,0 +1,20 @@
+A 2377 0.0852491
+C 383 0.013736
+D 1669 0.0598573
+E 1655 0.0593552
+F 1167 0.0418535
+G 2185 0.0783632
+H 627 0.0224868
+I 1455 0.0521823
+K 1614 0.0578847
+L 2360 0.0846394
+M 651 0.0233476
+N 1387 0.0497436
+P 1191 0.0427142
+Q 1022 0.0366532
+R 1282 0.0459778
+S 1664 0.0596779
+T 1599 0.0573468
+V 2052 0.0735932
+W 421 0.0150988
+Y 1119 0.040132
View
632 Tests/SubsMat/acc_rep_mat.pik
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+s.
View
20 Tests/SubsMat/protein_count.txt
@@ -0,0 +1,20 @@
+A 2377
+C 383
+D 1669
+E 1655
+F 1167
+G 2185
+H 627
+I 1455
+K 1614
+L 2360
+M 651
+N 1387
+P 1191
+Q 1022
+R 1282
+S 1664
+T 1599
+V 2052
+W 421
+Y 1119
View
20 Tests/SubsMat/protein_freq.txt
@@ -0,0 +1,20 @@
+A 0.0852491
+C 0.013736
+D 0.0598573
+E 0.0593552
+F 0.0418535
+G 0.0783632
+H 0.0224868
+I 0.0521823
+K 0.0578847
+L 0.0846394
+M 0.0233476
+N 0.0497436
+P 0.0427142
+Q 0.0366532
+R 0.0459778
+S 0.0596779
+T 0.0573468
+V 0.0735932
+W 0.0150988
+Y 0.040132
View
7 Tests/SubsMat/redAADistrib.txt
@@ -0,0 +1,7 @@
+F 9278 0.332748
+R 3334 0.119571
+O 5672 0.203422
+T 2896 0.103862
+N 3324 0.119212
+G 2185 0.0783632
+P 1191 0.0427142
View
8 Tests/SubsMat/redAltAADistrib.txt
@@ -0,0 +1,8 @@
+A 3411 0.2104153
+F 5867 0.1223327
+R 3334 0.119571
+O 5672 0.203422
+T 2896 0.103862
+N 3324 0.119212
+G 2185 0.0783632
+P 1191 0.0427142
View
1,140 Tests/output/test_SubsMat
@@ -0,0 +1,1140 @@
+test_SubsMat
+Check differences between derived and true frequencies for each
+letter. Differences should be very small
+A 0.000009
+C 0.000001
+D 0.000006
+E 0.000006
+F 0.000004
+G 0.000008
+H 0.000002
+I 0.000006
+K 0.000006
+L 0.000009
+M 0.000002
+N 0.000005
+P 0.000005
+Q 0.000004
+R 0.000005
+S 0.000006
+T 0.000006
+V 0.000008
+W 0.000002
+Y 0.000004
+A 0.011
+C 0.002 0.002
+D 0.009 0.001 0.008
+E 0.010 0.001 0.008 0.006
+F 0.006 0.002 0.003 0.003 0.004
+G 0.011 0.002 0.007 0.007 0.005 0.016
+H 0.003 0.001 0.003 0.002 0.002 0.003 0.003
+I 0.010 0.002 0.003 0.003 0.008 0.005 0.002 0.007
+K 0.010 0.001 0.008 0.008 0.003 0.007 0.003 0.004 0.006
+L 0.015 0.003 0.006 0.007 0.012 0.008 0.004 0.017 0.006 0.016
+M 0.004 0.001 0.001 0.002 0.003 0.002 0.001 0.004 0.002 0.008 0.001
+N 0.007 0.001 0.008 0.006 0.003 0.007 0.003 0.003 0.007 0.005 0.002 0.003
+P 0.006 0.001 0.005 0.005 0.003 0.005 0.001 0.003 0.005 0.004 0.001 0.005 0.006
+Q 0.006 0.001 0.006 0.005 0.002 0.004 0.002 0.003 0.005 0.004 0.001 0.004 0.003 0.002
+R 0.008 0.001 0.006 0.006 0.003 0.004 0.002 0.003 0.008 0.005 0.002 0.005 0.004 0.004 0.005
+S 0.010 0.001 0.008 0.007 0.005 0.008 0.003 0.004 0.007 0.008 0.002 0.006 0.005 0.005 0.005 0.006
+T 0.010 0.002 0.006 0.008 0.003 0.008 0.003 0.004 0.007 0.009 0.002 0.005 0.005 0.005 0.006 0.009 0.004
+V 0.013 0.003 0.005 0.006 0.008 0.007 0.003 0.016 0.007 0.022 0.005 0.005 0.005 0.003 0.004 0.006 0.007 0.012
+W 0.002 0.000 0.001 0.001 0.002 0.002 0.001 0.002 0.001 0.004 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.002 0.002
+Y 0.006 0.001 0.003 0.003 0.007 0.005 0.002 0.005 0.003 0.009 0.002 0.004 0.003 0.002 0.003 0.004 0.005 0.007 0.003 0.004
+ A C D E F G H I K L M N P Q R S T V W Y
+Diff between supplied and matrix-derived frequencies, should be small
+Y 0.00
+V 0.00
+W 0.00
+T 0.00
+R 0.00
+S 0.00
+P 0.00
+Q 0.00
+N 0.00
+L 0.01
+M 0.00
+K 0.00
+H 0.00
+I 0.01
+F 0.00
+G 0.01
+D 0.00
+E 0.00
+C 0.00
+A 0.00
+Calculating sum of letters for an observed frequency matrix
+Y 0.04
+V 0.08
+W 0.02
+T 0.06
+R 0.04
+S 0.06
+P 0.04
+Q 0.04
+N 0.05
+L 0.09
+M 0.02
+K 0.06
+H 0.02
+I 0.06
+F 0.04
+G 0.07
+D 0.06
+E 0.05
+C 0.02
+A 0.09
+Total sum 1.00 should be 1.0
+
+Log odds matrix
+A 1.60
+V -0.20 2.90
+I 0.10 2.30 3.30
+L -0.20 1.90 2.10 2.60
+M -0.10 1.10 2.00 2.30 2.90
+C -0.30 0.90 0.70 0.30 -0.20 9.50
+F -1.00 0.60 1.60 1.50 1.90 0.70 2.90
+W -0.70 -0.60 0.00 0.90 2.10 -0.90 1.70 7.80
+Y -0.60 0.10 -0.20 0.40 0.10 -1.30 2.80 2.70 3.70
+H -0.90 -1.40 -2.50 -1.10 -1.50 -1.70 -0.40 -0.80 0.30 6.90
+S 0.10 -2.00 -2.00 -1.30 -1.30 -1.80 -0.50 -2.30 -1.20 0.30 2.40
+T 0.10 -0.80 -1.70 -0.60 -1.90 -0.60 -1.70 -0.20 -0.20 1.10 1.20 1.20
+N -0.50 -1.90 -2.20 -2.30 -1.10 -0.70 -1.80 -0.10 -0.20 1.10 0.30 0.00 1.90
+Q 0.20 -2.10 -1.30 -2.30 -1.00 -1.40 -2.20 -1.90 -1.70 1.10 0.90 0.80 0.60 2.10
+K -0.10 -1.30 -2.20 -2.80 -2.30 -1.60 -1.90 -2.50 -1.60 0.60 0.40 0.40 1.20 1.20 2.70
+R 0.10 -1.90 -2.40 -1.80 -0.20 -2.50 -1.40 -0.90 -0.70 0.20 -0.30 0.60 0.50 0.60 1.80 4.00
+D -0.50 -2.70 -3.00 -2.50 -4.30 -3.60 -2.10 -2.20 -1.70 -0.20 1.10 -0.10 1.90 1.50 1.20 0.70 3.70
+E 0.50 -1.90 -3.00 -1.80 -2.00 -1.10 -2.90 -2.20 -1.80 -1.40 0.60 0.90 0.60 1.30 1.20 0.90 1.20 3.00
+G -0.20 -2.20 -2.50 -2.30 -1.30 -0.40 -0.90 -1.10 -0.70 -1.00 -0.00 -0.10 0.50 -0.50 -0.30 -1.80 -0.40 -0.20 5.10
+P -0.70 -0.70 -1.50 -2.90 -2.90 -0.80 -1.70 -1.70 -0.60 -2.30 0.40 -0.00 0.90 0.60 0.00 0.00 0.60 0.10 -0.30 5.60
+ A V I L M C F W Y H S T N Q K R D E G P
+
+Testing MatrixInfo
+
+benner6
+------------
+A 2
+C -1 12
+D 0 -3 5
+E 0 -4 4 5
+F -3 0 -5 -6 8
+G 0 -1 0 0 -5 5
+H -2 -1 0 0 0 -2 6
+I 0 -3 -4 -4 0 -3 -3 4
+K -1 -2 0 0 -6 -1 0 -3 5
+L -1 -3 -5 -5 2 -4 -2 2 -4 4
+M 0 -3 -4 -4 0 -3 -3 4 -2 -2 4
+N 0 -1 2 1 -3 0 1 -2 1 -3 -2 3
+P 1 -2 -2 -2 -3 -1 0 -2 -2 0 -1 -1 6
+Q -1 -3 0 2 -4 -1 3 -3 2 -2 -3 0 0 5
+R -1 0 -1 0 -4 0 1 -3 4 -3 -3 0 -1 2 5
+S 1 0 0 -1 -1 0 0 -1 -1 -1 -1 1 1 -1 0 2
+T 1 -1 -1 -1 -2 0 -1 0 -1 0 0 0 0 -1 -1 1 2
+V 0 -3 -3 -3 0 -2 -3 3 -3 1 3 -2 -1 -3 -3 0 0 4
+W -4 1 -6 -5 -1 -1 -2 -5 -1 -3 -4 -4 -4 -2 2 -2 -2 -4 14
+Y -4 2 -2 -4 5 -4 4 -3 -4 -1 -3 0 -3 -1 -2 -1 -3 -3 0 9
+ A C D E F G H I K L M N P Q R S T V W Y
+
+benner22
+------------
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+V 0 -2 -2 -2 -2 -1 -1 -2 4 -2 2 2 -2 -1 -2 -2 -1 0 4
+W -6 -5 -8 -7 -7 0 -7 -3 -5 -3 -2 -4 -4 -6 -5 2 -2 -5 -6 17
+X 0 -1 -3 -1 -1 -2 -1 -1 -1 -1 -1 -1 0 -1 -1 -1 0 0 -1 -4 -1
+Y -3 -3 0 -4 -4 7 -5 0 -1 -4 -1 -2 -2 -5 -4 -4 -3 -3 -2 0 -2 10
+Z 0 2 -5 3 3 -5 0 2 -2 0 -3 -2 1 0 3 0 0 -1 -2 -6 -1 -4 3
+ A B C D E F G H I K L M N P Q R S T V W X Y Z
+
+pam30
+------------
+A 6
+B -3 6
+C -6 -12 10
+D -3 6 -14 8
+E -2 1 -14 2 8
+F -8 -10 -13 -15 -14 9
+G -2 -3 -9 -3 -4 -9 6
+H -7 -1 -7 -4 -5 -6 -9 9
+I -5 -6 -6 -7 -5 -2 -11 -9 8
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+M -5 -10 -13 -11 -7 -4 -8 -10 -1 -2 1 11
+N -4 6 -11 2 -2 -9 -3 0 -5 -1 -7 -9 8
+P -2 -7 -8 -8 -5 -10 -6 -4 -8 -6 -7 -8 -6 8
+Q -4 -3 -14 -2 1 -13 -7 1 -8 -3 -5 -4 -3 -3 8
+R -7 -7 -8 -10 -9 -9 -9 -2 -5 0 -8 -4 -6 -4 -2 8
+S 0 -1 -3 -4 -4 -6 -2 -6 -7 -4 -8 -5 0 -2 -5 -3 6
+T -1 -3 -8 -5 -6 -9 -6 -7 -2 -3 -7 -4 -2 -4 -5 -6 0 7
+V -2 -8 -6 -8 -6 -8 -5 -6 2 -9 -2 -1 -8 -6 -7 -8 -6 -3 7
+W -13 -10 -15 -15 -17 -4 -15 -7 -14 -12 -6 -13 -8 -14 -13 -2 -5 -13 -15 13
+X -3 -5 -9 -5 -5 -8 -5 -5 -5 -5 -6 -5 -3 -5 -5 -6 -3 -4 -5 -11 -5
+Y -8 -6 -4 -11 -8 2 -14 -3 -6 -9 -7 -11 -4 -13 -12 -10 -7 -6 -7 -5 -7 10
+Z -3 0 -14 1 6 -13 -5 -1 -6 -4 -7 -5 -3 -4 6 -4 -5 -6 -6 -14 -5 -9 6
+ A B C D E F G H I K L M N P Q R S T V W X Y Z
+
+pam300
+------------
+A 2
+B 0 3
+C -2 -5 15
+D 0 3 -6 4
+E 0 3 -6 4 4
+F -4 -5 -5 -6 -6 11
+G 2 1 -4 1 0 -5 5
+H -1 1 -4 1 1 -2 -2 7
+I 0 -2 -3 -2 -2 1 -3 -2 5
+K -1 1 -6 0 0 -6 -2 0 -2 5
+L -2 -4 -7 -4 -4 3 -4 -2 3 -3 7
+M -1 -2 -6 -3 -2 1 -3 -2 3 0 4 6
+N 0 2 -4 2 2 -4 1 2 -2 1 -3 -2 2
+P 1 0 -3 -1 0 -5 0 0 -2 -1 -3 -2 0 6
+Q 0 2 -6 2 3 -5 -1 3 -2 1 -2 -1 1 0 4
+R -1 0 -4 -1 -1 -5 -2 2 -2 4 -3 0 0 0 2 7
+S 1 1 0 0 0 -4 1 -1 -1 0 -3 -2 1 1 0 0 1
+T 1 0 -2 0 0 -3 0 -1 0 0 -2 -1 0 1 -1 -1 1 2
+V 0 -2 -2 -2 -2 -1 -1 -2 4 -2 2 2 -2 -1 -2 -3 -1 0 5
+W -6 -6 -9 -7 -8 1 -8 -3 -6 -4 -2 -5 -5 -6 -5 3 -3 -6 -7 22
+X 0 0 -3 -1 -1 -2 -1 0 -1 -1 -1 -1 0 -1 0 -1 0 0 0 -4 -1
+Y -4 -4 1 -5 -5 9 -6 0 -1 -5 0 -2 -2 -5 -4 -5 -3 -3 -3 0 -2 12
+Z 0 2 -6 3 3 -5 0 2 -2 1 -3 -2 1 0 3 0 0 0 -2 -6 -1 -5 3
+ A B C D E F G H I K L M N P Q R S T V W X Y Z
+
+pam60
+------------
+A 5
+B -2 5
+C -5 -9 9
+D -2 5 -10 7
+E -1 2 -10 3 7
+F -6 -8 -9 -11 -10 8
+G 0 -2 -7 -2 -2 -7 6
+H -5 0 -6 -2 -3 -4 -6 8
+I -3 -4 -4 -5 -4 -1 -7 -6 7
+K -5 -1 -10 -2 -3 -10 -5 -4 -4 6
+L -4 -7 -11 -9 -7 -1 -8 -4 0 -6 6
+M -3 -6 -10 -7 -5 -2 -6 -7 1 0 2 10
+N -2 5 -7 2 0 -6 -1 1 -4 0 -5 -6 6
+P 0 -4 -6 -5 -3 -7 -4 -2 -6 -4 -5 -6 -4 7
+Q -3 -1 -10 -1 2 -9 -5 2 -5 -1 -3 -2 -2 -1 7
+R -5 -5 -6 -6 -6 -7 -7 0 -4 2 -6 -2 -3 -2 0 8
+S 1 0 -1 -2 -2 -5 0 -4 -4 -2 -6 -4 1 0 -3 -2 5
+T 1 -2 -5 -3 -4 -6 -3 -5 -1 -2 -5 -2 -1 -2 -4 -4 1 6
+V -1 -5 -4 -6 -4 -5 -4 -5 3 -6 -1 0 -5 -4 -5 -5 -4 -1 6
+W -10 -8 -12 -11 -12 -3 -11 -5 -10 -8 -4 -9 -6 -10 -9 0 -4 -9 -11 13
+X -2 -3 -6 -3 -3 -5 -3 -3 -3 -3 -4 -3 -2 -3 -3 -4 -2 -2 -3 -8 -3
+Y -6 -5 -2 -8 -7 3 -10 -2 -4 -7 -5 -7 -3 -10 -8 -8 -5 -5 -5 -3 -5 9
+Z -2 1 -10 2 5 -10 -3 0 -4 -2 -5 -4 -1 -2 6 -2 -3 -4 -5 -11 -3 -7 5
+ A B C D E F G H I K L M N P Q R S T V W X Y Z
+
+pam90
+------------
+A 4
+B -1 4
+C -3 -7 9
+D -1 5 -8 6
+E 0 2 -8 4 6
+F -5 -6 -7 -8 -8 8
+G 0 -1 -5 -1 -1 -6 5
+H -4 1 -5 -1 -1 -3 -5 8
+I -2 -3 -3 -4 -3 0 -5 -5 6
+K -3 0 -8 -2 -2 -8 -4 -2 -3 5
+L -3 -5 -9 -7 -5 0 -6 -3 1 -5 6
+M -2 -5 -8 -5 -4 -1 -5 -5 1 0 2 9
+N -1 4 -6 3 0 -5 -1 2 -3 1 -4 -4 5
+P 0 -3 -5 -4 -2 -6 -3 -2 -4 -3 -4 -4 -2 7
+Q -2 0 -8 0 2 -7 -3 2 -4 -1 -3 -2 -1 -1 6
+R -4 -3 -5 -5 -4 -6 -5 1 -3 2 -5 -2 -2 -1 0 7
+S 1 0 -1 -1 -2 -4 0 -3 -3 -1 -5 -3 1 0 -2 -1 4
+T 1 -1 -4 -2 -2 -5 -2 -3 0 -1 -3 -2 0 -1 -3 -3 2 5
+V 0 -4 -3 -4 -3 -4 -3 -4 3 -5 0 1 -4 -3 -4 -4 -3 -1 6
+W -8 -7 -10 -9 -10 -2 -9 -4 -8 -6 -3 -7 -5 -8 -7 0 -3 -7 -9 13
+Y -5 -4 -1 -6 -6 4 -8 -1 -3 -6 -3 -6 -2 -8 -6 -6 -4 -4 -4 -2 9
+Z -1 2 -8 3 5 -8 -2 1 -3 -1 -4 -3 0 -2 5 -1 -2 -2 -3 -8 -6 5
+ A B C D E F G H I K L M N P Q R S T V W Y Z
+
+rao
+------------
+A 16
+C 11 16
+D 9 8 16
+E 10 9 11 16
+F 10 10 4 6 16
+G 8 8 9 6 7 16
+H 11 10 9 11 9 7 16
+I 9 8 3 4 12 6 8 16
+K 10 9 11 11 6 7 11 4 16
+L 11 11 6 7 11 6 10 10 7 16
+M 11 10 5 8 10 4 10 9 8 11 16
+N 9 9 11 10 6 10 10 5 11 7 6 16
+P 6 7 8 5 4 11 5 3 6 4 2 9 16
+Q 11 10 11 11 7 8 11 6 12 9 9 11 7 16
+R 8 8 10 9 5 7 10 4 11 6 6 10 6 10 16
+S 10 10 10 9 8 11 10 8 10 8 7 11 10 10 9 16
+T 10 10 9 8 10 10 10 10 9 9 8 10 8 10 9 11 16
+V 9 8 3 4 11 6 9 12 5 10 9 5 3 6 5 8 10 16
+W 11 11 6 7 11 8 10 11 7 11 10 8 6 9 7 10 11 11 16
+Y 9 10 7 6 10 10 9 10 7 9 8 8 8 8 7 11 11 10 11 16
+ A C D E F G H I K L M N P Q R S T V W Y
+
+risler
+------------
+A 2
+C -1 2
+D 0 -1 2
+E 1 -1 1 2
+F 0 -1 0 0 2
+G 0 -1 0 0 0 2
+H 0 -1 -1 0 -1 -1 2
+I 1 -1 0 1 1 0 0 2
+K 1 -1 0 1 0 0 -1 1 2
+L 1 -1 0 0 1 0 0 2 0 2
+M 1 -1 0 0 0 0 -1 0 0 1 2
+N 1 -1 0 1 0 0 0 0 1 0 0 2
+P 0 -1 -1 0 -1 -1 -1 0 0 0 -1 -1 2
+Q 1 -1 0 2 0 0 0 1 1 1 1 1 0 2
+R 1 -1 0 1 0 0 0 1 2 1 1 1 0 2 2
+S 2 -1 0 1 0 0 0 1 1 1 0 1 0 1 2 2
+T 1 -1 0 1 0 0 0 1 1 1 0 1 0 1 1 2 2
+V 2 -1 0 1 0 0 0 2 1 2 0 1 0 1 1 1 1 2
+W 0 -1 -1 -1 0 -1 -1 0 -1 0 -1 -1 -1 -1 0 0 -1 0 2
+Y 0 -1 0 0 2 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 2
+ A C D E F G H I K L M N P Q R S T V W Y
+
+str
+------------
+A 4
+C -2 11
+D -1 -7 6
+E 0 -3 2 5
+F -3 -2 -5 -4 7
+G 0 -6 -1 -2 -6 5
+H -2 -6 0 -2 -2 -3 8
+I -2 -4 -3 -3 1 -5 -5 6
+K -1 -4 -1 1 -3 -3 0 -3 5
+L -2 -6 -6 -4 2 -5 -3 2 -2 5
+M 0 -5 -4 -2 0 -4 -2 1 -1 3 8
+N -1 -6 2 0 -3 -1 2 -3 0 -3 -2 5
+P -1 -8 -1 -1 -5 -2 -3 -4 -1 -3 -6 -2 7
+Q 0 -3 0 2 -4 -2 0 -5 1 -3 1 0 -2 6
+R -1 -2 -2 0 -4 -2 0 -3 2 -3 -4 -1 -2 1 7
+S 0 -4 0 -1 -3 -1 -2 -3 -1 -4 -4 0 -1 -1 0 4
+T -1 -5 -1 0 -3 -3 -2 -2 0 -3 -2 0 -1 0 -1 1 5
+V 0 -4 -4 -2 -1 -4 -2 2 -3 1 0 -4 -4 -2 -3 -3 -1 5
+W -3 -6 -6 -6 2 -4 -3 -2 -3 -1 -2 -5 -4 -5 -2 -5 -5 -4 10
+Y -3 -6 -3 -2 3 -3 0 -1 -2 -2 -1 -1 -6 -3 -1 -2 -2 -1 2 7
+ A C D E F G H I K L M N P Q R S T V W Y
View
40 Tests/test_SubsMat.py
@@ -0,0 +1,40 @@
+import cPickle
+import sys
+from Bio.SubsMat import *
+
+f = sys.stdout
+ftab_prot = FreqTable.read_count(open('SubsMat/protein_count.txt'))
+ctab_prot = FreqTable.read_freq(open('SubsMat/protein_freq.txt'))
+f.write("Check differences between derived and true frequencies for each\n")
+f.write("letter. Differences should be very small\n")
+for i in ftab_prot.alphabet.letters:
+ f.write("%s %f\n" % (i, abs(ftab_prot[i] - ctab_prot[i])))
+
+acc_rep_mat = cPickle.load(open('SubsMat/acc_rep_mat.pik'))
+acc_rep_mat = SubsMat.SeqMat(acc_rep_mat)
+obs_freq_mat = SubsMat._build_obs_freq_mat(acc_rep_mat)
+ftab_prot2 = SubsMat._exp_freq_table_from_obs_freq(obs_freq_mat)
+obs_freq_mat.print_mat(f=f,format=" %4.3f")
+
+
+f.write("Diff between supplied and matrix-derived frequencies, should be small\n")
+for i in ftab_prot.keys():
+ f.write("%s %.2f\n" % (i,abs(ftab_prot[i] - ftab_prot2[i])))
+
+s = 0.
+f.write("Calculating sum of letters for an observed frequency matrix\n")
+obs_freq_mat.all_letters_sum()
+for i in obs_freq_mat.sum_letters.keys():
+ f.write("%s\t%.2f\n" % (i, obs_freq_mat.sum_letters[i]))
+ s += obs_freq_mat.sum_letters[i]
+f.write("Total sum %.2f should be 1.0\n" % (s))
+lo_mat_prot = \
+SubsMat.make_log_odds_matrix(acc_rep_mat=acc_rep_mat,round_digit=1) #,ftab_prot
+f.write("\nLog odds matrix\n")
+lo_mat_prot.print_mat(f=f,format=" %.2f",alphabet='AVILMCFWYHSTNQKRDEGP')
+
+f.write("\nTesting MatrixInfo\n")
+for i in MatrixInfo.available_matrices:
+ mat = SubsMat.SeqMat(getattr(MatrixInfo,i))
+ f.write("\n%s\n------------\n" % i)
+ mat.print_mat(f=f)
View
7 Tests/test_align.py
@@ -12,10 +12,12 @@
import os
# biopython
+from Bio.Alphabet import IUPAC
from Bio.Clustalw import Clustalw
from Bio.Align.FormatConvert import FormatConverter
from Bio.Align import AlignInfo
from Bio.Fasta import FastaAlign
+from Bio.SubsMat import FreqTable
print "testing reading and writing clustal format..."
test_dir = os.path.join(os.getcwd(), 'Clustalw')
@@ -74,8 +76,11 @@
'A' : 0.25,
'T' : 0.25}
+e_freq_table = FreqTable.FreqTable(e_freq, FreqTable.FREQ,
+ IUPAC.unambiguous_dna)
+
print 'relative information:', align_info.information_content(
- expected_freqs = e_freq,
+ e_freq_table = e_freq_table,
chars_to_ignore = ['N'])
print "testing reading and writing fasta format..."

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